/usr/include/ncbi-vdb/ncbi/wgs-contig.h is in libncbi-vdb-dev 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.
*
* ===========================================================================
*
*/
#ifndef _h_ncbi_wgs_contig_
#define _h_ncbi_wgs_contig_
#ifndef _h_klib_defs_
#include <klib/defs.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*==========================================================================
* WGS Contig
*/
/*--------------------------------------------------------------------------
* types
* constants
*/
/* component_props
* a signed value describing either contigs or gaps
* where values >= 0 refer to contigs
* and negatives describe gaps
*/
typedef int16_t NCBI_WGS_component_props;
/* component description
* the sequencing status of the component
*
* These typically correspond to keywords in the INSDC submission.
* Current acceptable values are_
* A Active Finishing
* D Draft HTG (often phase1 and phase2 are called Draft,
* whether or not they have the draft keyword).
* F Finished HTG (phase3)
* G Whole Genome Finishing
* O Other sequence (typically means no HTG keyword)
* P Pre Draft
* W WGS contig
*/
enum
{
NCBI_WGS_component_WGS = 0,
NCBI_WGS_component_ActiveFinishing = 1,
NCBI_WGS_component_DraftHTG = 2,
NCBI_WGS_component_FinishedHTG = 3,
NCBI_WGS_component_WholeGenomeFinishing = 4,
NCBI_WGS_component_OtherSequence = 5,
NCBI_WGS_component_PreDraft = 6
};
/* strand
* specifies the orientation of the component relative to scaffold
* values given allow strand to be determined as "prop / 16"
* yielding_
* 0 unknown orientation
* 1 plus strand
* 2 negative strand
*/
enum
{
NCBI_WGS_strand_plus = 1 * 16,
NCBI_WGS_strand_minus = 2 * 16
};
/* gap description
* These typically correspond to keywords in the INSDC submission.
* Current acceptable values are_
* N gap with specified size
* U gap of unknown size, defaulting to 100 bases.
*/
enum
{
NCBI_WGS_gap_known = 1 * -1,
NCBI_WGS_gap_unknown = 2 * -1
};
/* gap_linkage
* Describes linkage and linkage evidence
*/
typedef int32_t NCBI_WGS_gap_linkage;
/* gap type
* scaffold a gap between two sequence contigs in a scaffold
* contig an unspanned gap between two sequence contigs
* centromere a gap inserted for the centromere
* short_arm a gap inserted at the start of an acrocentric chromosome
* heterochromatin a gap inserted for an especially large region of heterochromatic sequence
* telomere a gap inserted for the telomere
* repeat an unresolvable repeat
*/
enum
{
NCBI_WGS_gap_scaffold = 1 * -4,
NCBI_WGS_gap_contig = 2 * -4,
NCBI_WGS_gap_centromere = 3 * -4,
NCBI_WGS_gap_short_arm = 4 * -4,
NCBI_WGS_gap_heterochromatin = 5 * -4,
NCBI_WGS_gap_telomere = 6 * -4,
NCBI_WGS_gap_repeat = 7 * -4
};
/* gap linkage evidence
* paired-ends paired sequences from the two ends of a DNA fragment
* align_genus alignment to a reference genome within the same genus
* align_xgenus alignment to a reference genome within another genus
* align_trnscpt alignment to a transcript from the same species
* within_clone sequence on both sides of the gap is derived from
* the same clone, but the gap is not spanned by paired-ends
* clone_contig linkage is provided by a clone contig in the tiling path
* map linkage asserted using a non-sequence based map
* such as RH, linkage, fingerprint or optical
* strobe strobe sequencing (PacBio)
* unspecified
*/
enum
{
NCBI_WGS_gap_linkage_linked = 1,
NCBI_WGS_gap_linkage_evidence_paired_ends = 2,
NCBI_WGS_gap_linkage_evidence_align_genus = 4,
NCBI_WGS_gap_linkage_evidence_align_xgenus = 8,
NCBI_WGS_gap_linkage_evidence_align_trnscpt = 16,
NCBI_WGS_gap_linkage_evidence_within_clone = 32,
NCBI_WGS_gap_linkage_evidence_clone_contig = 64,
NCBI_WGS_gap_linkage_evidence_map = 128,
NCBI_WGS_gap_linkage_evidence_strobe = 256,
NCBI_WGS_gap_linkage_evidence_unspecified = 512,
NCBI_WGS_gap_linkage_evidence_pcr = 1024
};
/*--------------------------------------------------------------------------
* accession tokenization constants
*/
/* tokenize_nuc_accession
* tokenize_prot_accession
* scans name on input
* tokenizes into parts
*/
enum
{
NCBI_WGS_acc_token_unrecognized = 1,
NCBI_WGS_acc_token_prefix = 2,
NCBI_WGS_acc_token_contig = 3
};
#ifdef __cplusplus
}
#endif
#endif /* _h_ncbi_wgs_contig_ */
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