/usr/lib/ncbi-vdb/sra/pevents.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.
*
* ===========================================================================
*
*/
/*==========================================================================
* NCBI Likelihood & Event schema
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
typedef U8 INSDC:phred;
typedef ascii INSDC:event:text;
const INSDC:event:text INSDC:event:CHARSET = "ACGT0123B+-";
const INSDC:event:text INSDC:event:ACCEPTSET = "ACGTacgt0123B+-";
extern function < U32 dim >
U32 NCBI:SRA:sort_order #1.0 ( F32[dim] likelihoods );
extern function < U32 dim >
F32 NCBI:SRA:reorder #1.0 ( U32 sort_order, F32[dim] likelihoods );
extern function < U32 dim >
F32 NCBI:SRA:restore_order #1.0 ( U32 sort_order, F32[dim] likelihoods );
extern function < U32 sdim, U32 rdim >
INSDC:phred[rdim] NCBI:SRA:likelihood_to_phred #1.0 ( F32 like_scale, F32[sdim] likelihoods );
extern function < U32 sdim, U32 rdim >
F32[rdim] NCBI:SRA:phred_to_likelihood #1.0 ( F32 like_scale, F32[sdim] phred );
table NCBI:SRA:tbl:pevents #1.0
{
// event labels - single character events
extern column
INSDC:event:text PEVENTS = .PEVENTS;
physical column < INSDC:event:text >
zip_encoding #1.0 .PEVENTS = PEVENTS;
// likelihoods
extern default column
F32[4] LIKELIHOODS = likelihoods;
extern readonly column
INSDC:phred[4] LIKELIHOODS = phred;
U32 sort_encode = NCBI:SRA:sort_order < 4 > ( LIKELIHOODS );
physical column < U32 >
zip_encoding #1.0 < Z_RLE > .SORT_ORDER = sort_encode;
F32 reorder = NCBI:SRA:reorder < 4 > ( sort_encode, LIKELIHOODS );
F32 like_scale = vdb:fixed_vec_sum < F32, 4 > ( reorder );
physical column < F32 >
fzip_encoding #1.0 < 4 > .SCALE = like_scale;
INSDC:phred cut_phred = NCBI:SRA:likelihood_to_phred #1.0 < 4, 3 > ( like_scale, reorder );
physical column < INSDC:phred >
zip_encoding #1.0 < 5 > .PHRED = cut_phred;
// normalization scaling factors
extern readonly column
F32 LIKELIHOOD_NORM = .SCALE;
// phred scores
extern readonly column
INSDC:phred[4] PHRED = phred;
};
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