Mercurial > repos > charles_s_test > seqsero2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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 * NCBI PacBio Fastq Sequence Read Archive schema
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 'insdc/sra.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
33 include 'ncbi/sra.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
34
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 * NCBI:SRA:PacBio
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
38 * Pacific Biotech SRA Platform
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
39 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
40 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
41 * 1.0.2 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
42 * 1.0.3 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
43 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
44 table NCBI:SRA:PacBio:common #1.0.3 = NCBI:SRA:tbl:sra #2.1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
45 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
46 }
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 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
49 * 1.0.2 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
50 * 1.0.3 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
51 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
52 table NCBI:SRA:PacBio:smrt:fastq #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
53 = NCBI:SRA:PacBio:common #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
54 , NCBI:tbl:base_space #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
55 , NCBI:tbl:phred_quality #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
56 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
57 /* PLATFORM
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
58 * platform name is always "PACBIO_SMRT"
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 ascii platform_name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
61 = < ascii > echo < "PACBIO_SMRT" > ();
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 /* TRIMMED SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
64 * need to find the 0-based trim_start and trim_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
65 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
66 INSDC:coord:zero bio_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
67 = NCBI:SRA:bio_start ( out_read_start, out_read_type );
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 INSDC:coord:zero trim_start = bio_start;
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 U32 trim_left = ( U32 ) trim_start;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
72 INSDC:coord:len trim_len = ( INSDC:coord:len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
73 < U32 > diff ( spot_len, trim_left );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
74 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
75
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
76 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
77 * NCBI:SRA:PacBio:smrt:db
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
78 * Pacific Biotech SRA Platform
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
79 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
80 table NCBI:SRA:PacBio:smrt:indelsubst #1
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 // probability that the current base is an insertion
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
83 column < U8 > zip_encoding INSERTION_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
84
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
85 // probability of a deletion error following current base
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
86 // and identity of deleted base, if it exists
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
87 column < U8 > zip_encoding DELETION_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
88 column < INSDC:dna:text > zip_encoding DELETION_TAG;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
89
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
90 // probability of a substitution error
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
91 // and most likely alternative base call
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
92 column < U8 > zip_encoding SUBSTITUTION_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
93 column < INSDC:dna:text > zip_encoding SUBSTITUTION_TAG;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
94 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
95
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
96 typedef U8 PacBio:hole:status;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
97 const PacBio:hole:status PacBio:hole:SEQUENCING = 0;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
98 const PacBio:hole:status PacBio:hole:ANTIHOLE = 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
99 const PacBio:hole:status PacBio:hole:FIDUCIAL = 2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
100 const PacBio:hole:status PacBio:hole:SUSPECT = 3;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
101 const PacBio:hole:status PacBio:hole:ANTIMIRROR = 4;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
102 const PacBio:hole:status PacBio:hole:FDZMW = 5;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
103 const PacBio:hole:status PacBio:hole:FBZMW = 6;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
104 const PacBio:hole:status PacBio:hole:ANTIBEAMLET = 7;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
105 const PacBio:hole:status PacBio:hole:OUTSIDEFOV = 8;
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 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
108 * 1.0.1 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
109 * 1.0.2 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
110 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
111 table NCBI:SRA:PacBio:smrt:basecalls #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
112 = INSDC:SRA:tbl:spotcoord #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
113 , NCBI:tbl:base_space #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
114 , NCBI:tbl:phred_quality #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
115 , NCBI:SRA:PacBio:smrt:indelsubst #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
116 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
117 /* PLATFORM
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
118 * platform name is always "PACBIO_SMRT"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
119 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
120 ascii platform_name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
121 = < ascii > echo < "PACBIO_SMRT" > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
122
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
123 // basecalls will be routed to READ column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
124 readonly column INSDC:dna:text BASECALL
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
125 = out_dna_text;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
126
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
127 // quality value for each base
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
128 readonly column INSDC:quality:phred QUALITY_VALUE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
129 = out_qual_phred;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
130
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
131 // zero-based hole number
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
132 column < U32 > izip_encoding HOLE_NUMBER;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
133
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
134 // hole status
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
135 column < PacBio:hole:status > zip_encoding HOLE_STATUS;
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 // optional column pair to describe hole status
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
138 // when/if it does not line up with our constants above
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
139 column < ascii > zip_encoding HOLE_STATUS_VALUE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
140 column < INSDC:coord:len > izip_encoding HOLE_STATUS_VALUE_LEN;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
141
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
142 // hole ( X,Y ) pair will be split and sent to X and Y columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
143 column I16 [ 2 ] HOLE_XY
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
144 = < I16 > paste ( x_clip_I16, y_clip_I16 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
145 I16 x_clip_I16 = cast ( out_x_coord );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
146 I16 y_clip_I16 = cast ( out_y_coord );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
147
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
148 I16 in_x16_coord = < I16 > cut < 0 > ( HOLE_XY );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
149 I16 in_y16_coord = < I16 > cut < 1 > ( HOLE_XY );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
150
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
151 INSDC:coord:val in_x_coord = cast ( in_x16_coord );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
152 INSDC:coord:val in_y_coord = cast ( in_y16_coord );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
153
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
154 // the number of bases in ZMW
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
155 readonly column INSDC:coord:len NUM_EVENT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
156 = base_space_spot_len;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
157 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
158
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
159 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
160 * 1.0.1 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
161 * 1.0.2 - updated ancestry
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 table NCBI:SRA:PacBio:smrt:sequence #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
164 = NCBI:SRA:PacBio:smrt:basecalls #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
165 , NCBI:SRA:tbl:sra_nopos #2.1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
166 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
167 // pulse information
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
168 column < U16 > izip_encoding PRE_BASE_FRAMES;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
169 column < U16 > izip_encoding WIDTH_IN_FRAMES;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
170
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
171 // spot to pulse map
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
172 default column INSDC:position:zero PULSE_INDEX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
173 = .PULSE_INDEX;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
174 readonly column INSDC:position:one PULSE_INDEX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
175 = out_position;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
176 INSDC:position:one out_position
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
177 = ( INSDC:position:one ) < INSDC:position:zero > sum < 1 > ( .PULSE_INDEX );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
178
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
179 column NCBI:SRA:pos16 PULSE_INDEX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
180 = cast ( .PULSE_INDEX );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
181 NCBI:SRA:pos16 in_pulse_index16
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
182 = PULSE_INDEX;
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 INSDC:position:zero in_pulse_index32
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
185 = PULSE_INDEX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
186 | cast ( in_pulse_index16 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
187
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
188 physical column < INSDC:position:zero > izip_encoding .PULSE_INDEX
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
189 = in_pulse_index32;
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 /* clip quality */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
192 extern column < INSDC:coord:zero > izip_encoding CLIP_QUALITY_LEFT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
193 extern column < INSDC:coord:one > izip_encoding CLIP_QUALITY_RIGHT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
194
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
195 /* TRIMMED SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
196 * need to find the 0-based trim_start and trim_len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
197 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
198 INSDC:coord:zero trim_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
199 = .CLIP_QUALITY_LEFT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
200 | NCBI:SRA:bio_start ( out_read_start, out_read_type );
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 U32 trim_right
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
203 = ( U32 ) .CLIP_QUALITY_RIGHT
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
204 | spot_len;
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 U32 trim_left = ( U32 ) trim_start;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
207 INSDC:coord:len trim_len = ( INSDC:coord:len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
208 < U32 > diff ( trim_right, trim_left );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
211 /* history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
212 * 1.0.1 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
213 * 1.0.2 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
214 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
215 table NCBI:SRA:PacBio:smrt:cons #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
216 = NCBI:SRA:PacBio:smrt:basecalls #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
217 , NCBI:SRA:tbl:sra #2.1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
218 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
219 // documented in both hdf5 and xsd as signed...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
220 column < I32 > izip_encoding NUM_PASSES;
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 /* TRIMMED SEQUENCE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
223 * need to find the 0-based trim_start and trim_len
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 INSDC:coord:zero trim_start
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
226 = NCBI:SRA:bio_start ( out_read_start, out_read_type );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
227
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
228 U32 trim_left = ( U32 ) trim_start;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
229 INSDC:coord:len trim_len = ( INSDC:coord:len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
230 < U32 > diff ( spot_len, trim_left );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
231 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
232
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
233 /* these encoding rules attempt to compress the channels individually,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
234 although they may compress fine interleaved as they are... */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
235 physical
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
236 F32 [ 4 ] NCBI:SRA:PacBio:smrt:F32_4ch_encoding #1.0 < U32 mantissa >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
237 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
238 decode
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 fzip_fmt cmp0 = split < 0 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
241 fzip_fmt cmp1 = split < 1 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
242 fzip_fmt cmp2 = split < 2 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
243 fzip_fmt cmp3 = split < 3 > ( @ );
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 F32 ch0 = funzip ( cmp0 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
246 F32 ch1 = funzip ( cmp1 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
247 F32 ch2 = funzip ( cmp2 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
248 F32 ch3 = funzip ( cmp3 );
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 return < F32 > paste ( ch0, ch1, ch2, ch3 );
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
253 encode
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 F32 ch0 = < F32 > cut < 0 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
256 F32 ch1 = < F32 > cut < 1 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
257 F32 ch2 = < F32 > cut < 2 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
258 F32 ch3 = < F32 > cut < 3 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
259
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
260 fzip_fmt cmp0 = fzip < mantissa > ( ch0 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
261 fzip_fmt cmp1 = fzip < mantissa > ( ch1 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
262 fzip_fmt cmp2 = fzip < mantissa > ( ch2 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
263 fzip_fmt cmp3 = fzip < mantissa > ( ch3 );
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 return merge ( cmp0, cmp1, cmp2, cmp3 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
266 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
267 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
268
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
269 table NCBI:SRA:PacBio:smrt:zmw_metrics #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
270 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
271 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > BASE_FRACTION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
272 column < F32 > fzip_encoding < 24 > BASE_IPD;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
273 column < F32 > fzip_encoding < 24 > BASE_RATE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
274 column < F32 > fzip_encoding < 24 > BASE_WIDTH;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
275 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > CHAN_BASE_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
276 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > CHAN_DEL_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
277 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > CHAN_INS_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
278 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > CHAN_SUB_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
279 column < F32 > fzip_encoding < 24 > LOCAL_BASE_RATE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
280 column < F32 > fzip_encoding < 24 > DARK_BASE_RATE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
281 column < F32 > fzip_encoding < 24 > HQ_RGN_START_TIME;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
282 column < F32 > fzip_encoding < 24 > HQ_RGN_END_TIME;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
283 column NCBI:SRA:PacBio:smrt:F32_4ch_encoding < 24 > HQ_RGN_SNR;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
284 column < I8 > zip_encoding PRODUCTIVITY;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
285 column < F32 > fzip_encoding < 24 > READ_SCORE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
286 column < F32 > fzip_encoding < 24 > READ_BASE_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
287 column < F32 > fzip_encoding < 24 > READ_DEL_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
288 column < F32 > fzip_encoding < 24 > READ_INS_QV;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
289 column < F32 > fzip_encoding < 24 > READ_SUB_QV;
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
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
292 table NCBI:SRA:PacBio:smrt:passes #1
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 column < U8 > zip_encoding ADAPTER_HIT_BEFORE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
295 column < U8 > zip_encoding ADAPTER_HIT_AFTER;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
296 column < U8 > zip_encoding PASS_DIRECTION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
297 column < I32 > izip_encoding PASS_NUM_BASES;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
298 column < I32 > izip_encoding PASS_START_BASE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
299 };
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 database NCBI:SRA:PacBio:smrt:db #1.0.1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
302 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
303 table NCBI:SRA:PacBio:smrt:sequence #1.0 SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
304 table NCBI:SRA:PacBio:smrt:cons #1.0 CONSENSUS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
305 table NCBI:SRA:PacBio:smrt:passes #1.0 PASSES;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
306 table NCBI:SRA:PacBio:smrt:zmw_metrics #1.0 ZMW_METRICS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
307 };