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

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/seq.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 * Sequence schema implementation 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/ncbi.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	34 include 'insdc/sra.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	35
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	36
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	37 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	38 * n_encoding - implementation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	39 * introduces common virtual productions
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 table NCBI:tbl:n_encoding #1
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 U8 n_encoding_dummy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	44 = read_unpack
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	45 \| read_ndecode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	46 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	47
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 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	50 * seqloc
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	51 * NCBI sequence locator table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	52 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	53 table NCBI:tbl:seqloc #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	54 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	55 /* SEQ_ID
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	56 * a FASTA-style SeqId
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	57 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	58 extern column < ascii > zip_encoding SEQ_ID;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	59
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	60 /* SEQ_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	61 * provided in both 1 ( default ) and 0-based coordinates
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 extern default column < INSDC:coord:one > izip_encoding SEQ_START;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	64 readonly column INSDC:coord:zero SEQ_START
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	65 = ( INSDC:coord:zero ) < INSDC:coord:one > diff < 1 > ( .SEQ_START );
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 /* SEQ_LEN
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 extern column < INSDC:coord:len > izip_encoding SEQ_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	70 };
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	73 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	74 * base_space - implementation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	75 * READ column rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	76 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	77
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	78 /* color_from_dna
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	79 * use starting keys and color matrix to convert individual reads
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	80 * to base space.
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 extern function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	83 INSDC:x2cs:bin NCBI:color_from_dna #1 ( INSDC:x2na:bin bin_x2na,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	84 INSDC:coord:zero read_start, INSDC:coord:len read_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	85 INSDC:dna:text cs_key, U8 color_matrix );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	88 /* dcmp_base_space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	89 * table to introduce common virtual productions
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 table NCBI:tbl:dcmp_base_space #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	92 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	93 // rules to introduce purely virtual productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	94 // never expected to resolve...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	95 INSDC:dna:text dcmp_virtual_productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	96 = out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	97 \| out_dcmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	98 \| out_dcmp_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	99 \| out_dcmp_2na_packed;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	100 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	101
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	102 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	103 * 1.0.1 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	104 * 1.0.2 - spotdesc #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	105 * 1.0.3 - base upon dcmp_base_space for "out_dcmp_2na_bin"
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 table NCBI:tbl:base_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	108 = INSDC:tbl:sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	109 , INSDC:SRA:tbl:spotdesc #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	110 , INSDC:SRA:tbl:stats #1.1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	111 , NCBI:tbl:dcmp_base_space #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	112 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	113 /* INSDC:tbl:sequence inherited virtual productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	114 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	115
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	116 // cs_native - tells user color space is not native
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	117 bool cs_native = < bool > echo < false > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	118
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	119 // in_cs_key is not writable in base_space
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 // color-space key is completely artificial
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	122 INSDC:dna:text out_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	123 = .CS_KEY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	124 \| < INSDC:dna:text > echo < 'T' > ( out_read_type )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	125 \| < INSDC:dna:text > echo < 'T' > ( out_read_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	126 \| < INSDC:dna:text > echo < 'T' > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	127
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	128 // unambiguous synthesized 2cs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	129 INSDC:2cs:bin out_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	130 = < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_x2cs_bin );
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 // unambiguous unpacked 2na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	133 INSDC:2na:bin out_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	134 = out_dcmp_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	135 \| ( INSDC:2na:bin ) unpack ( out_2na_packed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	136
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	137 // synthesized color sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	138 INSDC:x2cs:bin out_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	139 = NCBI:color_from_dna ( out_x2na_bin, out_read_start, out_read_len, out_cs_key, out_color_matrix );
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 // synthesized packed 2cs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	142 INSDC:2cs:packed out_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	143 = ( INSDC:2cs:packed ) pack ( out_2cs_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	144
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	145 // synthesized packed 4na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	146 INSDC:4na:packed out_4na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	147 = ( INSDC:4na:packed ) pack ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	148
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	149 // synthesized color text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	150 INSDC:color:text out_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	151 = < 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	152
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	153 // published color matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	154 U8 out_color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	155 = < U8 > echo < INSDC:color:default_matrix > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	156
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	157 // spot_len and fixed_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	158 INSDC:coord:len base_space_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	159 = ( INSDC:coord:len ) row_len ( out_2na_packed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	160 INSDC:coord:len base_space_fixed_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	161 = ( INSDC:coord:len ) fixed_row_len ( out_2na_packed );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	164 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	165 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	166 * in_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	167 * out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	168 * out_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	169 * out_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	170 * out_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	171 */
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 /* INSDC:SRA:tbl:stats inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	174 * in_stats_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	175 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	176
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	177 /* NCBI:tbl:dcmp_base_space inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	178 * out_dcmp_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	179 * out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	180 * out_dcmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	181 * out_dcmp_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	182 */
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
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 /* base_space_nocol
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	187 * this table describes viewing rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	188 * but omits writing rules and physical column description
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	189 * in order to support older tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	190 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	191 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	192 * 1.0.1 - base explicitly upon base_space_common #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	193 * 1.0.2 - base explicitly upon base_space_common #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	194 * 1.0.3 - " " 1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	195 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	196 table NCBI:tbl:base_space_nocol #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	197 = NCBI:tbl:base_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	198 , NCBI:tbl:n_encoding #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	199 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	200 // incoming is disabled
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	201
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	202 // synthesized dna text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	203 INSDC:dna:text out_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	204 = < INSDC:x2na:bin, INSDC:dna:text > map < INSDC:x2na:map:BINSET, INSDC:x2na:map:CHARSET > ( out_x2na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	205
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	206 // synthesized 4na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	207 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	208 = < 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	209
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	210 // unpacked 2na with ambiguities
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	211 INSDC:x2na:bin out_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	212 = ( INSDC:x2na:bin ) read_ndecode;
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 // interface with n-encoded qualities
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	215 U8 read_unpack = out_2na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	216
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	217 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	218 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	219 * out_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	220 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	221
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	222 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	223 * read_ndecode
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	227 /* base_space #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	228 * this schema brings in standard .READ column for v1 tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	229 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	230 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	231 * 1.0.1 - base explicitly upon base_space_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	232 * 1.0.2 - base explicitly upon base_space_nocol #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	233 * 1.0.3 - base explicitly upon base_space_nocol #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	234 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	235 table NCBI:tbl:base_space #1.0.3 = NCBI:tbl:base_space_nocol #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	236 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	237 // 2-bit 2na representation (0..3)
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	238 INSDC:2na:packed out_2na_packed = .READ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	239
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	240 // no rules for writing to .READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	241
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	242 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	243 * out_signal
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	246 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	247 * read_ndecode
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 };
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	252 /* base_space #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	253 * standard current base-space table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	254 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	255 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	256 * 2.0.2 - base_space_common #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	257 * 2.0.3 - base_space_common #1.0.3 now has dcmp_base_space as well
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 table NCBI:tbl:base_space #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	260 = NCBI:tbl:base_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	261 , NCBI:tbl:dcmp_base_space #1
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 /* input rules
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	266 // input text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	267 INSDC:dna:text in_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	268 = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( READ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	269
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	270 // input 4na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	271 INSDC:4na:bin in_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	272 = < INSDC:4na:bin > range_validate < 0, 15 > ( READ )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	273 \| ( INSDC:4na:bin ) unpack ( in_4na_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	274 \| < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_dna_text )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	275 \| < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( in_x2na_bin );
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 // input 4na packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	278 INSDC:4na:packed in_4na_packed = READ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	279
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	280 // input x2na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	281 INSDC:x2na:bin in_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	282 = < INSDC:x2na:bin > range_validate < 0, 4 > ( READ )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	283 \| < 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 ] > ( in_4na_bin );
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 // input 2na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	286 INSDC:2na:bin in_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	287 = < INSDC:2na:bin > range_validate < 0, 3 > ( READ )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	288 \| ( INSDC:2na:bin ) unpack ( in_2na_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	289 \| INSDC:SEQ:rand_4na_2na ( in_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	290
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	291 // input 2na packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	292 INSDC:2na:packed in_2na_packed = READ;
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 // input 4na alt-read ( ambiguities )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	295 INSDC:4na:bin in_alt_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	296 = < INSDC:4na:bin, INSDC:4na:bin > map < INSDC:4na:map:BINSET, [ 15,0,0,3,0,5,6,7,0,9,10,11,12,13,14,15 ] > ( in_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	297
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	298 // preparing a feed into stats column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	299 U8 in_stats_bin = in_2na_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	300
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 /* physical columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	303 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	304
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	305 physical column INSDC:2na:packed .READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	306 = in_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	307 \| ( INSDC:2na:packed ) pack ( in_2na_bin );
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 physical column < INSDC:4na:bin > zip_encoding .ALTREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	310 = < INSDC:4na:bin > trim < 0, 0 > ( in_alt_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	311
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 /* output rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	314 */
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 // output 2na packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	317 INSDC:2na:packed out_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	318 = .READ
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	319 \| out_dcmp_2na_packed;
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 // output x2na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	322 INSDC:x2na:bin out_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	323 = out_dcmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	324 \| < 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_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	325
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	326 // output 2na->4na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	327 INSDC:4na:bin out_2na_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	328 = < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_2na_bin );
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 // output 4na bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	331 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	332 = < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_2na_4na_bin, .ALTREAD )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	333 \| out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	334 \| out_2na_4na_bin;
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 // output text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	337 INSDC:dna:text out_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	338 = < 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	339
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	340
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	341 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	342 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	343 */
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 /* NCBI:tbl:dcmp_base_space inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	346 * out_dcmp_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	347 * out_dcmp_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	348 * out_dcmp_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	349 * out_dcmp_2na_packed
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 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	352
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	353
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	356 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	357 * color_space - implementation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	358 * nucleotide sequences in color space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	359 */
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	362 INSDC:x2na:bin NCBI:dna_from_color #1 ( INSDC:x2cs:bin color_bin,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	363 INSDC:coord:zero read_start, INSDC:coord:len read_len,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	364 INSDC:dna:text cs_key, U8 color_matrix );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	365
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	366
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	367 /* dcmp_color_space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	368 * declares common virtual productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	369 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	370 table NCBI:tbl:dcmp_color_space #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	371 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	372 // rules to introduce purely virtual productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	373 // never expected to resolve...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	374 INSDC:dna:text dcmp_virtual_productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	375 = out_dcmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	376 \| out_dcmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	377 \| out_dcmp_2cs_packed;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	378 }
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 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	381 * 1.0.1 - base explicitly upn sequence #1.0.1, spotdesc #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	382 * 1.0.2 - spotdesc #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	383 * 1.0.3 - base upon dcmp_color_space for "out_dcmp_2cs_bin"
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 table NCBI:tbl:color_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	386 = INSDC:tbl:sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	387 , INSDC:SRA:tbl:spotdesc #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	388 , INSDC:SRA:tbl:stats #1.1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	389 , NCBI:tbl:dcmp_color_space #1.0.0
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 // cs_native - tells user color space is native
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	392 bool cs_native = < bool > echo < true > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	393
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	394 // unambiguous unpacked 2cs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	395 INSDC:2cs:bin out_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	396 = out_dcmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	397 \| ( INSDC:2cs:bin ) unpack ( out_2cs_packed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	398
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	399 // unambiguous synthesized 2na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	400 INSDC:2na:bin out_2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	401 = < 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	402
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	403 // synthesized unpacked 4na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	404 INSDC:4na:bin out_4na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	405 = < 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	406
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	407 // synthesized dna text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	408 INSDC:dna:text out_dna_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	409 = < INSDC:x2na:bin, INSDC:dna:text > map < INSDC:x2na:map:BINSET, INSDC:x2na:map:CHARSET > ( out_x2na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	410
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	411 // synthesized dna sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	412 INSDC:x2na:bin out_x2na_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	413 = NCBI:dna_from_color ( out_x2cs_bin, out_read_start, out_read_len, out_cs_key, out_color_matrix );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	414
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	415 // synthesized packed 2na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	416 INSDC:2na:packed out_2na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	417 = ( INSDC:2na:packed ) pack ( out_2na_bin );
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 // synthesized packed 4na
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	420 INSDC:4na:packed out_4na_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	421 = ( INSDC:4na:packed ) pack ( out_4na_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	422
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	423 // synthesized color text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	424 INSDC:color:text out_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	425 = < 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	426
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	427 // spot_len and fixed_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	428 INSDC:coord:len color_space_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	429 = ( INSDC:coord:len ) row_len ( out_2cs_packed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	430 INSDC:coord:len color_space_fixed_spot_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	431 = ( INSDC:coord:len ) fixed_row_len ( out_2cs_packed );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	432
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	433 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	434 * in_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	435 * out_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	436 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	437 * out_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	438 * in_color_text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	439 * out_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	440 * out_color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	441 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	442
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	443 /* INSDC:SRA:tbl:stats inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	444 * in_stats_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	445 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	446
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	447 /* NCBI:tbl:dcmp_color_space inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	448 * out_dcmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	449 * out_dcmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	450 * out_dcmp_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	451 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	452 };
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 /* color_space_nocol
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	455 * this table describes viewing rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	456 * but omits writing rules and physical column description
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	457 * in order to support older tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	458 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	459 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	460 * 1.0.1 - base explicitly upon color_space_common #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	461 * 1.0.2 - color_space_common #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	462 * 1.0.3 - color_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	463 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	464 table NCBI:tbl:color_space_nocol #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	465 = NCBI:tbl:color_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	466 , NCBI:tbl:n_encoding #1
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 // incoming is disabled
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 // v1 color matrix was stored in metadata
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	471 U8 out_color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	472 = < U8 > meta:read < "COLOR_MATRIX" > ()
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	473 \| < U8 > echo < INSDC:color:default_matrix > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	474
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	475 // unpacked 2cs with ambiguities
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	476 INSDC:x2cs:bin out_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	477 = ( INSDC:x2cs:bin ) read_ndecode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	478
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	479 // interface with n-encoded qualities
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	480 U8 read_unpack = out_2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	481
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	482 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	483 * out_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	484 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	485 * out_2cs_packed
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 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	489 * read_ndecode
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 };
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 /* color_space #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	494 * this schema brings in .CSREAD and .CS_KEY columns for v1 tables
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	495 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	496 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	497 * 1.0.1 - base explicitly upon color_space_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	498 * 1.0.2 - color_space_nocol #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	499 * 1.0.3 - color_space_nocol #1.0.3
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 table NCBI:tbl:color_space #1.0.3 = NCBI:tbl:color_space_nocol #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	502 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	503 // stored as text
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	504 INSDC:dna:text out_cs_key = .CS_KEY;
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 // stored color sequence
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	507 INSDC:2cs:packed out_2cs_packed = .CSREAD;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	508
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	509 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	510 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	511 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	512
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	513 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	514 * read_ndecode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	515 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	516 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	517
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	518 /* color_space #2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	519 * standard current color-space table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	520 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	521 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	522 * 2.0.1 - base explicitly upon color_space_common #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	523 * 2.0.2 - base explicitly upon color_space_common #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	524 * 2.1.0 - introduce hooks for compressed color space
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	525 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	526 table NCBI:tbl:color_space #2.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	527 = NCBI:tbl:color_space_common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	528 , NCBI:tbl:dcmp_color_space #1.0.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	529 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	530 /* input rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	531 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	532
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	533 // input text is not modified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	534 // illegal values are not detected here
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	535 INSDC:color:text in_color_text = CSREAD;
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 // input x2cs bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	538 // illegal values will be caught here
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	539 INSDC:x2cs:bin in_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	540 = < INSDC:x2cs:bin > range_validate < 0, 4 > ( CSREAD )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	541 \| < INSDC:color:text, INSDC:x2cs:bin > map < INSDC:x2cs:map:CHARSET, INSDC:x2cs:map:BINSET > ( in_color_text );
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 // input 2cs bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	544 INSDC:2cs:bin in_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	545 = < INSDC:2cs:bin > range_validate < 0, 3 > ( CSREAD )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	546 \| ( INSDC:2cs:bin ) unpack ( in_2cs_packed )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	547 \| < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( in_x2cs_bin );
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 // input 2cs packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	550 INSDC:2cs:packed in_2cs_packed = CSREAD;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	551
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	552 // input x2cs alt-csread ( ambiguity )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	553 INSDC:x2cs:bin in_alt_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	554 = < INSDC:x2cs:bin, INSDC:x2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 0, 0, 0, 4 ] > ( in_x2cs_bin );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	555
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	556 // color-space keys ARE modified on input
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	557 INSDC:dna:text in_cs_key
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	558 = < INSDC:dna:text, INSDC:dna:text > map < 'acgt', 'ACGT' > ( CS_KEY );
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 // color matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	561 U8 in_color_matrix = < U8 > range_validate < 0, 4 > ( COLOR_MATRIX );
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 // prepairing a feed into stats column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	564 U8 in_stats_bin = in_2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	565
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	566
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	567 /* physical columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	568 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	569
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	570 physical column INSDC:2cs:packed .CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	571 = in_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	572 \| ( INSDC:2cs:packed ) pack ( in_2cs_bin );
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 physical column < INSDC:x2cs:bin > zip_encoding .ALTCSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	575 = < INSDC:x2cs:bin > trim < 0, 0 > ( in_alt_x2cs_bin );
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 physical column < INSDC:dna:text > zip_encoding .CS_KEY = in_cs_key;
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 physical column < U8 > zip_encoding .COLOR_MATRIX = in_color_matrix;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	580
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 /* output rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	583 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	584
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	585 // output 2cs packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	586 INSDC:2cs:packed out_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	587 = .CSREAD
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	588 \| out_dcmp_2cs_packed;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	589
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	590 // unpacked 2cs with ambiguity
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	591 INSDC:x2cs:bin out_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	592 = ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_2cs_bin, .ALTCSREAD )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	593 \| out_dcmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	594 \| ( INSDC:x2cs:bin ) out_2cs_bin;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	595
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	596 // read directly from physical column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	597 INSDC:dna:text out_cs_key = .CS_KEY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	598
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	599 // color matrix may be synthesized
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	600 U8 out_color_matrix
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	601 = .COLOR_MATRIX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	602 \| < U8 > echo < INSDC:color:default_matrix > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	603
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	604
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	605 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	606 * out_signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	607 */
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 /* NCBI:tbl:dcmp_color_space inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	610 * out_dcmp_2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	611 * out_dcmp_x2cs_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	612 * out_dcmp_2cs_packed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	613 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	614 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	615
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	616
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	617 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	618 * protein
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	619 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	620 table NCBI:tbl:protein #1 = INSDC:tbl:protein
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 /* upper-case letters */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	623 INSDC:protein:text in_protein_text = < INSDC:protein:text, INSDC:protein:text >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	624 map < 'abcdefghijklmnopqrstvwxyzu','ABCDEFGHIJKLMNOPQRSTVWXYZU' > ( PROTEIN );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	625
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	626 /* std aa */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	627 INSDC:aa:bin in_aa_bin
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	628 = < INSDC:aa:bin > range_validate < 1, 27 > ( PROTEIN )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	629 \| < INSDC:protein:text, INSDC:aa:bin > map < INSDC:aa:map:CHARSET, INSDC:aa:map:BINSET > ( in_protein_text );
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 /* physical column */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	632 physical column < INSDC:aa:bin > zip_encoding .PROTEIN = in_aa_bin;
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 /* output rules */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	635 INSDC:aa:bin out_aa_bin = .PROTEIN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	636 INSDC:protein:text out_protein_text = < INSDC:aa:bin, INSDC:protein:text >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	637 map < INSDC:aa:map:BINSET, INSDC:aa:map:CHARSET > ( out_aa_bin );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	640
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 * phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	643 * standard phred quality representation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	644 * limits values on input to 1..63
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	645 * reserves value 0 as ambiguity symbol for reads
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	648
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	649 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	650 * 1.0.1 - base explicitly upon sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	651 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	652 table NCBI:tbl:phred_quality_nocol #1.0.1 = INSDC:tbl:sequence #1.0.1, NCBI:tbl:n_encoding #1
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 /* [CS]READ - decoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	655 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	656 U8 read_ndecode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	657 = < INSDC:quality:phred, U8 > map < 0, 4 > ( out_qual_phred, read_unpack );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	658
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	659 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	660 * out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	661 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	662 * out_qual_text_phred_64
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	665 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	666 * read_unpack
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	667 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	668 };
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 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	671 * 1.0.1 - base explicitly upon phred_quality_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	672 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	673 table NCBI:tbl:phred_quality #1.0.1 = NCBI:tbl:phred_quality_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	674 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	675 // read directly as n-encoded phred is compatible with phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	676 NCBI:quality:n_encoded:phred out_qual_phred = .QUALITY;
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:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	679 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	680 * out_qual_text_phred_64
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	681 */
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 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	684 * read_unpack
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	685 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	686 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	687
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	688 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	689 * 2.0.1 - added feed of in_stats_qual
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	690 * 2.0.2 - added input of text encodings
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	691 * 2.0.3 - base explicitly upon sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	692 * 2.0.4 - change compression from izip to zip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	693 * 2.0.5 - change from zip to delta_average_zip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	694 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	695 table NCBI:tbl:phred_quality #2.0.4 = INSDC:tbl:sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	696 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	697 // read directly quality as phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	698 INSDC:quality:phred out_qual_phred = .QUALITY;
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 // input rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	701 INSDC:quality:text:phred_33 in_qual_text_phred_33 = QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	702 INSDC:quality:text:phred_64 in_qual_text_phred_64 = QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	703
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	704 INSDC:quality:phred in_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	705 = QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	706 \| ( INSDC:quality:phred ) < B8 > diff < 33 > ( in_qual_text_phred_33 )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	707 \| ( INSDC:quality:phred ) < B8 > diff < 64 > ( in_qual_text_phred_64 );
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 // physical storage
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	710 /* next line is for future change in production, but we have to wait until supporting code is released to the public */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	711 // physical column < INSDC:quality:phred > delta_average_zip_encoding .QUALITY = in_qual_phred;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	712 /* NB * MUST change table version to 2.0.5 and propagate to all derived tables ***/
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	713 physical column < INSDC:quality:phred > zip_encoding .QUALITY = in_qual_phred;
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 // feed to compressed statistics
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	716 INSDC:quality:phred in_stats_qual = in_qual_phred;
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 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	719 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	720 * out_qual_text_phred_64
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	721 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	722 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	723
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	724
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 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	727 * log_odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	728 * log-odds quality score support
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	729 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	730 * conversion from log-odds to phred is via formula
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	731 * 10 * log ( 1 + pow ( 10, x / 10 ) ) / log ( 10 ) + 0.499
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	732 * for x = -4..40 : when x = -5, phred = 0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	733 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	734
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	735 // the map function requires two lookup tables:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	736 // the first table detects every legal value...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	737 const INSDC:quality:log_odds NCBI:quality:from:log_odds =
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	738 [
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	739 -6,-5,-4,-3,-2,-1, 0,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	740 1, 2, 3, 4, 5, 6, 7, 8, 9,10,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	741 11,12,13,14,15,16,17,18,19,20,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	742 21,22,23,24,25,26,27,28,29,30,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	743 31,32,33,34,35,36,37,38,39,40
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	744 ];
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	745
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	746 // ...the second table gives positional translations
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	747 const INSDC:quality:phred NCBI:quality:to:phred =
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 0, 1, 1, 2, 2, 3, 3,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	750 4, 4, 5, 5, 6, 7, 8, 9,10,10,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	751 11,12,13,14,15,16,17,18,19,20,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	752 21,22,23,24,25,26,27,28,29,30,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	753 31,32,33,34,35,36,37,38,39,40
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	754 ];
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 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	757 INSDC:quality:phred NCBI:log_odds_to_phred #1 ( INSDC:quality:log_odds qual_log_odds )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	758 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	759 // this range enforcement may not be required
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	760 INSDC:quality:log_odds log_odds_clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	761 = < INSDC:quality:log_odds > clip < -6, 40 > ( qual_log_odds );
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 // use the tables above to map from log-odds to phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	764 return < INSDC:quality:log_odds, INSDC:quality:phred >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	765 map < NCBI:quality:from:log_odds, NCBI:quality:to:phred > ( log_odds_clip );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	766 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	767
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	768 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	769 * 1.0.1 - base explicitly upon sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	770 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	771 table NCBI:tbl:log_odds_quality_nocol #1.0.1 = INSDC:tbl:sequence #1.0.1, NCBI:tbl:n_encoding #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	772 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	773 /* READ - decoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	774 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	775 U8 read_ndecode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	776 = < INSDC:quality:log_odds, U8 > map < -6, 4 > ( out_qual_log_odds, read_unpack );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	777
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	778 /* QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	779 * declared in INSDC:tbl:sequence as phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	780 * introduce here as log-odds
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:quality:log_odds QUALITY = out_qual_log_odds;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	783
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	784 // resolve for phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	785 INSDC:quality:phred out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	786 = out_qual2_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	787 \| NCBI:log_odds_to_phred ( out_qual_log_odds );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	788
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	789 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	790 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	791 * out_qual_text_phred_64
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	794 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	795 * read_unpack
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	798 /* NCBI:tbl:log_odds_quality_nocol productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	799 * out_qual2_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	800 * out_qual_log_odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	801 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	802 };
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 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	805 * 1.0.1 - base explicitly upon log_odds_quality_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	806 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	807 table NCBI:tbl:log_odds_quality #1.0.1 = NCBI:tbl:log_odds_quality_nocol #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	808 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	809 // read directly as n-encoded log_odds is compatible with log_odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	810 NCBI:quality:n_encoded:log_odds out_qual_log_odds = .QUALITY;
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 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	813 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	814 * out_qual_text_phred_64
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	817 /* NCBI:tbl:n_encoding inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	818 * read_unpack
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	821 /* NCBI:tbl:log_odds_quality_nocol inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	822 * out_qual2_phred
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 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	825
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	826 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	827 * 2.0.1 - base explicitly upon sequence #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	828 * 2.1.0 - added production of in_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	829 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	830 table NCBI:tbl:log_odds_quality_nocol #2.1.0 = INSDC:tbl:sequence #1.0.1
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 /* QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	833 * declared in INSDC:tbl:sequence as phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	834 * introduce here as log-odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	835 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	836 extern column INSDC:quality:log_odds QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	837 = out_qual_log_odds;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	838
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	839 // resolve for phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	840 INSDC:quality:phred in_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	841 = NCBI:log_odds_to_phred ( in_qual_log_odds );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	842
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	843 INSDC:quality:phred out_qual_phred
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	844 = NCBI:log_odds_to_phred ( out_qual_log_odds );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	847 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	848 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	849 * out_qual_text_phred_64
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	852 /* NCBI:tbl:log_odds_quality_nocol productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	853 * out_qual_log_odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	854 */
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	857 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	858 * 2.0.1 - added feed of in_stats_qual
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	859 * 2.0.2 - added input of text encodings
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	860 * 2.0.3 - base explicitly upon log_odds_quality_nocol #2.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	861 * 2.0.4 - changed compression from izip to zip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	862 * 2.1.0 - base explicitly upon log_odds_quality_nocol #2.1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	863 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	864 table NCBI:tbl:log_odds_quality #2.1.0 = NCBI:tbl:log_odds_quality_nocol #2.1.0
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 INSDC:quality:log_odds out_qual_log_odds= .QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	867
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	868 extern column INSDC:quality:text:log_odds_64 QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	869 = out_qual_text_log_odds_64
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	870 \| ( INSDC:quality:text:log_odds_64 ) < B8 > sum < 64 > ( out_qual_log_odds );
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 // input rules
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	873 INSDC:quality:text:log_odds_64 in_qual_text_log_odds_64 = QUALITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	874
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	875 INSDC:quality:log_odds in_qual_log_odds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	876 = QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	877 \| ( INSDC:quality:log_odds ) < B8 > diff < 64 > ( in_qual_text_log_odds_64 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	878
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	879 physical column < INSDC:quality:log_odds > zip_encoding .QUALITY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	880 = in_qual_log_odds;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	881
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	882 // feed to compressed statistics
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	883 INSDC:quality:log_odds in_stats_qual = in_qual_log_odds;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	884
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	885
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	886 /* INSDC:tbl:sequence inherited productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	887 * out_qual_text_phred_33
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	888 * out_qual_text_phred_64
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	889 */
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 /* NCBI:tbl:log_odds_quality productions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	892 * out_qual_text_log_odds_64
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 };

Mercurial > repos > charles_s_test > seqsero2

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