Mercurial > repos > charles_s_test > seqsero2

comparison libs/sratoolkit.2.8.0-centos_linux64/schema/align/qstat.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
comparison
equal deleted inserted replaced
2:0d65b71ff8df 3:38ad1130d077
1 /*===========================================================================
2 *
3 * PUBLIC DOMAIN NOTICE
4 * National Center for Biotechnology Information
5 *
6 * This software/database is a "United States Government Work" under the
7 * terms of the United States Copyright Act. It was written as part of
8 * the author's official duties as a United States Government employee and
9 * thus cannot be copyrighted. This software/database is freely available
10 * to the public for use. The National Library of Medicine and the U.S.
11 * Government have not placed any restriction on its use or reproduction.
12 *
13 * Although all reasonable efforts have been taken to ensure the accuracy
14 * and reliability of the software and data, the NLM and the U.S.
15 * Government do not and cannot warrant the performance or results that
16 * may be obtained by using this software or data. The NLM and the U.S.
17 * Government disclaim all warranties, express or implied, including
18 * warranties of performance, merchantability or fitness for any particular
19 * purpose.
20 *
21 * Please cite the author in any work or product based on this material.
22 *
23 * ===========================================================================
24 *
25 */
26
27 /*==========================================================================
28 * VDB Quality Statistics Table
29 */
30 version 1;
31
32 include 'vdb/vdb.vschema';
33 include 'ncbi/ncbi.vschema';
34
35 table NCBI:align:tbl:qstat #1.0
36 {
37 /* SPOT_GROUP
38 */
39 extern column < ascii > zip_encoding SPOT_GROUP;
40
41 /* CYCLE
42 * machine cycle
43 */
44 extern column < U32 > izip_encoding CYCLE;
45
46 /* KMER
47 * use dimer
48 */
49 extern column INSDC:dna:text KMER;
50
51 /* HPRUN
52 * homopolymer run
53 * number of bases of the same type preceding the current base
54 */
55 extern column < INSDC:coord:len > izip_encoding HPRUN;
56
57 /* GC_CONTENT
58 * number of G's or C's in the 7 bases preceding the current base
59 */
60 extern column < U32 > izip_encoding GC_CONTENT;
61
62 /* ORIG_QUAL
63 * original quality scores
64 */
65 extern column < INSDC:quality:phred > zip_encoding ORIG_QUAL;
66
67 /* MAX_QUAL
68 * max. quality score in read
69 */
70 extern column < INSDC:quality:phred > zip_encoding MAX_QUAL;
71
72 /* NREAD
73 * number of the read
74 */
75 extern column < U8 > zip_encoding NREAD;
76
77 /* TOTAL_COUNT
78 * total count of observed events
79 */
80 extern column < U32 > izip_encoding TOTAL_COUNT;
81
82 /* MISMATCH_COUNT
83 * count of observed mismatches
84 */
85 extern column < U32 > izip_encoding MISMATCH_COUNT;
86
87 };