seqsero2: libs/sratoolkit.2.8.0-centos_linux64/schema/align/align.vschema annotate

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/align.vschema @ 3:38ad1130d077 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
parents
children

rev	line source
3 38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1 /*===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	2 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	3 * PUBLIC DOMAIN NOTICE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	4 * National Center for Biotechnology Information
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	5 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	6 * This software/database is a "United States Government Work" under the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	7 * terms of the United States Copyright Act. It was written as part of
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	8 * the author's official duties as a United States Government employee and
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	9 * thus cannot be copyrighted. This software/database is freely available
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	10 * to the public for use. The National Library of Medicine and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	11 * Government have not placed any restriction on its use or reproduction.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	12 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	13 * Although all reasonable efforts have been taken to ensure the accuracy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	14 * and reliability of the software and data, the NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	15 * Government do not and cannot warrant the performance or results that
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	16 * may be obtained by using this software or data. The NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	17 * Government disclaim all warranties, express or implied, including
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	18 * warranties of performance, merchantability or fitness for any particular
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	19 * purpose.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	20 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	21 * Please cite the author in any work or product based on this material.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	22 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	23 * ===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	24 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	25 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	26
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	27 /*==========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	28 * VDB Alignment types, functions and tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	29 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	30 version 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	31
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	32 include 'vdb/vdb.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	33 include 'ncbi/seq.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	34 include 'ncbi/sra.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	35 include 'ncbi/stats.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	36 include 'align/seq.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	37 include 'align/qstat.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	38 include 'sra/abi.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	39 include 'align/mate-cache.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	40
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	41
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	42 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	43 * data types
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	44 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	45
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	46 /* ploidy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	47 * the number of sets of chromosomes in a cell
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	48 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	49 typedef U32 NCBI:align:ploidy;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	50
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	51 /* ro_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	52 * the type of event causing ref-offset
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	53 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	54 typedef U8 NCBI:align:ro_type;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	55
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	56 const NCBI:align:ro_type NCBI:align:ro_normal = 0; // normal ref-offset
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	57 const NCBI:align:ro_type NCBI:align:ro_soft_clip = 1; // soft-clipping
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	58 const NCBI:align:ro_type NCBI:align:ro_intron_plus = 2; // intron on positive strand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	59 const NCBI:align:ro_type NCBI:align:ro_intron_minus = 3; // intron on negative strand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	60 const NCBI:align:ro_type NCBI:align:ro_intron_unknown = 4; // intron strand not specified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	61 const NCBI:align:ro_type NCBI:align:ro_complete_genomics = 5; //
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	62
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	63
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	64 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	65 * functions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	66 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	67
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	68
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	69 /* cigar
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	70 * construct "cigar" alignment string or length arrays
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	71 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	72 * "ctype" [ CONST ] - select variant of format
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	73 * 0 => both matches and mismatches represented as M
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	74 * 1 => matches represented as '=' mismatches as 'X'
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	75 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	76 * "has_mismatch" [ DATA ] - a boolean for each base in aligned sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	77 * where a value of false means the base aligned to the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	78 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	79 * "has_ref_offset" [ DATA ] - a boolean for each base in the aligned sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	80 * where a value of true means there is a corresponding offset to position on reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	81 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	82 * "ref_offset" [ DATA ] - a packed sequence of signed offsets to aligned position
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	83 * one entry for every true in "has_ref_offset"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	84 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	85 * "read_len" [ DATA ] - v2: elem_count defines PLOIDY and values are an actual length of reads in spot
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	86 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	87 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	88 ascii NCBI:align:cigar #1 < U8 ctype > ( bool has_mismatch, bool has_ref_offset,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	89 I32 ref_offset, * INSDC:coord:len ref_len ) = ALIGN:cigar;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	90
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	91 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	92 * 2.1 - added "ref_offset_type" optional parameter
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	93 * NB - reverting to 2.0 due to linker bug in older code
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	94 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	95 extern function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	96 T NCBI:align:cigar #2.0 < U8 ctype > ( bool has_mismatch, bool has_ref_offset,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	97 I32 ref_offset, INSDC:coord:len read_len, * INSDC:coord:len ref_len, NCBI:align:ro_type ref_offset_type )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	98 = ALIGN:cigar_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	99
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	100 extern function U32 NCBI:align:edit_distance #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	101 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	102
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	103 extern function U32 NCBI:align:edit_distance #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	104 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset, INSDC:coord:len ref_len, *INSDC:coord:len read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	105 = NCBI:align:edit_distance_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	106
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	107 extern function U32 NCBI:align:edit_distance #3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	108 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset, NCBI:align:ro_type ref_offset_type, INSDC:coord:len read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	109 = NCBI:align:edit_distance_3;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	110
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	111 /* rna_orientation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	112 * reads column REF_OFFSET_TYPE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	113 * returns '+' if has:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	114 * at least one NCBI:align:ro_intron_plus
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	115 * none of NCBI:align:ro_intron_minus
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	116 * returns '-' if has:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	117 * at least one NCBI:align:ro_intron_minus
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	118 * none of NCBI:align:ro_intron_plus
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	119 * returns empty string otherwise
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	120 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	121 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	122 ascii NCBI:align:rna_orientation #1 ( NCBI:align:ro_type ref_offset_type );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	123
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	124 /* project_from_sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	125 * projects column from SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	126 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	127 * "T" [ TYPE ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	128 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	129 * "col" [ CONST ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	130 * "use_read_len" [ CONST ] whether subset by read_len or by read_id only
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	131 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	132 * "seq_spot_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	133 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	134 * "seq_read_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	135 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	136 extern function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	137 T NCBI:align:project_from_sequence #1 < ascii col> ( I64 seq_spot_id, INSDC:coord:one seq_read_id )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	138 = ALIGN:project_from_sequence;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	139
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	140
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	141 /* align_restore_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	142 * restores read by applying alignment-based difference to ref_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	143 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	144 * "ref_read" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	145 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	146 * "has_mismatch" [ DATA ] and "mismatch" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	147 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	148 * "has_ref_offset" [ DATA ] and "ref_offset" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	149 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	150 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	151 INSDC:4na:bin NCBI:align:align_restore_read #1 ( INSDC:4na:bin ref_read, bool has_mismatch,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	152 INSDC:4na:bin mismatch, bool has_ref_offset, I32 ref_offset * INSDC:coord:len read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	153 = ALIGN:align_restore_read;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	154
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	155
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	156 /* raw_restore_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	157 * restores read by applying alignment-based difference to align_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	158 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	159 * "align_read" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	160 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	161 * "ref_orientation" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	162 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	163 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	164 INSDC:4na:bin NCBI:align:raw_restore_read #1 ( INSDC:4na:bin align_read, bool ref_orientation )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	165 = ALIGN:raw_restore_read;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	166
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	167
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	168 /* raw_restore_qual
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	169 * restores quality by applying alignment-based difference to align_qual
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	170 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	171 * "align_qual" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	172 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	173 * "ref_orientation" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	174 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	175 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	176 INSDC:quality:phred NCBI:align:raw_restore_qual #1 ( INSDC:quality:phred align_qual, bool ref_orientation );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	177
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	178
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	179 /* ref_sub_select
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	180 * projects reference from sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	181 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	182 * "id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	183 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	184 * "start" [ DATA ] and "len" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	185 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	186 * "ref_ploidy" [ DATA, OPTIONAL ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	187 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	188 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	189 INSDC:4na:bin NCBI:align:ref_sub_select #1 ( I64 id, INSDC:coord:zero start,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	190 INSDC:coord:len len * U32 ref_ploidy)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	191 = ALIGN:ref_sub_select;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	192
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	193
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	194 /* ref_restore_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	195 * restores read from central storage
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	196 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	197 * "cmp_rd" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	198 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	199 * "seq_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	200 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	201 * "seq_start" [ DATA ] and "seq_len" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	202 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	203 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	204 INSDC:4na:bin NCBI:align:ref_restore_read #1 ( INSDC:4na:bin cmp_rd, ascii seq_id,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	205 INSDC:coord:one seq_start, INSDC:coord:len seq_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	206 = ALIGN:ref_restore_read;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	207
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	208
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	209 /* seq_restore_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	210 * projects read from align_deflate table to SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	211 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	212 * "cmp_rd" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	213 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	214 * "align_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	215 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	216 * "read_len" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	217 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	218 * "rd_type" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	219 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	220 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	221 INSDC:4na:bin NCBI:align:seq_restore_read #1 ( INSDC:4na:bin cmp_rd, I64 align_id,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	222 INSDC:coord:len read_len, INSDC:SRA:xread_type rd_type )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	223 = ALIGN:seq_restore_read;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	224
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	225
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	226 /* seq_restore_linkage_group
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	227 * projects LINKAGE_GROUP from PRIMARY_ALIGNMENT table to SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	228 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	229 * "cmp_linkage_group" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	230 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	231 * "align_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	232 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	233 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	234 ascii NCBI:align:seq_restore_linkage_group #1 ( ascii cmp_linkage_group,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	235 I64 align_id )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	236 = ALIGN:seq_restore_linkage_group;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	237
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	238
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	239 /* generate_has_mismatch
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	240 * generates has mismatch by doing actual compare of reference and subject,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	241 * *ref_offsets move comparisons reference-wise
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	242 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	243 * "reference" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	244 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	245 * "subject" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	246 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	247 * "has_ref_offset" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	248 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	249 * "ref_offset" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	250 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	251 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	252 bool NCBI:align:generate_has_mismatch #1 ( INSDC:4na:bin reference,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	253 INSDC:4na:bin subject, bool has_ref_offset, I32 ref_offset)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	254 = ALIGN:generate_has_mismatch;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	255
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	256
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	257 /* generate_mismatch
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	258 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	259 * "reference" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	260 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	261 * "subject" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	262 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	263 * "has_ref_offset" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	264 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	265 * "ref_offset" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	266 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	267 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	268 INSDC:4na:bin NCBI:align:generate_mismatch #1 ( INSDC:4na:bin reference,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	269 INSDC:4na:bin subject, bool has_ref_offset, I32 ref_offset )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	270 = ALIGN:generate_mismatch;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	271
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	272
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	273 /* ref_pos
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	274 * retrieves the alignment's positions on the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	275 * one per PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	276 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	277 * "ref_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	278 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	279 * "ref_start" [ DATA ] - one per PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	280 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	281 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	282 INSDC:coord:zero NCBI:align:ref_pos #1 ( I64 ref_id, INSDC:coord:zero ref_start );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	283
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	284
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	285 /* ref_name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	286 * retrieve the name from the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	287 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	288 * "ref_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	289 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	290 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	291 ascii NCBI:align:ref_name #1 ( I64 ref_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	292
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	293
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	294 /* ref_seq_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	295 * retrieve the seq_id from the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	296 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	297 * "ref_id" [ DATA ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	298 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	299 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	300 ascii NCBI:align:ref_seq_id #1 ( I64 ref_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	301
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	302
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	303 /* local_ref_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	304 * convert global ref_start into ref_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	305 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	306 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	307 I64 NCBI:align:local_ref_id #1 ( U64 global_ref_start );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	308
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	309
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	310 /* global_ref_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	311 * convert global ref_start into ref_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	312 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	313 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	314 INSDC:coord:zero NCBI:align:local_ref_start #1 ( U64 global_ref_start );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	315
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	316 /* not_my_row
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	317 * removes current row_id from the list
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	318 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	319 extern function I64 NCBI:align:not_my_row #1 ( I64 list );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	320
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	321 /* template_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	322 * compute template length, i.e. the distance from the left-most to the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	323 * right-most matching reference position
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	324 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	325 extern function I32 NCBI:align:template_len #1 (
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	326 INSDC:coord:zero pos, INSDC:coord:zero mate_pos,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	327 INSDC:coord:len reflen, INSDC:coord:len mate_reflen,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	328 ascii ref_name, ascii mate_ref_name, INSDC:coord:one read_id);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	329
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	330 /* get_sam_flags
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	331 * compute the flags that would be in a SAM file
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	332 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	333 * version 1 works with full Alignment databases.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	334 * version 2 works with Alignment databases that have had SEQUENCE removed.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	335 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	336 extern function U32 NCBI:align:get_sam_flags #1 (
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	337 INSDC:coord:len read_len, INSDC:coord:one read_id, I32 template_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	338 bool strand, bool mate_strand, bool is_secondary, * INSDC:SRA:read_filter filter);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	339
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	340 extern function U32 NCBI:align:get_sam_flags #2 (
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	341 I64 mate_id, INSDC:coord:one read_id, I32 template_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	342 bool strand, bool mate_strand, bool is_secondary, * INSDC:SRA:read_filter filter)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	343 = NCBI:align:get_sam_flags_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	344
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	345 /* get_left_soft_clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	346 * compute the length of the soft clip on the left edge of the alignment
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	347 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	348 extern function INSDC:coord:len NCBI:align:get_left_soft_clip #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	349 ( bool has_ref_offset, I32 ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	350
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	351 extern function INSDC:coord:len NCBI:align:get_left_soft_clip #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	352 ( bool has_ref_offset, I32 ref_offset, INSDC:coord:len read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	353 = NCBI:align:get_left_soft_clip_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	354
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	355 /* get_right_soft_clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	356 * compute the length of the soft clip on the right edge of the alignment
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	357 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	358 extern function INSDC:coord:len NCBI:align:get_right_soft_clip #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	359 ( bool has_mismatch, INSDC:coord:len left_clip * bool has_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	360
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	361 extern function INSDC:coord:len NCBI:align:get_right_soft_clip #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	362 ( bool has_mismatch, INSDC:coord:len left_clip, bool has_ref_offset, I32 ref_offset )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	363 = NCBI:align:get_right_soft_clip_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	364
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	365 extern function INSDC:coord:len NCBI:align:get_right_soft_clip #3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	366 ( bool has_ref_offset, I32 ref_offset, INSDC:coord:len ref_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	367 = NCBI:align:get_right_soft_clip_3;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	368
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	369 extern function INSDC:coord:len NCBI:align:get_right_soft_clip #4
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	370 ( bool has_ref_offset, I32 ref_offset, INSDC:coord:len read_len, INSDC:coord:len ref_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	371 = NCBI:align:get_right_soft_clip_4;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	372
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	373 extern function INSDC:coord:len NCBI:align:get_right_soft_clip #5
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	374 ( bool has_ref_offset, I32 ref_offset, NCBI:align:ro_type ref_offset_type, INSDC:coord:len read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	375 = NCBI:align:get_right_soft_clip_5;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	376
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	377 /* get_clipped_cigar
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	378 * compute the CIGAR string with the soft clipping removed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	379 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	380 extern function ascii NCBI:align:get_clipped_cigar #1 ( ascii cigar );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	381
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	382 extern function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	383 T NCBI:align:get_clipped_cigar #2 ( ascii cigar, INSDC:coord:len cigar_len ) = NCBI:align:get_clipped_cigar_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	384
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	385 /* get_clipped_ref_offset
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	386 * compute the reference offsets with the soft clipping removed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	387 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	388 extern function I32 NCBI:align:get_clipped_ref_offset #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	389 ( bool has_ref_offset, I32 ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	390
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	391 /* clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	392 * remove the soft clipped bases (or qualities, or has_mismatch, or cetera)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	393 * works with things whose lengths are the same as SEQUENCE.READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	394 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	395 extern function < type T > T NCBI:align:clip #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	396 ( T object, INSDC:coord:len left_clip, INSDC:coord:len right_clip);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	397
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	398 extern function < type T > T NCBI:align:clip #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	399 ( T object, INSDC:coord:len read_len, INSDC:coord:len left_clip, INSDC:coord:len right_clip)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	400 = NCBI:align:clip_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	401
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	402 /* get_ref_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	403 * compute reference length from alignment information
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	404 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	405 extern function INSDC:coord:len NCBI:align:get_ref_len #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	406 ( bool has_ref_offset, I32 ref_offset, * INSDC:coord:len right_clip );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	407
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	408 extern function INSDC:coord:len NCBI:align:get_ref_len_2 #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	409 ( bool has_ref_offset, I32 ref_offset)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	410 = NCBI:align:get_ref_len_2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	411
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	412
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	413 /* get_mismatch_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	414 * generate the READ with matching bases replaced with '='
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	415 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	416 extern function ascii NCBI:align:get_mismatch_read #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	417 ( bool has_mismatch, INSDC:dna:text mismatch );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	418
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	419 /* get_ref_mismatch
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	420 * shows mismatch positions in reference space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	421 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	422 function bool NCBI:align:get_ref_mismatch #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	423 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	424 INSDC:coord:len ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	425
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	426 /* get_ref_insert
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	427 * shows positions of inserts in reference space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	428 * i.e. an insert occurs between each pair of true's
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	429 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	430 function bool NCBI:align:get_ref_insert #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	431 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	432 INSDC:coord:len ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	433
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	434 /* get_ref_delete
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	435 * shows positions of deleted bases in reference space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	436 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	437 function bool NCBI:align:get_ref_delete #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	438 ( bool has_mismatch, bool has_ref_offset, I32 ref_offset,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	439 INSDC:coord:len ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	440
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	441 extern function INSDC:quality:phred NCBI:align:compress_quality #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	442 ( INSDC:quality:phred quality, bool preserved );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	443
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	444 extern function INSDC:quality:phred NCBI:align:decompress_quality #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	445 < INSDC:quality:phred restored_qual_value >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	446 ( INSDC:quality:phred cmp_quality, bool preserved );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	447
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	448 /* make_cmp_read_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	449 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	450 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	451 extern function INSDC:coord:zero NCBI:align:make_read_start #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	452 (INSDC:coord:len read_len);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	453
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	454 /* make_cmp_read_desc
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	455 * determines whether an element of "operand" is aligned
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	456 * by looking at the corresponding element of "align_id"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	457 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	458 * zeros out unaligned elements of operand, unless "invert" is true,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	459 * in which case it zeros out aligned elements.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	460 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	461 * "T" [ TYPE ] - type of operand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	462 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	463 * "invert" [ CONST ] - if true, invert the logic of which elements
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	464 * to zero out.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	465 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	466 * "operand" [ DATA ] - uncompressed data
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	467 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	468 * "align_id" [ DATA ] - indication of alignment
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	469 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	470 extern function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	471 T NCBI:align:make_cmp_read_desc #1 <bool invert>(T operand, I64 align_id);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	472
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	473 /* seq_construct_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	474 * assembles read from aligned and unaligned parts
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	475 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	476 extern function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	477 T NCBI:align:seq_construct_read #1 (
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	478 T aligned, INSDC:coord:len aligned_read_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	479 T unaligned, INSDC:coord:len unaligned_read_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	480
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	481 extern function I64 NCBI:align:get_mate_align_id #1 ( I64 spot_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	482
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	483 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	484 * tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	485 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	486
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	487
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	488 /* ref_block_cmn
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	489 * common implementation ancestor for reference block
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	490 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	491 table NCBI:align:tbl:ref_block_cmn #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	492 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	493 readonly column ascii REF_TABLE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	494 = < ascii > meta:read < "CONFIG/REF_TABLE" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	495 \| < ascii > echo < 'REFERENCE' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	496
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	497 // REF_ID is rowid in Reference Table REF_TABLE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	498 extern column I64 REF_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	499 = out_ref_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	500
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	501 // this is a redefinition of REF_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	502 // REF_START is the offset within REFERENCE.READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	503 extern column INSDC:coord:zero REF_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	504 = out_ref_start;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	505
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	506 // global REF_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	507 extern column U64 GLOBAL_REF_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	508 = out_global_ref_start;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	509
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	510 // REF_LEN the length of a read projection on reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	511 INSDC:coord:len out_ref_len_internal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	512 = NCBI:align:get_ref_len_2 ( out_has_ref_offset, out_ref_offset )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	513 \| NCBI:align:get_ref_len ( out_has_ref_offset, out_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	514
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	515 INSDC:coord:len out_ref_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	516 = .REF_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	517 /* \| NCBI:align:get_ref_len ( out_has_ref_offset, out_ref_offset, out_right_clip ) */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	518 \| out_ref_len_internal;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	519
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	520 physical column < INSDC:coord:len > izip_encoding .REF_LEN = REF_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	521 extern column INSDC:coord:len REF_LEN = out_ref_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	522
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	523 // REF_ORIENTATION - relative orientation of original raw read to the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	524 // false -> same orientation, true -> opposite orientation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	525 // alignment and reference are always in the same orientation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	526 extern column bool_encoding REF_ORIENTATION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	527
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	528 // REF_PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	529 extern column < U32 > izip_encoding REF_PLOIDY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	530
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	531 /* REF_POS
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	532 * per PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	533 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	534 readonly column INSDC:coord:zero REF_POS
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	535 = NCBI:align:ref_pos ( out_ref_id, out_ref_start );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	536
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	537 /* REF_NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	538 * the name of the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	539 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	540 readonly column ascii REF_NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	541 = NCBI:align:ref_name ( out_ref_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	542
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	543 /* REF_SEQ_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	544 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	545 readonly column ascii REF_SEQ_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	546 = NCBI:align:ref_seq_id ( out_ref_id )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	547 \| < ascii > echo < '' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	548 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	549
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	550
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	551 /* global_ref_block
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	552 * reference block favoring global ref-start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	553 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	554 table NCBI:align:tbl:global_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	555 = NCBI:align:tbl:ref_block_cmn #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	556 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	557 U64 out_global_ref_start = .GLOBAL_REF_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	558 physical < U64 > izip_encoding .GLOBAL_REF_START = GLOBAL_REF_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	559
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	560 I64 out_ref_id = NCBI:align:local_ref_id ( .GLOBAL_REF_START );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	561 INSDC:coord:zero out_ref_start = NCBI:align:local_ref_start ( .GLOBAL_REF_START );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	562 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	563
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	564
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	565 /* local_ref_block
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	566 * reference block favoring local ref-start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	567 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	568 table NCBI:align:tbl:local_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	569 = NCBI:align:tbl:ref_block_cmn #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	570 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	571 I64 out_ref_id = .REF_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	572 physical < I64 > izip_encoding .REF_ID = REF_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	573
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	574 INSDC:coord:zero out_ref_start = .REF_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	575 physical < INSDC:coord:zero > izip_encoding .REF_START = REF_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	576 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	577
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	578
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	579 /* align_cmn
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	580 * common interface and implementation for alignment object
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	581 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	582 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	583 * 2.1 - added REF_OFFSET_TYPE and RNA_ORIENTATION columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	584 * updated all cigar calculations
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	585 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	586 table NCBI:align:tbl:align_cmn #2.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	587 = NCBI:tbl:base_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	588 , NCBI:SRA:tbl:stats #1.2.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	589 , NCBI:align:tbl:ref_block_cmn #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	590 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	591 bool is_secondary = out_is_secondary;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	592 // temporary key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	593 extern column < U32 > izip_encoding TMP_KEY_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	594
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	595 extern column <ascii> zip_encoding LINKAGE_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	596
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	597
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	598 /* Raw Sequence Block */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	599 // Points to sequence table, which may contain more information about the raw sequence.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	600 // row id in SEQUENCE table; 0 if not linked
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	601 extern column < I64 > izip_encoding SEQ_SPOT_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	602
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	603 // read number in SEQUENCE table; { SEQ_SPOT_ID, SEQ_READ_ID } is the unique link to the sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	604 extern column < INSDC:coord:one > izip_encoding SEQ_READ_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	605
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	606
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	607 /* Soft-Clipped data block */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	608
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	609 readonly column INSDC:coord:len LEFT_SOFT_CLIP
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	610 = NCBI:align:get_left_soft_clip ( HAS_REF_OFFSET, REF_OFFSET, out_read_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	611
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	612 INSDC:coord:len out_right_clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	613 = NCBI:align:get_right_soft_clip #5 ( out_has_ref_offset, out_ref_offset, out_ro_type, out_read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	614 \| NCBI:align:get_right_soft_clip #4 ( out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	615 \| NCBI:align:get_right_soft_clip #3 ( out_has_ref_offset, out_ref_offset, out_ref_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	616 \| NCBI:align:get_right_soft_clip #2 ( out_has_mismatch, LEFT_SOFT_CLIP, out_has_ref_offset, out_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	617 readonly column INSDC:coord:len RIGHT_SOFT_CLIP = out_right_clip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	618
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	619 readonly column ascii CLIPPED_CIGAR_LONG
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	620 = < ascii > NCBI:align:get_clipped_cigar ( CIGAR_LONG, CIGAR_LONG_LEN );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	621
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	622 readonly column INSDC:coord:len CLIPPED_CIGAR_LONG_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	623 = < INSDC:coord:len > NCBI:align:get_clipped_cigar ( CIGAR_LONG, CIGAR_LONG_LEN );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	624
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	625 readonly column ascii CLIPPED_CIGAR_SHORT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	626 = < ascii > NCBI:align:get_clipped_cigar ( CIGAR_SHORT, CIGAR_SHORT_LEN );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	627
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	628 readonly column INSDC:coord:len CLIPPED_CIGAR_SHORT_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	629 = < INSDC:coord:len > NCBI:align:get_clipped_cigar ( CIGAR_SHORT, CIGAR_SHORT_LEN );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	630
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	631 bool out_clipped_has_mismatch
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	632 = < bool > NCBI:align:clip (out_has_mismatch, out_read_len, LEFT_SOFT_CLIP, RIGHT_SOFT_CLIP);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	633
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	634 readonly column ascii CLIPPED_HAS_MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	635 = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_clipped_has_mismatch );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	636
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	637 readonly column bool CLIPPED_HAS_MISMATCH = out_clipped_has_mismatch;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	638
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	639 bool out_clipped_has_ref_offset
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	640 = < bool > NCBI:align:clip (HAS_REF_OFFSET, out_read_len, LEFT_SOFT_CLIP, RIGHT_SOFT_CLIP);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	641
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	642 readonly column ascii CLIPPED_HAS_REF_OFFSET
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	643 = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_clipped_has_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	644
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	645 readonly column bool CLIPPED_HAS_REF_OFFSET = out_clipped_has_ref_offset;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	646
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	647 // TBD cannot be computed right unless HAS_MISMATCH and! READ_LEN is used
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	648 readonly column INSDC:dna:text CLIPPED_MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	649 = < INSDC:dna:text > NCBI:align:clip #1 ( out_mismatch_dna_text, LEFT_SOFT_CLIP, RIGHT_SOFT_CLIP);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	650
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	651 readonly column I32 CLIPPED_REF_OFFSET
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	652 = NCBI:align:get_clipped_ref_offset ( HAS_REF_OFFSET, REF_OFFSET );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	653
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	654 readonly column INSDC:quality:phred CLIPPED_QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	655 = < INSDC:quality:phred > NCBI:align:clip (out_qual_phred, out_read_len, LEFT_SOFT_CLIP, RIGHT_SOFT_CLIP);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	656
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	657 readonly column INSDC:dna:text CLIPPED_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	658 = < INSDC:dna:text > NCBI:align:clip (READ, out_read_len, LEFT_SOFT_CLIP, RIGHT_SOFT_CLIP);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	659
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	660 /* Sequence Block */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	661
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	662 extern column < NCBI:align:ploidy > izip_encoding PLOIDY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	663
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	664 // Number of reads per spot; corresponds to the number of alternative alignments
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	665 // all alternative alignments are computed against the same reference region
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	666 U32 out_nreads
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	667 = .PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	668 \| < U32 > echo < 1 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	669
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	670 // READ_START and READ_LEN are position and length of the sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	671 physical < INSDC:coord:zero > izip_encoding .READ_START = READ_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	672 INSDC:coord:zero out_read_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	673 = .READ_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	674 \| < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	675
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	676 physical < INSDC:coord:len > izip_encoding .READ_LEN = READ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	677
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	678 INSDC:coord:len align_spot_len = ( INSDC:coord:len ) row_len ( out_has_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	679 INSDC:coord:len out_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	680 = .READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	681 \| align_spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	682
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	683 // associated qualities
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	684 extern column INSDC:quality:phred CMP_QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	685 = .CMP_QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	686 \| out_cmp_quality;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	687 physical column < INSDC:quality:phred > zip_encoding .CMP_QUALITY = CMP_QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	688
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	689 INSDC:quality:phred out_raw_qual = < INSDC:quality:phred >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	690 NCBI:align:project_from_sequence < '( INSDC:quality:phred ) QUALITY'> ( .SEQ_SPOT_ID, .SEQ_READ_ID );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	691 INSDC:quality:phred out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	692 = NCBI:align:raw_restore_qual ( out_raw_qual, .REF_ORIENTATION )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	693 \| < INSDC:quality:phred > echo < 30 > ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	694 readonly column INSDC:quality:text:phred_33 SAM_QUALITY = QUALITY ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	695
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	696 // project read group and name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	697 ascii out_spot_group = < ascii > simple_sub_select < 'SEQUENCE','SPOT_GROUP'> (.SEQ_SPOT_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	698
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	699
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	700 INSDC:SRA:spotid_t tmp_seq_spot_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	701 = cast ( .SEQ_SPOT_ID )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	702 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	703 physical <ascii> zip_encoding .SEQ_NAME = SEQ_NAME;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	704 extern column ascii SEQ_NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	705 = .SEQ_NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	706 \| < ascii > simple_sub_select < 'SEQUENCE','NAME'> (.SEQ_SPOT_ID)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	707 \| sprintf < "%u" > ( tmp_seq_spot_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	708
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	709 // compute sam flags
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	710 /* blows up parser: starts at schema-tbl.c:2138
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	711 readonly column U32 SAM_FLAGS = NCBI:align:get_sam_flags(MATE_ALIGN_ID,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	712 .SEQ_READ_ID, out_template_len, REF_ORIENTATION,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	713 out_mate_ref_orientation, is_secondary);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	714 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	715 INSDC:coord:len projected_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	716 = < INSDC:coord:len > simple_sub_select < 'SEQUENCE', 'READ_LEN' > ( .SEQ_SPOT_ID );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	717
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	718 readonly column U32 SAM_FLAGS
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	719 = NCBI:align:get_sam_flags #1 (projected_read_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	720 .SEQ_READ_ID, out_template_len, REF_ORIENTATION,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	721 out_mate_ref_orientation, is_secondary, out_rd_filter)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	722 \| NCBI:align:get_sam_flags #2 (out_mate_align_id,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	723 .SEQ_READ_ID, out_template_len, REF_ORIENTATION,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	724 out_mate_ref_orientation, is_secondary, out_rd_filter);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	725
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	726 ascii out_name_fmt = < ascii > echo < '$R' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	727
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	728 INSDC:coord:zero trim_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	729 = < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	730 INSDC:coord:len trim_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	731 = align_spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	732
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	733 ascii out_label
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	734 = .LABEL
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	735 \| < ascii > echo < "ploidy1" > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	736 INSDC:coord:zero out_label_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	737 = .LABEL_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	738 \| < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	739 INSDC:coord:len out_label_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	740 = .LABEL_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	741 \| < INSDC:coord:len > echo < 7 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	742
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	743 physical < INSDC:SRA:read_filter > zip_encoding .RD_FILTER = READ_FILTER;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	744 INSDC:SRA:read_filter out_rd_filter
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	745 = .RD_FILTER
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	746 \| < INSDC:SRA:read_filter > NCBI:align:project_from_sequence < 'READ_FILTER' > ( .SEQ_SPOT_ID, .SEQ_READ_ID )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	747 \| < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	748
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	749 INSDC:SRA:platform_id out_platform
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	750 = .PLATFORM
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	751 \| < INSDC:SRA:platform_id > simple_sub_select < 'SEQUENCE','PLATFORM'> (.SEQ_SPOT_ID)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	752 \| < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	753
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	754 U8 out_alignment_count = <U8> NCBI:align:project_from_sequence < 'ALIGNMENT_COUNT' > ( .SEQ_SPOT_ID, .SEQ_READ_ID );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	755
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	756 /* out_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	757 * set to SRA_READ_TYPE_FORWARD + SRA_READ_TYPE_BIOLOGICAL
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	758 * which has a constant value of 3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	759 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	760 INSDC:SRA:xread_type out_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	761 = < INSDC:SRA:xread_type > echo < 3 > ( out_read_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	762
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	763 // stats inputs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	764 bool in_stats_bin = HAS_REF_OFFSET;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	765
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	766 INSDC:coord:len _alt_in_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	767 = READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	768 \| ( INSDC:coord:len ) row_len #1 ( HAS_REF_OFFSET );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	769
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	770 INSDC:SRA:xread_type _alt_in_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	771 = READ_TYPE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	772 \| < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > (_alt_in_read_len);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	773
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	774 readonly column ascii MISMATCH_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	775 = NCBI:align:get_mismatch_read ( out_has_mismatch, out_mismatch_dna_text );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	776
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	777 /* Alignment block */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	778
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	779 // MAPQ - single value quality of the mapping; the scale is submitter specific
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	780 extern column < I32 > izip_encoding MAPQ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	781
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	782 extern column INSDC:coord:zero MATE_REF_POS = out_mate_ref_pos;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	783 extern column INSDC:coord:len MATE_REF_LEN = out_mate_ref_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	784 extern column I64 MATE_REF_ID = out_mate_ref_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	785 extern column I32 TEMPLATE_LEN = out_template_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	786 extern column bool MATE_REF_ORIENTATION = out_mate_ref_orientation;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	787 readonly column ascii MATE_REF_NAME = NCBI:align:ref_name ( out_mate_ref_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	788 readonly column ascii MATE_REF_SEQ_ID = NCBI:align:ref_seq_id( out_mate_ref_id );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	789 readonly column U8 ALIGNMENT_COUNT = out_alignment_count;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	790
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	791
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	792 /********************************
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	793 * Columns representing CIGARs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	794 ********************************/
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	795
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	796
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	797 // one value per base i.e. length is same as sum of READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	798 // partitioned by READ_START and READ_LEN into alternative alignments
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	799 // flags the shifts in reference position preceeding the base
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	800 // if sequence of a partitioned read starts with a ref_offset and one or more mismatches
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	801 // then it represents a left soft clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	802 // any run of mismatches at the end represents a right soft clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	803
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	804 readonly column ascii HAS_REF_OFFSET = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_has_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	805 extern column bool_encoding HAS_REF_OFFSET;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	806 bool out_has_ref_offset = .HAS_REF_OFFSET;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	807
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	808 // has number of elements equal to number of true elements in HAS_REF_OFFSET
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	809 extern column < I32 > izip_encoding REF_OFFSET;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	810 I32 out_ref_offset = .REF_OFFSET;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	811
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	812 // the type of offset recorded in REF_OFFSET
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	813 extern column < NCBI:align:ro_type > izip_encoding REF_OFFSET_TYPE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	814 NCBI:align:ro_type out_ro_type = .REF_OFFSET_TYPE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	815
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	816 // DISPLAY Columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	817
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	818 readonly column I64 ALIGN_ID = row_id ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	819
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	820 // get projection of the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	821 readonly column INSDC:dna:text REF_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	822 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( REF_READ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	823
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	824 readonly column INSDC:4na:bin REF_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	825 = NCBI:align:ref_sub_select (out_ref_id, out_ref_start, out_ref_len, .REF_PLOIDY)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	826 \| NCBI:align:ref_sub_select (out_ref_id, out_ref_start, out_ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	827
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	828 INSDC:4na:bin ref_read_internal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	829 = NCBI:align:ref_sub_select (out_ref_id, out_ref_start, out_ref_len_internal, .REF_PLOIDY)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	830 \| NCBI:align:ref_sub_select (out_ref_id, out_ref_start, out_ref_len_internal);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	831
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	832 // text forms of reads
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	833 INSDC:dna:text out_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	834 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	835 readonly column INSDC:dna:text RAW_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	836 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_raw_read );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	837 readonly column INSDC:4na:bin RAW_READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	838 = out_raw_read;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	839
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	840 // CIGARs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	841 readonly column ascii CIGAR_LONG
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	842 = < ascii > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len, out_ro_type)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	843 \| < ascii > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	844 \| < ascii > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	845 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	846 readonly column INSDC:coord:len CIGAR_LONG_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	847 = < INSDC:coord:len > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len, out_ro_type)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	848 \| < INSDC:coord:len > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	849 \| < INSDC:coord:len > NCBI:align:cigar #2 < 1 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	850 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	851 readonly column ascii CIGAR_SHORT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	852 = < ascii > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len, out_ro_type)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	853 \| < ascii > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	854 \| < ascii > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	855 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	856 readonly column INSDC:coord:len CIGAR_SHORT_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	857 = < INSDC:coord:len > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len, out_ro_type)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	858 \| < INSDC:coord:len > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len, out_ref_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	859 \| < INSDC:coord:len > NCBI:align:cigar #2 < 0 > (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	860 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	861
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	862 readonly column ascii RNA_ORIENTATION
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	863 = NCBI:align:rna_orientation ( out_ro_type )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	864 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	865
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	866 readonly column U32 EDIT_DISTANCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	867 = NCBI:align:edit_distance #3 (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ro_type, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	868 \| NCBI:align:edit_distance #2 (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ref_len, out_read_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	869 \| NCBI:align:edit_distance #2 (out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ref_len)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	870 \| NCBI:align:edit_distance #1 (out_has_mismatch, out_has_ref_offset, out_ref_offset);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	871
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	872 readonly column ascii HAS_MISMATCH = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_has_mismatch );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	873
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	874 // needed for backward compatibility
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	875 readonly column ascii SEQ_SPOT_GROUP = out_spot_group;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	876
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	877
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	878 /* These columns are purely informational. */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	879 bool out_ref_mismatch = NCBI:align:get_ref_mismatch ( out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	880 readonly column ascii REF_MISMATCH = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_ref_mismatch );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	881 readonly column bool REF_MISMATCH = out_ref_mismatch;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	882
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	883 bool out_ref_insert = NCBI:align:get_ref_insert ( out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	884 readonly column ascii REF_INSERT = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_ref_insert );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	885 readonly column bool REF_INSERT = out_ref_insert;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	886
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	887 bool out_ref_delete = NCBI:align:get_ref_delete ( out_has_mismatch, out_has_ref_offset, out_ref_offset, out_ref_len );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	888 readonly column ascii REF_DELETE = < U8 , ascii > map < [ 0 , 1 ] , '01' > ( out_ref_delete );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	889 readonly column bool REF_DELETE = out_ref_delete;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	890
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	891 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	892
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	893
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	894 /* align_full
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	895 * aligns externally stored sequence against reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	896 * alignment transcript is calculated
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	897 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	898 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	899 * 1.1 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	900 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	901 table NCBI:align:tbl:align_full #1.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	902 = NCBI:align:tbl:align_cmn #2.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	903 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	904 bool out_is_secondary = <bool> echo < true > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	905 // restore reads to its raw form (orientation is restored)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	906
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	907 INSDC:4na:bin out_raw_read
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	908 = < INSDC:4na:bin > simple_sub_select < 'PRIMARY_ALIGNMENT', '( INSDC:4na:bin ) RAW_READ' > (.PRIMARY_ALIGNMENT_ID)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	909 \| < INSDC:4na:bin > NCBI:align:project_from_sequence < '( INSDC:4na:bin ) READ'> ( .SEQ_SPOT_ID, .SEQ_READ_ID );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	910
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	911 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	912 = NCBI:align:align_restore_read ( ref_read_internal, out_has_mismatch, tmp_out_mismatch_4na_bin, out_has_ref_offset, out_ref_offset, .READ_LEN )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	913 \| NCBI:align:align_restore_read ( ref_read_internal, out_has_mismatch, tmp_out_mismatch_4na_bin, out_has_ref_offset, out_ref_offset )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	914 \| NCBI:align:raw_restore_read ( out_raw_read, .REF_ORIENTATION );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	915
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	916
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	917 // flags mismatches with the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	918 // produced by actual comparison of REF_READ and READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	919 // TMP_HAS_MISMATCH is a hack to speed up retrieval during coverage recalculation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	920 column bool_encoding TMP_HAS_MISMATCH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	921 bool out_has_mismatch
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	922 = .TMP_HAS_MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	923 \| NCBI:align:generate_has_mismatch ( REF_READ, READ, out_has_ref_offset, out_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	924 readonly column bool HAS_MISMATCH = out_has_mismatch;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	925
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	926 INSDC:4na:bin out_mismatch_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	927 = NCBI:align:generate_mismatch ( REF_READ, READ, out_has_ref_offset, out_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	928
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	929 INSDC:4na:bin tmp_out_mismatch_4na_bin = < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( .TMP_MISMATCH );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	930
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	931 // temporary column for reference coverage calculation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	932 column < INSDC:dna:text> zip_encoding TMP_MISMATCH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	933
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	934 INSDC:dna:text out_mismatch_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	935 = .TMP_MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	936 \| < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_mismatch_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	937
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	938 readonly column INSDC:dna:text MISMATCH = out_mismatch_dna_text;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	939 readonly column INSDC:4na:bin MISMATCH = out_mismatch_4na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	940
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	941 physical column < INSDC:coord:zero > izip_encoding .MATE_REF_POS = MATE_REF_POS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	942 INSDC:coord:zero out_mate_ref_pos = .MATE_REF_POS
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	943 \| < INSDC:coord:zero > simple_sub_select < '','REF_POS'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	944
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	945 physical column < I64 > izip_encoding .MATE_REF_ID = MATE_REF_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	946 I64 out_mate_ref_id = .MATE_REF_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	947 \| < I64 > simple_sub_select < '','REF_ID'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	948
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	949 INSDC:coord:len out_mate_ref_len = < INSDC:coord:len > simple_sub_select < '','REF_LEN'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	950 physical column < I32 > izip_encoding .TEMPLATE_LEN = TEMPLATE_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	951 I32 out_template_len = .TEMPLATE_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	952 \| NCBI:align:template_len(REF_POS,out_mate_ref_pos,out_ref_len,out_mate_ref_len,REF_NAME,MATE_REF_NAME,SEQ_READ_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	953
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	954 physical column < bool > izip_encoding .MATE_REF_ORIENTATION = MATE_REF_ORIENTATION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	955 bool out_mate_ref_orientation = .MATE_REF_ORIENTATION
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	956 \| < bool > simple_sub_select < '','REF_ORIENTATION'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	957
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	958 I64 out_mate_align_id = .MATE_ALIGN_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	959 physical column <I64> izip_encoding .MATE_ALIGN_ID = MATE_ALIGN_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	960 extern column I64 MATE_ALIGN_ID = out_mate_align_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	961
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	962 physical column < I64 > izip_encoding .PRIMARY_ALIGNMENT_ID = PRIMARY_ALIGNMENT_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	963
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	964 I32 read_idx = <I32> cast (.SEQ_READ_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	965 extern column I64 PRIMARY_ALIGNMENT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	966 = .PRIMARY_ALIGNMENT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	967 \| <I64> simple_sub_select < 'SEQUENCE','PRIMARY_ALIGNMENT_ID' > (.SEQ_SPOT_ID,.SEQ_READ_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	968
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	969 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	970
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	971
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	972 /* compressed_by_reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	973 * aligns internally represented sequence against reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	974 * alignment transcript is stored
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	975 * original sequence is reconstructed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	976 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	977 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	978 * 1.2 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	979 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	980 table NCBI:align:tbl:compressed_by_reference #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	981 = NCBI:align:tbl:align_cmn #2.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	982 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	983 bool out_is_secondary = <bool> echo < false > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	984
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	985 // one value per base i.e. length is same as sum of READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	986 // partitioned by READ_START and READ_LEN into alternative alignments
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	987 // flags mismatches with the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	988 extern default column bool_encoding HAS_MISMATCH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	989 bool out_has_mismatch = .HAS_MISMATCH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	990
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	991 // has number of elements equal to number of true elements in HAS_MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	992 extern column INSDC:dna:text MISMATCH
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	993 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	994 read = out_mismatch_dna_text;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	995 validate = < INSDC:dna:text > compare ( in_mismatch_dna_text, out_mismatch_dna_text );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	996 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	997
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	998 INSDC:dna:text in_mismatch_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	999 = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( MISMATCH );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1000
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1001 INSDC:4na:bin in_mismatch_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1002 = < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_mismatch_dna_text );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1003
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1004 extern column < ascii > zip_encoding ALIGN_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1005
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1006 physical column < INSDC:4na:bin > zip_encoding .MISMATCH = in_mismatch_4na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1007
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1008 INSDC:4na:bin out_mismatch_4na_bin = .MISMATCH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1009 INSDC:dna:text out_mismatch_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1010 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_mismatch_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1011
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1012 I64 out_mate_align_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1013 = .MATE_ALIGN_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1014 \| NCBI:align:get_mate_align_id (.SEQ_SPOT_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1015
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1016 physical column <I64> izip_encoding .MATE_ALIGN_ID = MATE_ALIGN_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1017 extern column I64 MATE_ALIGN_ID = out_mate_align_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1018
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1019 // restore reads from alignment columns and the reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1020 // optional .READ_LEN size defines PLOIDY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1021 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1022 = NCBI:align:align_restore_read ( ref_read_internal, out_has_mismatch, .MISMATCH, out_has_ref_offset, out_ref_offset, .READ_LEN )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1023 \| NCBI:align:align_restore_read ( ref_read_internal, out_has_mismatch, .MISMATCH, out_has_ref_offset, out_ref_offset );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1024
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1025 // restore reads to its raw form (orientation is restored)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1026 INSDC:4na:bin out_raw_read = NCBI:align:raw_restore_read (out_4na_bin,.REF_ORIENTATION);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1027
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1028 I64 primary_align_pair = < I64 > simple_sub_select < 'SEQUENCE','PRIMARY_ALIGNMENT_ID'> (.SEQ_SPOT_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1029 I64 out_mate_ref_id = < I64 > simple_sub_select < '','REF_ID'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1030 bool out_mate_ref_orientation = < bool > simple_sub_select < '','REF_ORIENTATION'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1031 INSDC:coord:zero out_mate_ref_pos = < INSDC:coord:zero > simple_sub_select < '','REF_POS'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1032 INSDC:coord:len out_mate_ref_len = < INSDC:coord:len > simple_sub_select < '','REF_LEN'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1033 readonly column U32 MATE_EDIT_DISTANCE = < U32 > simple_sub_select < '','EDIT_DISTANCE'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1034 readonly column ascii MATE_CIGAR_LONG = < ascii > simple_sub_select < '','CIGAR_LONG'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1035 readonly column ascii MATE_CIGAR_SHORT = < ascii > simple_sub_select < '','CIGAR_SHORT'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1036 readonly column INSDC:coord:len MATE_CIGAR_LONG_LEN = < INSDC:coord:len > simple_sub_select < '','CIGAR_LONG_LEN'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1037 readonly column INSDC:coord:len MATE_CIGAR_SHORT_LEN = < INSDC:coord:len > simple_sub_select < '','CIGAR_SHORT_LEN'> (MATE_ALIGN_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1038
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1039 I32 out_template_len = NCBI:align:template_len (REF_POS,out_mate_ref_pos,out_ref_len,out_mate_ref_len,REF_NAME,MATE_REF_NAME,SEQ_READ_ID);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1040 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1041
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1042
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1043 /* align_sorted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1044 * deflated alignment data sorted against reference
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1045 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1046 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1047 * 1.2 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1048 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1049 table NCBI:align:tbl:align_sorted #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1050 = NCBI:align:tbl:compressed_by_reference #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1051 , NCBI:align:tbl:global_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1052 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1053 // 128K
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1054 column default limit = 131072;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1055 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1056
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1057
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1058 /* align_unsorted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1059 * deflated alignment unsorted data
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1060 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1061 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1062 * 1.2 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1063 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1064 table NCBI:align:tbl:align_unsorted #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1065 = NCBI:align:tbl:compressed_by_reference #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1066 , NCBI:align:tbl:local_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1067 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1068 // 128K
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1069 column default limit = 131072;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1070 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1071
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1072
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1073 /* align_mate_sorted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1074 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1075 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1076 * 1.1 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1077 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1078 table NCBI:align:tbl:align_mate_sorted #1.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1079 = NCBI:align:tbl:align_full #1.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1080 , NCBI:align:tbl:global_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1081 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1082 // 128K
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1083 column default limit = 131072;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1084 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1085
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1086
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1087 /* align_mate_unsorted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1088 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1089 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1090 * 1.1 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1091 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1092 table NCBI:align:tbl:align_mate_unsorted #1.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1093 = NCBI:align:tbl:align_full #1.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1094 , NCBI:align:tbl:local_ref_block #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1095 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1096 // 128K
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1097 column default limit = 131072;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1098 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1099
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1100 /* align_allele
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1101 * alleles coverage extension
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1102 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1103 * History:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1104 * 1.2 - respond to changes in base table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1105 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1106 table NCBI:align:tbl:align_allele #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1107 = NCBI:align:tbl:align_unsorted #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1108 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1109 extern column < I64 > izip_encoding EVIDENCE_ALIGNMENT_IDS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1110
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1111 /*
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1112 INSDC:quality:phred out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1113 = < INSDC:quality:phred > echo < 30 > ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1114 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1115 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1116
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1117 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1118 * seq
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1119 * alignment sequence table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1120 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1121 physical
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1122 I64 NCBI:align:sorted:alignment_id_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1123 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1124 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1125 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1126 I64 outliers_removed = iunzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1127 return < I64 > outlier_decode < 0 > ( outliers_removed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1128 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1129
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1130 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1131 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1132 I64 outliers_removed = < I64 > outlier_encode < 0 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1133 return izip ( outliers_removed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1134 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1135 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1136
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1137
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1138 table NCBI:align:tbl:seq #1.1 =
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1139 NCBI:tbl:base_space #2.0.3,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1140 NCBI:tbl:phred_quality #2.0.4,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1141 NCBI:align:tbl:cmp_base_space #1,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1142 NCBI:SRA:tbl:spotdesc #1.0.2,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1143 NCBI:SRA:tbl:stats #1.2.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1144 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1145 // 128K
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1146 column default limit = 131072;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1147
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1148 // gets primary record in alignment table (size of column is NREADS)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1149 // if sorted - should used special encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1150 extern column <I64> izip_encoding PRIMARY_ALIGNMENT_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1151
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1152 INSDC:coord:zero trim_start = < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1153 INSDC:coord:len trim_len = _spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1154
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1155 // size is NREADS
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1156 extern column < U8 > zip_encoding ALIGNMENT_COUNT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1157
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1158 // auto-generate name from row-id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1159 ascii out_name_fmt = < ascii > echo < '$R' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1160
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1161 // temparary column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1162 extern column < U64 > izip_encoding TMP_KEY_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1163
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1164 // restored READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1165 INSDC:4na:bin out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1166 = NCBI:align:seq_restore_read (out_cmp_4na_bin, .PRIMARY_ALIGNMENT_ID, .READ_LEN, .READ_TYPE);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1167
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1168 extern column < U64 > izip_encoding TI;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1169
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1170 extern column <ascii> zip_encoding CMP_LINKAGE_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1171
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1172 // restored LINKAGE_GROUP
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1173 readonly column ascii LINKAGE_GROUP = NCBI:align:seq_restore_linkage_group(.CMP_LINKAGE_GROUP, .PRIMARY_ALIGNMENT_ID)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1174 \| .CMP_LINKAGE_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1175 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1176
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1177
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1178 table NCBI:align:tbl:cs_seq #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1179 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1180 /* writable columns */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1181 extern column INSDC:color:text CMP_CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1182 = out_cmp_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1183 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1184
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1185 extern column < INSDC:dna:text > zip_encoding CS_KEY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1186
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1187 extern default column < INSDC:quality:phred > zip_encoding QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1188
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1189 extern column < I64 > izip_encoding PRIMARY_ALIGNMENT_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1190
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1191 extern column < U8 > zip_encoding ALIGNMENT_COUNT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1192
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1193 extern column < INSDC:SRA:platform_id > zip_encoding PLATFORM;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1194
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1195 extern column < ascii > zip_encoding LABEL;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1196 extern column < INSDC:coord:zero > izip_encoding LABEL_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1197 extern column < INSDC:coord:len > izip_encoding LABEL_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1198
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1199 extern column < INSDC:SRA:xread_type > zip_encoding READ_TYPE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1200 extern column < INSDC:coord:zero > izip_encoding READ_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1201 extern column < INSDC:coord:len > izip_encoding READ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1202 extern column < INSDC:SRA:read_filter > zip_encoding READ_FILTER;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1203
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1204 extern column < U64 > izip_encoding TMP_KEY_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1205
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1206 extern column < ascii > zip_encoding SPOT_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1207
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1208 extern column < U64 > izip_encoding TI;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1209
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1210 /* writing rules */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1211 INSDC:x2cs:bin in_cmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1212 = < INSDC:color:text, INSDC:x2cs:bin > map < INSDC:x2cs:map:CHARSET, INSDC:x2cs:map:BINSET > ( CMP_CSREAD )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1213 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1214 INSDC:2cs:bin in_cmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1215 = < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( in_cmp_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1216 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1217 INSDC:x2cs:bin in_cmp_alt_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1218 = < INSDC:x2cs:bin, INSDC:x2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 0, 0, 0, 4 ] > ( in_cmp_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1219 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1220 physical column INSDC:2cs:packed .CMP_CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1221 = ( INSDC:2cs:packed ) pack ( in_cmp_2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1222 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1223 physical column < INSDC:x2cs:bin > zip_encoding .CMP_ALTCSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1224 = < INSDC:x2cs:bin > trim < ALIGN_LEFT, 0 > ( in_cmp_alt_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1225 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1226
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1227 /* reading rules */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1228 INSDC:2cs:packed phys_cmp_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1229 = .CMP_CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1230 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1231 INSDC:x2cs:bin phys_cmp_alt_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1232 = .CMP_ALTCSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1233 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1234 INSDC:2cs:packed phys_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1235 = .CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1236 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1237 INSDC:x2cs:bin phys_alt_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1238 = .ALTCSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1239 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1240 INSDC:2cs:bin out_cmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1241 = ( INSDC:2cs:bin ) unpack ( phys_cmp_2cs_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1242 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1243 INSDC:2cs:bin out_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1244 = ( INSDC:2cs:bin ) unpack ( phys_2cs_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1245 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1246 INSDC:x2cs:bin out_cmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1247 = ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_cmp_2cs_bin, phys_cmp_alt_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1248 \| ( INSDC:x2cs:bin ) out_cmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1249 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1250 INSDC:x2cs:bin out_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1251 = ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_2cs_bin, phys_alt_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1252 \| ( INSDC:x2cs:bin ) out_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1253 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1254 INSDC:color:text out_cmp_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1255 = < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_cmp_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1256 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1257 INSDC:color:text out_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1258 = < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1259 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1260
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1261 /* triggers from stats */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1262 INSDC:quality:phred in_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1263 = QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1264 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1265 INSDC:coord:len in_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1266 = READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1267 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1268 INSDC:SRA:xread_type in_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1269 = READ_TYPE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1270 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1271 ascii in_spot_group
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1272 = SPOT_GROUP
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1273 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1274 trigger meta_stats
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1275 = NCBI:SRA:cmp_stats_trigger ( in_cmp_x2cs_bin, in_qual_phred, in_read_len, in_read_type, in_spot_group )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1276 \| NCBI:SRA:cmp_stats_trigger ( in_cmp_x2cs_bin, in_qual_phred, in_read_len, in_read_type )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1277 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1278 trigger qual_stats
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1279 = NCBI:SRA:phred_stats_trigger #1 ( in_qual_phred )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1280 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1281
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1282 extern column <ascii> zip_encoding CMP_LINKAGE_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1283
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1284 // restored LINKAGE_GROUP
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1285 readonly column ascii LINKAGE_GROUP = NCBI:align:seq_restore_linkage_group(.CMP_LINKAGE_GROUP, .PRIMARY_ALIGNMENT_ID)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1286 \| .CMP_LINKAGE_GROUP;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1287 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1288
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1289 table NCBI:align:view:cs_seq #1.1 = NCBI:align:tbl:cs_seq #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1290 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1291 // various READ columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1292 default readonly column INSDC:dna:text READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1293 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_dcmp_4na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1294 \| < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_4na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1295 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1296 readonly column INSDC:4na:bin READ = out_dcmp_4na_bin \| out_4na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1297 readonly column INSDC:4na:packed READ = pack ( out_dcmp_4na_bin ) \| pack ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1298 readonly column INSDC:x2na:bin READ = out_dcmp_x2na_bin \| out_x2na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1299 readonly column INSDC:2na:bin READ = out_dcmp_2na_bin \| out_2na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1300 INSDC:2na:bin out_dcmp_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1301 = < INSDC:x2na:bin, INSDC:2na:bin > map < INSDC:x2na:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_dcmp_x2na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1302 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1303 INSDC:2na:bin out_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1304 = < INSDC:x2na:bin, INSDC:2na:bin > map < INSDC:x2na:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_x2na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1305 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1306 readonly column INSDC:2na:packed READ = pack ( out_dcmp_2na_bin ) \| pack ( out_2na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1307
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1308 // decompression in base space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1309 INSDC:coord:len cmp_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1310 = < INSDC:coord:len > NCBI:align:make_cmp_read_desc #1 < true > ( .READ_LEN, .PRIMARY_ALIGNMENT_ID )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1311 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1312 INSDC:coord:zero cmp_read_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1313 = NCBI:align:make_read_start #1 ( cmp_read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1314 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1315 INSDC:x2na:bin out_cmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1316 = NCBI:dna_from_color #1 ( out_cmp_x2cs_bin, cmp_read_start, cmp_read_len, .CS_KEY, color_matrix )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1317 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1318 INSDC:x2na:bin out_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1319 = NCBI:dna_from_color #1 ( out_x2cs_bin, .READ_START, .READ_LEN, .CS_KEY, color_matrix )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1320 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1321 INSDC:4na:bin out_cmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1322 = < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( out_cmp_x2na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1323 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1324 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1325 = < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( out_x2na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1326 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1327 INSDC:4na:bin out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1328 = NCBI:align:seq_restore_read ( out_cmp_4na_bin, .PRIMARY_ALIGNMENT_ID, .READ_LEN, .READ_TYPE )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1329 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1330
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1331
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1332 // various CSREAD columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1333 default readonly column INSDC:color:text CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1334 = < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_dcmp_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1335 \| out_color_text;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1336 readonly column INSDC:x2cs:bin CSREAD = out_dcmp_x2cs_bin \| out_x2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1337 readonly column INSDC:2cs:bin CSREAD = out_dcmp_2cs_bin \| out_2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1338 INSDC:2cs:bin out_dcmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1339 = < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_dcmp_x2cs_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1340 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1341 readonly column INSDC:2cs:packed CSREAD = pack ( out_dcmp_2cs_bin ) \| out_2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1342
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1343
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1344 // decompression in color space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1345 INSDC:x2na:bin out_dcmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1346 = < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( out_dcmp_4na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1347 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1348 INSDC:x2cs:bin out_dcmp_x2na_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1349 = NCBI:color_from_dna #1 ( out_dcmp_x2na_bin, .READ_START, .READ_LEN, .CS_KEY, color_matrix )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1350 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1351 INSDC:coord:len aligned_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1352 = < INSDC:coord:len > NCBI:align:make_cmp_read_desc #1 < false > ( .READ_LEN, .PRIMARY_ALIGNMENT_ID )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1353 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1354 INSDC:x2cs:bin out_dcmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1355 = < INSDC:x2cs:bin > NCBI:align:seq_construct_read #1 ( out_dcmp_x2na_x2cs_bin, .READ_LEN, out_cmp_x2cs_bin, cmp_read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1356 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1357
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1358 // CS_NATIVE - dynamic
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1359 U32 cmp_csread_row_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1360 = row_len #1 ( phys_cmp_2cs_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1361 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1362 U32 cmp_csread_not_zero
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1363 = < U32 > clip < 0, 1 > ( cmp_csread_row_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1364 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1365 readonly column bool CS_NATIVE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1366 = < U32, bool > map < [ 0, 1 ], [ false, true ] > ( cmp_cs_read_not_zero )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1367 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1368
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1369 // COLOR_MATRIX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1370 readonly column U8 COLOR_MATRIX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1371 = color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1372 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1373 U8 color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1374 = < U8 > echo < INSDC:color:default_matrix > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1375 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1376
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1377 // various QUALITY types
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1378 readonly column INSDC:quality:text:phred_33 QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1379 = out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1380 \| ( INSDC:quality:text:phred_33 ) < B8 > sum < 33 > ( .QUALITY );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1381 readonly column INSDC:quality:text:phred_64 QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1382 = out_qual_text_phred_64
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1383 \| ( INSDC:quality:text:phred_64 ) < B8 > sum < 64 > ( .QUALITY );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1384
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1385 // SPOT_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1386 INSDC:coord:len spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1387 = ( INSDC:coord:len ) row_len ( out_dcmp_4na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1388 \| ( INSDC:coord:len ) row_len ( out_4na_bin )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1389 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1390 readonly column INSDC:coord:len SPOT_LEN = spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1391
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1392 // TRIM_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1393 readonly column INSDC:coord:zero TRIM_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1394 = < INSDC:coord:zero > echo < 0 > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1395 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1396 readonly column INSDC:coord:one TRIM_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1397 = < INSDC:coord:one > echo < 1 > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1398 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1399 // TRIM_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1400 readonly column INSDC:coord:len TRIM_LEN = spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1401
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1402 // MIN_SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1403 readonly column INSDC:SRA:spotid_t MIN_SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1404 = < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MIN" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1405 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1406 // MAX_SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1407 readonly column INSDC:SRA:spotid_t MAX_SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1408 = < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MAX" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1409 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1410 // SPOT_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1411 readonly column U64 SPOT_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1412 = < U64 > meta:value < "STATS/TABLE/SPOT_COUNT" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1413 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1414 // BASE_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1415 U64 base_count
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1416 = < U64 > meta:value < "STATS/TABLE/BASE_COUNT" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1417 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1418 readonly column U64 BASE_COUNT = base_count;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1419 // BIO_BASE_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1420 readonly column U64 BIO_BASE_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1421 = < U64 > meta:value < "STATS/TABLE/BIO_BASE_COUNT" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1422 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1423 // CMP_BASE_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1424 readonly column U64 CMP_BASE_COUNT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1425 = < U64 > meta:value < "STATS/TABLE/CMP_BASE_COUNT" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1426 \| base_count
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1427 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1428
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1429 // various PLATFORM
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1430 // TBD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1431
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1432 // SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1433 I64 rowid_64 = row_id ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1434 readonly column INSDC:SRA:spotid_t SPOT_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1435 = cast ( rowid_64 )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1436 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1437
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1438 readonly column ascii NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1439 = sprintf < "%u" > ( SPOT_ID )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1440 ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1441
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1442 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1443
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1444
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1445 /***********************************
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1446 * Reference table - to store reference sequences
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1447 * Sequences are divided in chunks. Two sequences never share a chunk.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1448 * SEQ_LEN - real size of a chunk should never exceed MAX_SEQ_LEN when it is set
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1449 * READ - inherited from NCBI:tbl:base_space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1450 * CMP_READ,CMP_ALTREAD - are inherited from NCBI:align:tbl:cmp_base_space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1451 * SEQ_ID,SEQ_START,SEQ_LEN are inherited from NCBI:align:tbl:seqloc
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1452 * .skey contains NAME of the chunk - it corresponds to actual name used in BAM (chr1,chr2, etc....)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1453 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1454 * SEQ_START,SEQ_LEN,MAX_SEQ_LEN,SEQID and rowlen(READ) operate the following way
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1455 * - SEQ_LEN < MAX_SEQ_LEN - should only happen on the last chunk of the sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1456 * - .READ is absent - there should be a retrieval from external services by SEQ_ID,SEQ_START,SEQ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1457 * - rowlen(.READ) = 0 && SEQ_START==0 (used as flag) - the sequence is SEQ_LEN repetition of 'N'
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1458 * - rowlen(.READ) = 0 && SEQ_START >= 1 - the sequence have to be fetched from external sources
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1459 * - 0 < rowlen(.READ)< SEQ_LEN -- the sequence have to be filled with 'N's
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1460 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1461 v***********************************/
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1462 table NCBI:align:tbl:reference #2 =
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1463 NCBI:align:tbl:cmp_base_space #1,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1464 NCBI:tbl:base_space #2.0.3,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1465 NCBI:tbl:seqloc #1,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1466 NCBI:SRA:tbl:stats #1.2.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1467 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1468 INSDC:quality:phred out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1469 = < INSDC:quality:phred > echo < 30 > ( out_dcmp_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1470
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1471 // MAX_SEQ_LEN - should be a constant == static column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1472 extern column < U32 > izip_encoding MAX_SEQ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1473
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1474 // indicates if sequence has circular structure
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1475 // copied from refSeq
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1476 extern column bool_encoding CIRCULAR;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1477
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1478 // make CS_KEY writable
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1479 INSDC:dna:text in_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1480 = < INSDC:dna:text, INSDC:dna:text > map < 'acgtn', 'ACGTN' > ( CS_KEY );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1481 physical column < INSDC:dna:text > zip_encoding .CS_KEY = in_cs_key;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1482
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1483 U32 in_spot_len = SEQ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1484
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1485 INSDC:coord:len _alt_in_read_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1486 = READ_LEN
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1487 \| SEQ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1488
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1489 INSDC:SRA:xread_type _alt_in_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1490 = READ_TYPE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1491 \| < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1492
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1493 // extra columns needed for CS conversion
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1494 INSDC:coord:zero out_read_start = < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1495 INSDC:coord:len out_read_len = .SEQ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1496
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1497 extern column utf8 NAME = out_spot_name_utf8;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1498 physical utf8 .NAME = idx:text:insert #1.0 < 'i_name' > ( NAME );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1499
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1500 utf8 out_spot_name_utf8 = idx:text:project #1.0 < 'i_name' > (.NAME );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1501
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1502 ascii out_spot_name = cast ( out_spot_name_utf8 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1503
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1504 INSDC:coord:zero trim_start = < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1505 INSDC:coord:len trim_len = base_space_spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1506
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1507 ascii out_label
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1508 = < ascii > echo < "reference" > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1509 INSDC:coord:zero out_label_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1510 = < INSDC:coord:zero > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1511 INSDC:coord:len out_label_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1512 = < INSDC:coord:len > echo < 9 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1513
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1514 U32 out_nreads
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1515 = < U32 > echo < 1 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1516 INSDC:SRA:xread_type out_read_type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1517 = < INSDC:SRA:xread_type > echo < 3 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1518 INSDC:SRA:read_filter out_rd_filter
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1519 = < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1520
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1521
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1522 // Columns of computed coverages by alignment
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1523
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1524 // TBD: use percentiles instead of min/max?
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1525 // maximum value clipped at 255 of the coverage density
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1526 // for a chunk
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1527 extern column < U8 > izip_encoding CGRAPH_HIGH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1528
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1529 // minimum value clipped at 255 of the coverage density
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1530 // for a chunk
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1531 extern column < U8 > izip_encoding CGRAPH_LOW;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1532
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1533 // count of the number of mismatches in the chunk
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1534 extern column < U32 > izip_encoding CGRAPH_MISMATCHES;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1535
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1536 // count of the number of inserts and deletes in the chunk
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1537 extern column < U32 > izip_encoding CGRAPH_INDELS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1538
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1539 // List of row ids from alignment tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1540 extern column < I64 > izip_encoding PRIMARY_ALIGNMENT_IDS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1541 extern column < I64 > izip_encoding SECONDARY_ALIGNMENT_IDS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1542 extern column < I64 > izip_encoding EVIDENCE_INTERVAL_IDS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1543
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1544 // both OVERLAP_REF_* columns are array of three elements, matching number of *_IDS columns above.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1545 // points back to an offset where the alignments to this chunk start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1546 extern column < INSDC:coord:zero > izip_encoding OVERLAP_REF_POS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1547 // indicates the length of the longest tail of the alignmnent to this chunk which start in previous chunks
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1548 // if value of an element in this col is zero corresponding value of OVERLAP_REF_POS is meaningless
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1549 extern column < INSDC:coord:len > izip_encoding OVERLAP_REF_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1550
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1551 // Mechanism to seach for NAME
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1552 readonly column vdb:row_id_range NAME_RANGE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1553 = idx:text:lookup #1.0 < 'i_name', 'QUERY_SEQ_NAME' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1554
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1555 // Fully instantiates READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1556 INSDC:4na:bin out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1557 = NCBI:align:ref_restore_read (out_cmp_4na_bin, .SEQ_ID, .SEQ_START, .SEQ_LEN);
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1558 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1559
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1560 // THE DATABASES
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1561 database NCBI:align:db:alignment_sorted #1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1562 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1563 table NCBI:align:tbl:reference #2 REFERENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1564 table NCBI:align:tbl:align_sorted #1.2 PRIMARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1565 table NCBI:align:tbl:align_mate_sorted #1.1 SECONDARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1566 table NCBI:align:tbl:seq #1.1 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1567 table NCBI:align:view:cs_seq #1.1 CS_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1568 table NCBI:align:tbl:qstat #1.0 QUAL_STAT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1569 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1570
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1571 database NCBI:align:db:alignment_unsorted #1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1572 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1573 table NCBI:align:tbl:reference #2 REFERENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1574 table NCBI:align:tbl:align_unsorted #1.2 PRIMARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1575 table NCBI:align:tbl:align_mate_unsorted #1.1 SECONDARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1576 table NCBI:align:tbl:seq #1.1 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1577 table NCBI:align:view:cs_seq #1.1 CS_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1578 table NCBI:align:tbl:qstat #1.0 QUAL_STAT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1579 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1580
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1581 database NCBI:align:db:alignment_evidence #1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1582 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1583 table NCBI:align:tbl:reference #2 REFERENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1584 table NCBI:align:tbl:align_unsorted #1.2 PRIMARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1585 table NCBI:align:tbl:align_mate_unsorted #1.1 SECONDARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1586 table NCBI:align:tbl:align_allele #1.2 EVIDENCE_INTERVAL;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1587 table NCBI:align:tbl:align_mate_unsorted #1.1 EVIDENCE_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1588 table NCBI:align:tbl:seq #1.1 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1589 table NCBI:align:view:cs_seq #1.1 CS_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1590 table NCBI:align:tbl:qstat #1.0 QUAL_STAT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1591 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1592
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1593 database NCBI:align:db:alignment_evidence_sorted #1.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1594 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1595 table NCBI:align:tbl:reference #2 REFERENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1596 table NCBI:align:tbl:align_sorted #1.2 PRIMARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1597 table NCBI:align:tbl:align_mate_sorted #1.1 SECONDARY_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1598 table NCBI:align:tbl:align_allele #1.2 EVIDENCE_INTERVAL;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1599 table NCBI:align:tbl:align_mate_unsorted #1.1 EVIDENCE_ALIGNMENT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1600 table NCBI:align:tbl:seq #1.1 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1601 table NCBI:align:view:cs_seq #1.1 CS_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1602 table NCBI:align:tbl:qstat #1.0 QUAL_STAT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1603 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1604
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1605 database NCBI:align:db:unaligned #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1606 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1607 table NCBI:align:tbl:seq #1.1 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1608 table NCBI:SRA:ABI:tbl:v2 #1.0.4 CS_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1609 table NCBI:align:tbl:qstat #1.0 QUAL_STAT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1610 };

Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/align.vschema @ 3:38ad1130d077 draft