/usr/lib/ncbi-vdb/align/seq.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.
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*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* Sequence schema
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/ncbi/seq.vschema';
/* cmp_base_space
* table representing compressed reads in base space,
* where the bases are only stored for unaligned reads
*/
table NCBI:align:tbl:cmp_base_space #1
= INSDC:tbl:sequence #1.0.1
, NCBI:tbl:dcmp_base_space #1
{
/* CMP_READ
* read compressed against a reference sequence
*/
// default is IUPAC character representation
extern default column INSDC:dna:text CMP_READ
{
read = out_cmp_dna_text;
validate = < INSDC:dna:text > compare ( in_cmp_dna_text, out_cmp_dna_text );
}
// 4na representation
extern column INSDC:4na:bin CMP_READ = out_cmp_4na_bin;
extern column INSDC:4na:packed CMP_READ = out_cmp_4na_packed;
// x2na representation - 2na with ambiguity
extern column INSDC:x2na:bin CMP_READ = out_cmp_x2na_bin;
// 2na representation - 2na with no ambiguity
extern column INSDC:2na:bin CMP_READ = out_cmp_2na_bin;
extern column INSDC:2na:packed CMP_READ = out_cmp_2na_packed;
/* input processing rules
*/
// compressed input text
INSDC:dna:text in_cmp_dna_text
= < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( CMP_READ );
// compressed input 4na bin
INSDC:4na:bin in_cmp_4na_bin
= < INSDC:4na:bin > range_validate < 0, 15 > ( CMP_READ )
| ( INSDC:4na:bin ) unpack ( in_cmp_4na_packed )
| < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_cmp_dna_text )
| < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( in_cmp_x2na_bin );
// compressed input 4na packed
INSDC:4na:packed in_cmp_4na_packed = CMP_READ;
// compressed input x2na bin
INSDC:x2na:bin in_cmp_x2na_bin
= < INSDC:x2na:bin > range_validate < 0, 4 > ( CMP_READ )
| < 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_cmp_4na_bin );
// compressed input 2na bin
INSDC:2na:bin in_cmp_2na_bin
= < INSDC:2na:bin > range_validate < 0, 3 > ( CMP_READ )
| ( INSDC:2na:bin ) unpack ( in_cmp_2na_packed )
| INSDC:SEQ:rand_4na_2na ( in_cmp_4na_bin );
// compressed input 2na packed
INSDC:2na:packed in_cmp_2na_packed = CMP_READ;
// input 4na alt-read ( ambiguities )
INSDC:4na:bin in_cmp_alt_4na_bin
= < 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_cmp_4na_bin );
// preparing a feed into stats column
U8 in_cmp_stats_bin = in_cmp_2na_bin;
/* physical columns
*/
physical column INSDC:2na:packed .CMP_READ
= in_cmp_2na_packed
| ( INSDC:2na:packed ) pack ( in_cmp_2na_bin );
physical column < INSDC:4na:bin > zip_encoding .CMP_ALTREAD
= < INSDC:4na:bin > trim < 0, 0 > ( in_cmp_alt_4na_bin );
/* output processing rules
*/
// output 2na packed
INSDC:2na:packed out_cmp_2na_packed = .CMP_READ;
// unambiguous unpacked 2na
INSDC:2na:bin out_cmp_2na_bin
= ( INSDC:2na:bin ) unpack ( out_cmp_2na_packed );
// output x2na bin
INSDC:x2na:bin out_cmp_x2na_bin
= < 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_cmp_4na_bin );
// output 2na->4na bin
INSDC:4na:bin out_cmp_2na_4na_bin
= < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_cmp_2na_bin );
// output 4na bin
INSDC:4na:bin out_cmp_4na_bin
= < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_cmp_2na_4na_bin, .CMP_ALTREAD )
| out_cmp_2na_4na_bin;
// synthesized packed 4na
INSDC:4na:packed out_cmp_4na_packed
= ( INSDC:4na:packed ) pack ( out_cmp_4na_bin );
// output text
INSDC:dna:text out_cmp_dna_text
= < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_cmp_4na_bin );
/* decompressed sequences
* source is out_dcmp_4na_bin - a virtual production
*/
// synthesize x2na_bin, 2na_bin and 2na_packed
INSDC:x2na:bin out_dcmp_x2na_bin
= < 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_dcmp_4na_bin );
INSDC:2na:bin out_dcmp_2na_bin
= < INSDC:x2na:bin, INSDC:2na:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2na_bin );
INSDC:2na:packed out_dcmp_2na_packed
= ( INSDC:2na:packed ) pack ( out_dcmp_2na_bin );
/* INSDC:tbl:sequence inherited productions
* cs_native
* out_cs_key
* out_signal
* out_2cs_bin
* out_2na_bin
* out_4na_bin
* out_dna_text
* out_x2cs_bin
* out_x2na_bin
* out_2cs_packed
* out_2na_packed
* out_4na_packed
* out_color_text
* out_color_matrix
*/
/* NCBI:tbl:dcmp_base_space inherited productions
* out_dcmp_4na_bin
*/
}
/* cmp_color_space
* table representing compressed reads in color space,
* where the colors are only stored for unaligned reads
*/
table NCBI:align:tbl:cmp_color_space #1 =
INSDC:tbl:sequence #1.0.1, NCBI:tbl:dcmp_color_space #1
{
/* CMP_CSREAD
* read compressed against a reference sequence
*/
// default is IUPAC character representation
extern default column INSDC:color:text CMP_CSREAD = out_cmp_color_text;
// x2cs representation - 2cs with ambiguity
extern column INSDC:x2cs:bin CMP_CSREAD = out_cmp_x2cs_bin;
// 2cs representation - 2cs with no ambiguity
extern column INSDC:2cs:bin CMP_CSREAD = out_cmp_2cs_bin;
extern column INSDC:2cs:packed CMP_CSREAD = out_cmp_2cs_packed;
/* input processing rules
*/
// compressed input text
INSDC:color:text in_cmp_color_text = CMP_CSREAD;
// compressed input x2cs bin
INSDC:x2cs:bin in_cmp_x2cs_bin
= < INSDC:x2cs:bin > range_validate < 0, 4 > ( CMP_CSREAD )
| < INSDC:color:text, INSDC:x2cs:bin > map < INSDC:x2cs:map:CHARSET, INSDC:x2cs:map:BINSET > ( in_cmp_color_text );
// compressed input 2cs bin
INSDC:2cs:bin in_cmp_2cs_bin
= < INSDC:2cs:bin > range_validate < 0, 3 > ( CMP_CSREAD )
| ( INSDC:2cs:bin ) unpack ( in_cmp_2cs_packed )
| < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( in_cmp_x2cs_bin );
// compressed input 2cs packed
INSDC:2cs:packed in_cmp_2cs_packed = CMP_CSREAD;
// compressed input x2cs alt-read ( ambiguities )
INSDC:x2cs:bin in_cmp_alt_x2cs_bin
= < INSDC:x2cs:bin, INSDC:x2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 0, 0, 0, 4 ] > ( in_cmp_x2cs_bin );
// preparing a feed into stats column
U8 in_cmp_stats_bin = in_cmp_2cs_bin;
/* physical columns
*/
physical column INSDC:2cs:packed .CMP_CSREAD
= in_cmp_2cs_packed
| ( INSDC:2cs:packed ) pack ( in_cmp_2cs_bin );
physical column < INSDC:x2cs:bin > zip_encoding .CMP_ALTCSREAD
= < INSDC:x2cs:bin > trim < 0, 0 > ( in_cmp_alt_x2cs_bin );
/* output processing rules
*/
// compressed output 2cs packed
INSDC:2cs:packed out_cmp_2cs_packed = .CMP_CSREAD;
// unambiguous unpacked 2cs
INSDC:2cs:bin out_cmp_2cs_bin
= ( INSDC:2cs:bin ) unpack ( out_cmp_2cs_packed );
// unpacked 2cs with ambiguity
INSDC:x2cs:bin out_cmp_x2cs_bin
= ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_cmp_2cs_bin, .CMP_ALTCSREAD )
| ( INSDC:x2cs:bin ) out_cmp_2cs_bin;
// output text
INSDC:color:text out_cmp_color_text
= < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_cmp_x2cs_bin );
/* decompressed sequences
* sources are out_dcmp_x2cs_bin - virtual production
*/
// synthesize 2cs_bin and 2cs_packed
INSDC:2cs:bin out_dcmp_2cs_bin
= < INSDC:x2cs:bin, INSDC:2cs:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2cs_bin );
INSDC:2cs:packed out_dcmp_2cs_packed
= ( INSDC:2cs:packed ) pack ( out_dcmp_2cs_bin );
/* INSDC:tbl:sequence inherited productions
* cs_native
* out_cs_key
* out_signal
* out_2cs_bin
* out_2na_bin
* out_4na_bin
* out_dna_text
* out_x2cs_bin
* out_x2na_bin
* out_2cs_packed
* out_2na_packed
* out_4na_packed
* out_color_text
* out_qual_phred
* out_color_matrix
* out_qual_text_phred_33
* out_qual_text_phred_64
*/
/* NCBI:tbl:dcmp_color_space inherited productions
* out_dcmp_x2cs_bin
*/
}
|