/usr/lib/ncbi-vdb/ncbi/ncbi.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.
*
* ===========================================================================
*
*/
/*==========================================================================
* VDB Schema intrinsic types and functions
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/insdc/insdc.vschema';
/*--------------------------------------------------------------------------
* data types
*/
// N-encoded phred has values limited to 1..63 and 0 used for N
typedef INSDC:quality:phred NCBI:quality:n_encoded:phred;
// N-encoded log-odds has values limite to -5..40 and -6 for N
typedef INSDC:quality:log_odds NCBI:quality:n_encoded:log_odds;
// these types have been restated
alias INSDC:dna:text INSDC:fasta;
alias INSDC:4na:packed INSDC:dna:4na;
alias INSDC:2na:packed INSDC:dna:2na;
alias INSDC:2na:packed NCBI:2na;
alias INSDC:2cs:packed INSDC:color:2cs;
alias INSDC:2cs:packed NCBI:2cs;
alias INSDC:quality:phred NCBI:qual1;
alias NCBI:quality:n_encoded:phred NCBI:SRA:enc_qual1;
// 16-bit integer sample data
typedef I16 NCBI:isamp1, NCBI:isamp4 [ 4 ];
// 32-bit floating point sample data
typedef F32 NCBI:fsamp1, NCBI:fsamp4 [ 4 ];
// ASN.1
typedef B8 NCBI:asn:binary;
typedef ascii NCBI:asn:text;
// GenInfo id - 64 bit because we are almost out of 32 bit ids
typedef U64 NCBI:gi;
// Taxonomy id
typedef U32 NCBI:taxid;
// Genbank status
typedef U32 NCBI:gb_state;
/*--------------------------------------------------------------------------
* formats
* many of these formats are older than the current corresponding vdb fmts
*/
fmtdef merged_t;
fmtdef fp_encoded_t;
fmtdef rl_encoded_t;
fmtdef NCBI:zlib_encoded_t;
fmtdef NCBI:fp_encoded_t;
/*--------------------------------------------------------------------------
* functions
*/
/* merge
* split
* the original versions of these functions
* used a slightly different format giving them
* a different signature from their vdb counterparts.
*
* here to maintain backward compatibility for
* column schema functions
*/
extern function
merged_t NCBI:merge #1.0 ( any in, ... );
extern function
any NCBI:split #1.0 < U32 idx > ( merged_t in )
= vdb:split;
/* cut
* paste
* these have no compiler type-checking
*/
extern function
any NCBI:cut #1.0 < U32 idx, ... > ( any in )
= vdb:cut;
extern function
any NCBI:paste #1.0 ( any in, ... )
= vdb:paste;
/* pack
* unpack
* wildcard typed
*/
extern function
any NCBI:pack #1.0 < U32 from, U32 to > ( any in );
extern function
any NCBI:unpack #1.0 < U32 from, U32 to > ( any in );
/* fp_decode
* OBSOLETE
* here to handle anything encoded with fp_encode
*/
extern function
any NCBI:fp_decode #1.0 ( fp_encoded_t in );
/* fp_extend
* OBSOLETE
* here to handle anything encoded with fp_truncate
*/
extern function
any NCBI:fp_extend #1.0 < U32 bits > ( NCBI:fp_encoded_t in );
/* run_length_encode
* run_length_decode
*/
extern function
rl_encoded_t NCBI:run_length_encode #1.0 ( any in )
= vdb:rlencode;
extern function
any NCBI:run_length_decode #1.0 ( rl_encoded_t in )
= vdb:rldecode;
/* zlib
* unzip
* variation on the formatting
*/
extern function
NCBI:zlib_encoded_t NCBI:zlib #1.0 < * I32 strategy, I32 level > ( any in )
= vdb:zip;
extern function
any NCBI:unzip #1.0 ( NCBI:zlib_encoded_t in );
/* zlib_huffman_compress
* invokes zlib in huffman + rle mode
*/
schema function
NCBI:zlib_encoded_t NCBI:zlib_huffman_compress #1.0 ( any in )
{
// named as Huffman, but apply RLE as well
return NCBI:zlib < Z_RLE > ( in );
}
/* zlib_compress
* standard zlib
*/
schema function
NCBI:zlib_encoded_t NCBI:zlib_compress #1.0 ( any in )
{
return NCBI:zlib < Z_DEFAULT_STRATEGY > ( in );
}
/* zlib_decompress
* alternate name for unzip
*/
alias NCBI:unzip NCBI:zlib_decompress;
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