/usr/lib/ncbi-vdb/align/pileup-stats.vschema is in libncbi-vdb2 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 | /*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/built-in.vschema';
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/insdc/insdc.vschema';
/*--------------------------------------------------------------------------
* tables
*/
table NCBI:pileup:tbl:pileup_stats #1
{
/* RUN_NAME
* expected to be a single value for entire object
*/
extern column ascii RUN_NAME;
/* REFERENCE_SPEC
* the canonical reference accession
* an index is stored in 'ref_spec'.
*/
extern column ascii REFERENCE_SPEC = out_reference_spec;
physical < ascii > zip_encoding .REFERENCE_SPEC
= idx:text:insert #1.0 < 'ref_spec' > ( REFERENCE_SPEC );
ascii out_reference_spec
= idx:text:project #1.0 < 'ref_spec' > ( .REFERENCE_SPEC );
/* REF_POS
* we dedicate a row to every position on the reference
* some rows are empty, other than their position
*/
extern column I64 REF_POS = out_ref_pos;
physical < I64 > izip_encoding .REF_POS = in_ref_pos;
I64 in_ref_pos
= < I64 > sub_row_id ( REF_POS )
;
I64 out_ref_pos
= < I64 > add_row_id ( .REF_POS )
| < I64 > add_row_id ( .REF_POS_TRANS )
;
/* REF_POS_TRANS
* records the translation between current row-id
* and REF_POS, such that
* row-id () + REF_POS_TRANS == REF_POS
*/
extern column I64 REF_POS_TRANS = out_ref_pos_trans;
physical < I64 > izip_encoding .REF_POS_TRANS = in_ref_pos_trans;
I64 in_ref_pos_trans
= REF_POS_TRANS
;
I64 out_ref_pos_trans
= .REF_POS_TRANS
| < I64 > sub_row_id ( .REF_POS )
;
/* REF_BASE
* this optional column records data extracted from reference
* it is the base at REF_POS
*/
extern column < INSDC:dna:text > zip_encoding REF_BASE;
/* DEPTH
* depth of coverage at REF_POS
*/
extern column < U32 > izip_encoding DEPTH;
/* MISMATCH_COUNTS
* the number of pileup bases that do not match against REF_BASE
* the normal vector MISMATCH_COUNTS [ 4 ] is recorded as MISMATCH_COUNTS [ 3 ]
* where the element representing REF_BASE has been eliminated.
*/
extern column < U32 > izip_encoding MISMATCH_COUNTS;
/* INSERTION_COUNTS
* the number of insertions-before-bases
*/
extern column < U32 > izip_encoding INSERTION_COUNTS;
/* DELETION_COUNT
* the number of deletions at REF_POS
*/
extern column < U32 > izip_encoding DELETION_COUNT;
}
/*--------------------------------------------------------------------------
* databases
*/
database NCBI:pileup:db:pileup_stats #1
{
table NCBI:pileup:tbl:pileup_stats #1 STATS;
}
|