/usr/lib/ncbi-vdb/align/mate-cache.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 | /*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* VDB mate-cache types, functions and tables
*/
version 1;
include '/usr/lib/ncbi-vdb/insdc/insdc.vschema';
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/insdc/sra.vschema';
/*--------------------------------------------------------------------------
* data types
*/
/*--------------------------------------------------------------------------
* functions
*/
/*--------------------------------------------------------------------------
* tables
*/
table NCBI:align:tbl:mate_cache #1.1
{
/* SAM_FLAGS
*/
extern column < U32 > izip_encoding SAM_FLAGS_CACHE;
/* SAM_QUALITY
*/
extern column < INSDC:quality:text:phred_33 > zip_encoding SAM_QUALITY_CACHE;
/* TEMPLATE_LEN
*/
extern column < I32 > izip_encoding TEMPLATE_LEN_CACHE;
/* MATE_ALIGN_ID
*/
extern column < I64 > izip_encoding MATE_ALIGN_ID_CACHE;
/* MATE_REF_NAME
*/
extern column < ascii > zip_encoding MATE_REF_NAME_CACHE;
/* MATE_REF_POS
*/
extern column < INSDC:coord:zero > izip_encoding MATE_REF_POS_CACHE;
/* ALIGNMENT_COUNT
*/
extern column < U8 > izip_encoding ALIGNMENT_COUNT_CACHE;
/* RD_FILTER
*/
extern column < INSDC:SRA:read_filter > zip_encoding RD_FILTER_CACHE;
readonly column INSDC:SRA:read_filter READ_FILTER_CACHE = .RD_FILTER_CACHE;
/* SPOT_GROUP
*/
extern column < ascii > zip_encoding SPOT_GROUP_CACHE;
readonly column ascii SEQ_SPOT_GROUP_CACHE = .SPOT_GROUP_CACHE;
};
/*--------------------------------------------------------------------------
* databases
*/
database NCBI:align:db:mate_cache #1
{
table NCBI:align:tbl:mate_cache #1.1 PRIMARY_ALIGNMENT;
};
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