/usr/lib/ncbi/schema/clip.vschema is in sra-toolkit 2.1.7a-1ubuntu2.
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 Sequence Read Archive schema
*/
version 1;
include 'ncbi/sra.vschema';
include 'ncbi/spotname.vschema';
/*--------------------------------------------------------------------------
* NCBI:SRA:tbl:clip
* common clip column processing
* shared by 454 and ion-torrent
*
* uses spotdesc because it has a dependency upon spot_len
*
* history:
* 1.0.1 - base explicitly upon spotdesc #1.0.1
* 1.0.2 - base explicitly upon spotdesc #1.0.2
*/
table NCBI:SRA:tbl:clip #1.0.2 = INSDC:SRA:tbl:spotdesc #1.0.2
{
/* CLIP_ADAPTER_LEFT, CLIP_ADAPTER_RIGHT
* adapter clips in 1-based coordinates
* when value is 0, implies that they are NOT SET
*/
column INSDC:coord:one CLIP_ADAPTER_LEFT = out_clip_adapt_left;
column INSDC:coord:one CLIP_ADAPTER_RIGHT = out_clip_adapt_right;
// casts are required to allow multple storage formats
INSDC:coord:one out_clip_adapt_left = cast ( .CLIP_ADAPTER_LEFT );
INSDC:coord:one out_clip_adapt_right = cast ( .CLIP_ADAPTER_RIGHT );
/* CLIP_QUALITY_LEFT, CLIP_QUALITY_RIGHT
* quality clips in 1-based coordinates
* when value is 0, implies that they are NOT SET
*/
column INSDC:coord:one CLIP_QUALITY_LEFT = out_clip_qual_left;
column INSDC:coord:one CLIP_QUALITY_RIGHT = out_clip_qual_right;
// casts are required to allow multple storage formats
INSDC:coord:one out_clip_qual_left
= cast ( .CLIP_QUALITY_LEFT )
| < INSDC:coord:one > echo < 1 > ();
INSDC:coord:one out_clip_qual_right
= cast ( .CLIP_QUALITY_RIGHT )
| cast ( spot_len );
// support for reading 16-bit clips, as in v1 schema
readonly column U16 CLIP_ADAPTER_LEFT
= .CLIP_ADAPTER_LEFT
| cast ( out_clip_adapt_left );
readonly column U16 CLIP_ADAPTER_RIGHT
= .CLIP_ADAPTER_RIGHT
| cast ( out_clip_adapt_right );
readonly column U16 CLIP_QUALITY_LEFT = cast ( out_clip_qual_left );
readonly column U16 CLIP_QUALITY_RIGHT = cast ( out_clip_qual_right );
/* CLIP-MANIA
*/
// 1-based fully-closed right edge is row-length
INSDC:coord:one spot_right = ( INSDC:coord:one ) spot_len;
// processed 1-based coordinates >= 1
INSDC:coord:one lim_clip_adapt_left
= < INSDC:coord:one > clip < 1, 0x7FFFFFFF > ( out_clip_adapt_left );
INSDC:coord:one max_clip_adapt_right
= < INSDC:coord:one, INSDC:coord:one > map < 0, 0x7FFFFFFF > ( out_clip_adapt_right );
INSDC:coord:one lim_clip_adapt_right
= < INSDC:coord:one > min ( spot_right, max_clip_adapt_right );
INSDC:coord:one lim_clip_qual_left
= < INSDC:coord:one > clip < 1, 0x7FFFFFFF > ( out_clip_qual_left );
INSDC:coord:one max_clip_qual_right
= < INSDC:coord:one, INSDC:coord:one > map < 0, 0x7FFFFFFF > ( out_clip_qual_right );
INSDC:coord:one lim_clip_qual_right
= < INSDC:coord:one > min ( spot_right, max_clip_qual_right );
// read-only columns with 0-based coordinates
readonly column INSDC:coord:zero CLIP_ADAPTER_LEFT
= ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_adapt_left );
readonly column INSDC:coord:zero CLIP_ADAPTER_RIGHT
= ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_adapt_right );
readonly column INSDC:coord:zero CLIP_QUALITY_LEFT
= ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_qual_left );
readonly column INSDC:coord:zero CLIP_QUALITY_RIGHT
= ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_qual_right );
// combined clips
INSDC:coord:one max_clip_left
= < INSDC:coord:one > max ( lim_clip_adapt_left, lim_clip_qual_left )
| lim_clip_adapt_left
| lim_clip_qual_left;
INSDC:coord:zero max_zclip_left
= ( INSDC:coord:zero ) < I32 > diff < 1 > ( max_clip_left );
INSDC:coord:one min_clip_right
= < INSDC:coord:one > min ( lim_clip_adapt_right, lim_clip_qual_right )
| lim_clip_adapt_right
| lim_clip_qual_right;
/* TRIMMED SEQUENCE
* need to find the 0-based trim_start and trim_len
*/
INSDC:coord:zero bio_start
= NCBI:SRA:bio_start ( out_read_start, out_read_type );
INSDC:coord:zero trim_start
= < INSDC:coord:zero > max ( bio_start, max_zclip_left )
| bio_start;
I32 trim_stop
= < I32 > max ( min_clip_right, trim_start )
| spot_right;
INSDC:coord:len trim_len
= ( INSDC:coord:len ) < I32 > diff ( trim_stop, trim_start );
};
|