/usr/include/ncbi-vdb/align/bam.h is in libncbi-vdb-dev 2.8.1+dfsg-2.
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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_align_bam_
#define _h_align_bam_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#ifndef _h_klib_defs_
#include <klib/defs.h>
#endif
#include <stdarg.h>
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct KDirectory;
struct KFile;
struct VPath;
struct AlignAccessDB;
struct AlignAccessAlignmentEnumerator;
/*--------------------------------------------------------------------------
* BAMAlignment
*/
typedef struct BAMAlignment BAMAlignment;
/* GetBAMAlignment
* get property
*
* Release with BAMAlignmentRelease.
*/
ALIGN_EXTERN rc_t CC AlignAccessAlignmentEnumeratorGetBAMAlignment
( const struct AlignAccessAlignmentEnumerator *self, const BAMAlignment **result );
/* AddRef
* Release
*/
ALIGN_EXTERN rc_t CC BAMAlignmentAddRef ( const BAMAlignment *self );
ALIGN_EXTERN rc_t CC BAMAlignmentRelease ( const BAMAlignment *self );
/* GetReadLength
* get the sequence length
* i.e. the number of elements of both sequence and quality
*
* "length" [ OUT ] - length in bases of query sequence and quality
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetReadLength ( const BAMAlignment *self, uint32_t *length );
/* GetSequence
* get the sequence data [0..ReadLength)
* caller provides buffer of ReadLength bytes
*
* "sequence" [ OUT ] - pointer to a buffer of at least ReadLength bytes
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetSequence ( const BAMAlignment *self, char *sequence );
/* GetSequence2
* get the sequence data [0..ReadLength)
* caller provides buffer of ReadLength bytes
*
* "sequence" [ OUT ] - pointer to a buffer of at least ReadLength bytes
*
* "start" [ IN ] and "stop" [ IN ] - zero-based coordinates, half-closed interval
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetSequence2 ( const BAMAlignment *self, char *sequence, uint32_t start, uint32_t stop);
/* GetQuality
* get the raw quality data [0..ReadLength)
* values are unsigned with 0xFF == missing
*
* "quality" [ OUT ] - return param for quality sequence
* held internally, validity is guaranteed for the life of the BAMAlignment
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetQuality ( const BAMAlignment *self, const uint8_t **quality );
/* GetQuality2
* get the raw quality data [0..ReadLength) from OQ if possible else from QUAL
* values are unsigned with 0xFF == missing
*
* "quality" [ OUT ] - return param for quality sequence
* held internally, validity is guaranteed for the life of the BAMAlignment
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetQuality2(const BAMAlignment *self, const uint8_t **quality, uint8_t *offset);
/* GetRefSeqId
* get id of reference sequence
* pass result into BAMFileGetRefSeqById to get the Reference Sequence record
*
* "refSeqId" [ OUT ] - zero-based id of reference sequence
* returns -1 if set as invalid within BAM ( rc may be zero )
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetRefSeqId ( const BAMAlignment *self, int32_t *refSeqId );
/* GetMateRefSeqId
* get id of mate's reference sequence
* pass result into BAMFileGetRefSeqById to get the Reference Sequence record
*
* "refSeqId" [ OUT ] - zero-based id of reference sequence
* returns -1 if invalid
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetMateRefSeqId ( const BAMAlignment *self, int32_t *refSeqId );
/* GetPosition
* get the aligned position on the ref. seq.
*
* "n" [ IN ] - zero-based position index for cases of multiple alignments
*
* "pos" [ OUT ] - zero-based position on reference sequence
* returns -1 if invalid
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetPosition ( const BAMAlignment *self, int64_t *pos );
/* GetPosition2
* get the aligned start position on the ref. seq.
* get the aligned length on the ref. seq.
*
* "n" [ IN ] - zero-based position index for cases of multiple alignments
*
* "pos" [ OUT ] - zero-based position on reference sequence
* returns -1 if invalid
*
* "length" [ OUT ] - length of alignment on reference sequence
* returns 0 if invalid
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetPosition2 ( const BAMAlignment *self, int64_t *pos, uint32_t *length );
/* GetMatePosition
* starting coordinate of mate's alignment on ref. seq.
*
* "pos" [ OUT ] - zero-based position on reference sequence
* returns -1 if invalid
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetMatePosition ( const BAMAlignment *self, int64_t *pos );
/* IsMapped
* is the alignment mapped to something
*/
ALIGN_EXTERN bool CC BAMAlignmentIsMapped ( const BAMAlignment *self );
/* GetReadGroupName
* get the name of the read group (i.e. accession)
* pass result into BAMFileGetReadGroupByName to get the Read Group record
*
* "name" [ OUT ] - return param for NUL-terminated read group name
* held internally, validity is guaranteed for the life of the BAMAlignment
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetReadGroupName ( const BAMAlignment *self, const char **name );
/* GetReadName
* get the read name (i.e. spot name)
* GetReadName2
* get the read name and length in bytes
*
* "name" [ OUT ] - return param for NUL-terminated read name
* held internally, validity is guaranteed for the life of the BAMAlignment
*
* "length" [ OUT ] - return the number of bytes in "name"
* excluding terminating NUL.
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetReadName ( const BAMAlignment *self, const char **name );
ALIGN_EXTERN rc_t CC BAMAlignmentGetReadName2 ( const BAMAlignment *self, const char **name, size_t *length );
/* GetReadName3
* get the read name and length in bytes
* applies fixups to name
*
* "name" [ OUT ] - return param for read name
* held internally, validity is guaranteed for the life of the BAMAlignment
*
* "length" [ OUT ] - return the number of bytes in "name"
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetReadName3 ( const BAMAlignment *self, const char **name, size_t *length );
/* HasColorSpace
* Does the alignment have colorspace info
*/
ALIGN_EXTERN bool CC BAMAlignmentHasColorSpace ( const BAMAlignment *self );
/* GetCSKey
* get the colorspace key
*
* "cskey" [ OUT ] - return param
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetCSKey ( const BAMAlignment *self, char cskey[1] );
ALIGN_EXTERN rc_t CC BAMAlignmentGetCSSeqLen ( const BAMAlignment *self, uint32_t *seqLen );
/* GetCSSequence
* get the colorspace sequence data [0..seqLen)
* caller provides buffer of seqLen bytes
*
* "csseq" [ OUT ] - pointer to a buffer of at least seqLen bytes
* "seqLen" [ IN ] - length of sequence from BAMAlignmentGetCSSeqLen
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetCSSequence ( const BAMAlignment *self, char *csseq, uint32_t seqLen );
ALIGN_EXTERN rc_t CC BAMAlignmentGetCSQuality(BAMAlignment const *cself, uint8_t const **quality, uint8_t *offset);
/* GetFlags
* return the raw "flags" bitmap word
*
* "flags" [ OUT ] - return parameter for bitmap word
*/
enum BAMFlags
{
BAMFlags_bit_WasPaired = 0, /* was paired when sequenced */
BAMFlags_bit_IsMappedAsPair,
BAMFlags_bit_SelfIsUnmapped,
BAMFlags_bit_MateIsUnmapped,
BAMFlags_bit_SelfIsReverse,
BAMFlags_bit_MateIsReverse,
BAMFlags_bit_IsFirst, /* and mate exists */
BAMFlags_bit_IsSecond, /* and mate exists */
BAMFlags_bit_IsNotPrimary, /* a read having split hits may have multiple primary alignments */
BAMFlags_bit_IsLowQuality, /* fails platform/vendor quality checks */
BAMFlags_bit_IsDuplicate, /* PCR or optical dup */
BAMFlags_bit_IsSupplemental,
BAMFlags_WasPaired = (1 << BAMFlags_bit_WasPaired),
BAMFlags_IsMappedAsPair = (1 << BAMFlags_bit_IsMappedAsPair),
BAMFlags_SelfIsUnmapped = (1 << BAMFlags_bit_SelfIsUnmapped),
BAMFlags_MateIsUnmapped = (1 << BAMFlags_bit_MateIsUnmapped),
BAMFlags_SelfIsReverse = (1 << BAMFlags_bit_SelfIsReverse),
BAMFlags_MateIsReverse = (1 << BAMFlags_bit_MateIsReverse),
BAMFlags_IsFirst = (1 << BAMFlags_bit_IsFirst),
BAMFlags_IsSecond = (1 << BAMFlags_bit_IsSecond),
BAMFlags_IsNotPrimary = (1 << BAMFlags_bit_IsNotPrimary),
BAMFlags_IsLowQuality = (1 << BAMFlags_bit_IsLowQuality),
BAMFlags_IsDuplicate = (1 << BAMFlags_bit_IsDuplicate),
BAMFlags_IsSupplemental = (1 << BAMFlags_bit_IsSupplemental)
};
ALIGN_EXTERN rc_t CC BAMAlignmentGetFlags ( const BAMAlignment *self, uint16_t *flags );
/* GetMapQuality
* return the quality score of mapping
*
* "qual" [ OUT ] - return param for quality score
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetMapQuality ( const BAMAlignment *self, uint8_t *qual );
/* GetAlignmentDetail
* get the alignment details
*
* "rslt" [ OUT, NULL OKAY ] and "count" [ IN ] - array to hold detail records
*
* "actual" [ OUT, NULL OKAY ] - number of elements written to "rslt"
* required if "rslt" is not NULL
*
* "firstMatch" [ OUT, NULL OKAY ] - zero-based index into "rslt" of the first match to the refSeq
* or < 0 if invalid
*
* "lastMatch" [ OUT, NULL OKAY ] - zero-based index into "rslt" of the last match to the refSeq
* or < 0 if invalid
*/
typedef uint32_t BAMCigarType;
enum BAMCigarTypes
{
ct_Match = 'M', /* 0 */
ct_Insert = 'I', /* 1 */
ct_Delete = 'D', /* 2 */
ct_Skip = 'N', /* 3 */
ct_SoftClip = 'S', /* 4 */
ct_HardClip = 'H', /* 5 */
ct_Padded = 'P', /* 6 */
ct_Equal = '=', /* 7 */
ct_NotEqual = 'X', /* 8 */
ct_Overlap = 'B' /* Complete Genomics extension */
};
typedef struct BAMAlignmentDetail BAMAlignmentDetail;
struct BAMAlignmentDetail
{
int64_t refSeq_pos; /* position on refSeq where this alignment region starts or -1 if NA */
int32_t read_pos; /* position on read where this alignment region starts or -1 if NA */
uint32_t length; /* length of alignment region */
BAMCigarType type; /* type of alignment */
};
ALIGN_EXTERN rc_t CC BAMAlignmentGetAlignmentDetail ( const BAMAlignment *self,
BAMAlignmentDetail *rslt, uint32_t count, uint32_t *actual,
int32_t *firstMatch, int32_t *lastMatch );
/* GetCigarCount
* the number of CIGAR elements
* a CIGAR element consists of the pair of matching op code and op length
*
* "n" [ OUT ] - return param for cigar count
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetCigarCount ( const BAMAlignment *self, uint32_t *n );
ALIGN_EXTERN rc_t CC BAMAlignmentGetRawCigar(const BAMAlignment *cself, uint32_t const **rslt, uint32_t *length);
/* GetCigar
* get CIGAR element n [0..GetCigarCount)
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetCigar ( const BAMAlignment *self,
uint32_t n, BAMCigarType *type, uint32_t *length );
/* GetInsertSize
* distance in bases to start of mate's alignment on ref. seq.
*
* "size" [ OUT ] - >0 for first in pair, <0 for second
*/
ALIGN_EXTERN rc_t CC BAMAlignmentGetInsertSize ( const BAMAlignment *self, int64_t *size );
ALIGN_EXTERN rc_t CC BAMAlignmentFormatSAM(const BAMAlignment *self,
size_t *actsize,
size_t maxsize,
char *buffer);
/* OptDataForEach
* DANGER
* these optional fields are the weakest part of BAM.
*
* It is probably best to not use this info.
* You can't count on them being there.
* Moreover, you might need to interpret the types correctly.
*/
typedef uint32_t BAMOptDataValueType;
enum BAMOptDataValueTypes
{
dt_CSTRING = 'Z',
dt_INT8 = 'c',
dt_UINT8 = 'C',
dt_INT16 = 's',
dt_UINT16 = 'S',
dt_INT = 'i',
dt_UINT = 'I',
dt_FLOAT32 = 'f',
#if 0
dt_FLOAT64 = 'd', /* removed? not in Dec 19 2013 version of SAMv1.pdf */
#endif
dt_ASCII = 'A',
dt_HEXSTRING = 'H',
dt_NUM_ARRAY = 'B'
};
#define OPT_TAG_X "X?" /* end user data */
#define OPT_TAG_Y "Y?" /* end user data */
#define OPT_TAG_Z "Z?" /* end user data */
#define OPT_TAG_ReadGroup "RG" /* Read Group; same as BAMAlignmentGetReadGroupName */
#define OPT_TAG_Library "LB" /* LIbrary; also BAMReadGroup */
#define OPT_TAG_Unit "PU" /* Platform specific Unit; also BAMReadGroup */
#define OPT_TAG_Program "PG" /* Alignment software name */
#define OPT_TAG_AlignScore "AS" /* Alignment Score (MapQuality?) */
#define OPT_TAG_SecQual "SQ" /* second called base:2 and quality:6; length == ReadLength? warning */
#define OPT_TAG_MateMapQual "MQ" /* map Quality of mate */
#define OPT_TAG_NumMismatch "NM" /* Number of Mismatches */
#define OPT_TAG_Hits0 "H0" /* Number of perfect hits */
#define OPT_TAG_Hits1 "H1" /* Number of off-by-one */
#define OPT_TAG_Hits2 "H2" /* Number of off-by-two */
#define OPT_TAG_CondQual "UQ" /* conditional Quality of read */
#define OPT_TAG_CondQPair "PQ" /* conditional Quality of pair */
#define OPT_TAG_ReadHits "NH" /* Number of times this read (spot) aligns */
#define OPT_TAG_ReadHits2 "IH" /* Number of times this read (spot) aligns that are in this file */
#define OPT_TAG_HitIndex "HI" /* n-th hit for this read in this file */
#define OPT_TAG_Match2 "MD" /* another sort of matching string like CIGAR but different? */
#define OPT_TAG_ColorKey "CS" /* primer and first color */
#define OPT_TAG_ColorQual "CQ" /* quality of above */
#define OPT_TAG_ColorMisses "CM" /* Number of color-space Mismatches */
#define OPT_TAG_SeqOverlap "GS"
#define OPT_TAG_QualOverlap "GQ"
#define OPT_TAG_OverlapDesc "GC"
#define OPT_TAG_MateSeq "R2" /* sequence of the mate */
#define OPT_TAG_MateQual "Q2" /* quality scores of the mate */
#define OPT_TAG_OtherQual "S2"
#define OPT_TAG_NextHitRef "CC" /* Reference name of the next hit */
#define OPT_TAG_NextHitPos "CP" /* coordinate of the next hit */
#define OPT_TAG_SingleMapQ "SM" /* quality of mapping as if not paired */
#define OPT_TAG_AM "AM"
#define OPT_TAG_MAQFlag "MQ"
struct BAMOptData
{
BAMOptDataValueType type;
uint32_t element_count;
union {
int8_t i8[8];
uint8_t u8[8];
int16_t i16[4];
uint16_t u16[4];
int32_t i32[2];
uint32_t u32[2];
int64_t i64[2];
uint64_t u64[2];
float f32[2];
double f64[1];
char asciiz[8];
} u;
};
typedef struct BAMOptData BAMOptData;
typedef rc_t ( CC * BAMOptionalDataFunction )
( void *ctx, const char tag[2], const BAMOptData *value );
ALIGN_EXTERN rc_t CC BAMAlignmentOptDataForEach
( const BAMAlignment *self, void *ctx, BAMOptionalDataFunction callback );
ALIGN_EXTERN bool CC BAMAlignmentHasCGData(BAMAlignment const *self);
ALIGN_EXTERN
rc_t CC BAMAlignmentGetCGSeqQual(BAMAlignment const *self,
char sequence[/* 35 */],
uint8_t quality[/* 35 */]);
ALIGN_EXTERN
rc_t CC BAMAlignmentGetCGCigar(BAMAlignment const *self,
uint32_t *cigar,
uint32_t cig_max,
uint32_t *cig_act);
ALIGN_EXTERN rc_t BAMAlignmentGetTI(BAMAlignment const *self, uint64_t *ti);
/* strand = '+', '-', or ' ' */
ALIGN_EXTERN rc_t BAMAlignmentGetRNAStrand(BAMAlignment const *self, uint8_t *strand);
ALIGN_EXTERN rc_t BAMAlignmentGetCGAlignGroup(BAMAlignment const *self,
char buffer[],
size_t max_size,
size_t *act_size);
/*--------------------------------------------------------------------------
* BAMFile
*/
typedef struct BAMFile BAMFile;
typedef struct BAMRefSeq BAMRefSeq;
struct BAMRefSeq
{
uint64_t length;
const char *name; /* not null unique */
const char *assemblyId;
const uint8_t *checksum;
const char *uri;
const char *species;
uint32_t id;
uint8_t checksum_array[16];
};
typedef struct BAMReadGroup BAMReadGroup;
struct BAMReadGroup
{
const char *name; /* not null unique, accession e.g. SRR001138 */
const char *sample; /* not null */
const char *library;
const char *description;
const char *unit; /* platform specific identifier, e.g. BI.080214_SL-XAJ_0001_FC2044KAAXX.7 */
const char *insertSize;
const char *center; /* e.g. BI */
const char *runDate;
const char *platform; /* e.g. ILLUMINA */
uint32_t id;
};
/* 64-bit structure stored as an integer
* The high-order 48 bits store the position in the file at which a
* compressed block starts. The low-order 16 bits store the position
* in the decompressed block at which a record starts. This is the
* way that positions are represented in BAM indices.
*/
typedef uint64_t BAMFilePosition;
/* Make
* open the BAM file specified by path
*
* "path" [ IN ] - NUL terminated string or format
*/
ALIGN_EXTERN rc_t CC BAMFileMake ( const BAMFile **result, const char *path, ... );
ALIGN_EXTERN rc_t CC BAMFileMakeWithHeader ( const BAMFile **result,
char const headerText[],
char const path[], ... );
/* MakeWithDir
* open the BAM file specified by path and supplied directory
*
* "dir" [ IN ] - directory object used to open file
*
* "path" [ IN ] - NUL terminated string or format
*/
ALIGN_EXTERN rc_t CC BAMFileMakeWithDir ( const BAMFile **result,
struct KDirectory const *dir, const char *path, ... );
ALIGN_EXTERN rc_t CC BAMFileVMakeWithDir ( const BAMFile **result,
struct KDirectory const *dir, const char *path, va_list args );
/* Make
* open the BAM file specified by file
*
* "file" [ IN ] - an open KFile
*/
ALIGN_EXTERN rc_t CC BAMFileMakeWithKFile(const BAMFile **result,
struct KFile const *file);
/* Make
* open the BAM file specified by file
*
* "file" [ IN ] - an open KFile
*/
ALIGN_EXTERN rc_t CC BAMFileMakeWithVPath(const BAMFile **result,
struct VPath const *path);
/* ExportBAMFile
* export the BAMFile object in use by the AlignAccessDB, if any
* must be released via BAMFileRelease
*/
ALIGN_EXTERN rc_t CC AlignAccessDBExportBAMFile ( struct AlignAccessDB const *self,
const BAMFile **result );
/* AddRef
* Release
*/
ALIGN_EXTERN rc_t CC BAMFileAddRef ( const BAMFile *self );
ALIGN_EXTERN rc_t CC BAMFileRelease ( const BAMFile *self );
/* GetPosition
* get the position of the about-to-be read alignment
* this position can be stored
* this position can be passed into SetPosition to seek to the same alignment
*
* "pos" [ OUT ] - return parameter for position
*/
ALIGN_EXTERN rc_t CC BAMFileGetPosition ( const BAMFile *self, BAMFilePosition *pos );
/* GetProportionalPosition
* get the aproximate proportional position in the input file
* this is intended to be useful for computing progress
*
* NB - does not return rc_t
*/
ALIGN_EXTERN float CC BAMFileGetProportionalPosition ( const BAMFile *self );
/* Read
* read an aligment
*
* "result" [ OUT ] - return param for BAMAlignment object
* must be released with BAMAlignmentRelease
*
* returns RC(..., ..., ..., rcRow, rcNotFound) at end
*/
ALIGN_EXTERN rc_t CC BAMFileRead ( const BAMFile *self, const BAMAlignment **result );
/* Read
* read an aligment
*
* "result" [ OUT ] - return param for BAMAlignment object
* must be released with BAMAlignmentRelease, is invalidated or contents
* change on next call to BAMFileRead2. Unlike with BAMFileRead, no attempt is
* made to preserve this object.
*
* returns:
* RC(..., ..., ..., rcRow, rcNotFound) at end
* RC(..., ..., ..., rcRow, rcInvalid) and RC(..., ..., ..., rcRow, rcEmpty)
* are not fatal and are resumable
*
* tries to use static buffers and will log messages about parsing errors
*/
ALIGN_EXTERN rc_t CC BAMFileRead2 ( const BAMFile *self, const BAMAlignment **result );
/* Rewind
* reset the position back to the first aligment in the file
*/
ALIGN_EXTERN rc_t CC BAMFileRewind ( const BAMFile *self );
/* SetPosition
* set the position to a particular alignment
* pass in the values from GetPosition
*/
ALIGN_EXTERN rc_t CC BAMFileSetPosition ( const BAMFile *self, const BAMFilePosition *pos );
/* GetRefSeqCount
* get the number of Reference Sequences refered to in the header
* this is not necessarily the number of Reference Sequences referenced
* by the alignments
*/
ALIGN_EXTERN rc_t CC BAMFileGetRefSeqCount ( const BAMFile *self, uint32_t *count );
/* GetRefSeq
* get the n'th Ref. Seq. where n is [0..RefSeqCount)
* the resulting pointer is static-like; it is freed when the BAMFile is.
* IOW, it is good for precisely at long as the BAMFile is.
*/
ALIGN_EXTERN rc_t CC BAMFileGetRefSeq ( const BAMFile *self, uint32_t n, const BAMRefSeq **result );
/* GetRefSeqById
* get a Ref. Seq. by its id
* the resulting pointer is static-like; it is freed when the BAMFile is.
* IOW, it is good for precisely at long as the BAMFile is.
*/
ALIGN_EXTERN rc_t CC BAMFileGetRefSeqById ( const BAMFile *self, int32_t id, const BAMRefSeq **result );
/* GetReadGroupCount
* get the number of Read Groups (accessions, etc.) refered to in the header
* this is not necessarily the number of Read Groups referenced
* by the alignments
*/
ALIGN_EXTERN rc_t CC BAMFileGetReadGroupCount ( const BAMFile *self, uint32_t *count );
/* GetReadGroup
* get the n'th Read Group where n is [0..ReadGroupCount)
* the resulting pointer is static-like; it is freed when the BAMFile is.
* IOW, it is good for precisely at long as the BAMFile is.
*/
ALIGN_EXTERN rc_t CC BAMFileGetReadGroup ( const BAMFile *self, unsigned n, const BAMReadGroup **result );
/* GetHeaderText
* get the text of the BAM header file
* the resulting pointer is static-like; it is freed when the BAMFile is.
* IOW, it is good for precisely at long as the BAMFile is.
*/
ALIGN_EXTERN rc_t CC BAMFileGetHeaderText(BAMFile const *cself, char const **header, size_t *header_len);
/* GetReadGroupByName
* get a Read Group by its name
* the resulting pointer is static-like; it is freed when the BAMFile is.
* IOW, it is good for precisely at long as the BAMFile is.
*/
ALIGN_EXTERN rc_t CC BAMFileGetReadGroupByName ( const BAMFile *self,
const char *name, const BAMReadGroup **result );
/* OpenIndex
* takes a simple path...
*/
ALIGN_EXTERN rc_t CC BAMFileOpenIndex ( const BAMFile *self, const char *path );
ALIGN_EXTERN rc_t CC BAMFileOpenIndexWithVPath ( const BAMFile *self, struct VPath const *path );
/* IsIndexed
* returns true if true
*/
ALIGN_EXTERN bool CC BAMFileIsIndexed ( const BAMFile *self );
/* IndexHasRefSeqId
*/
ALIGN_EXTERN bool CC BAMFileIndexHasRefSeqId ( const BAMFile *self, uint32_t refSeqId );
/* Seek
* seeks a half-open zero-based interval on a particular reference
* rcSelf, rcIncomplete
*/
ALIGN_EXTERN rc_t CC BAMFileSeek ( const BAMFile *self, uint32_t refSeqId, uint64_t alignStart, uint64_t alignEnd );
typedef uint32_t BAMValidateOption;
enum BAMValidateOptions {
/* this is the minimum level of BAM file validation; just walks the compressed block headers */
bvo_BlockHeaders = 1,
/* decompresses each block */
bvo_BlockCompression = 2,
/* within each block, walks the records without examining the contents */
bvo_BlockStructure = 3,
/* within each record, validate the structure vis-a-vis the record size */
bvo_RecordStructure = 4,
/* verify that the extra fields a parsable */
bvo_ExtraFields = 8,
/* confirm that no alignment starts before the alignment preceeding it */
bvo_Sorted = 16,
/* verify that flags are consistent with itself and the other fields in the record
* NB. can not verify secondary alignment flag 0x100
*/
bvo_FlagsConsistency = 32,
/* verify CIGAR against sequence length */
bvo_CIGARConsistency = 64,
/* verify that bin number corresponds to position and alignment length */
bvo_BinConsistency = 128,
/* verify that mapQ is consistent with flags and refSeqID */
bvo_MapQuality = 256,
/* verify Quality values >= 33 */
bvo_QualityValues = 512,
/* verify that sequence length != 0 */
bvo_MissingSequence = 1024,
/* verify that Quality values != 255 */
bvo_MissingQuality = 2048,
/* compute flagstats */
bvo_FlagsStats = 4096,
/* verify that index is parsable
* NB. this can be done without a BAM file
*/
bvo_IndexStructure = 1 << 16,
/* verify that the file offsets in the index are valid for the given BAM file
* NB. does not cause decompression of the BAM file but will cause referenced
* block headers to be validated
*/
bvo_IndexOffsets1 = 2 << 16,
/* in addition to verifying that the file offsets in the index are valid for
* the given BAM file, verify that the record offsets with the blocks are valid.
* NB. will cause referenced blocks to be decompressed and structurally validated.
*/
bvo_IndexOffsets2 = 3 << 16,
/* verify that index's reference number and bin number agree with the
* referenced record
*/
bvo_IndexBins = 4 << 16,
bvo_IndexOptions = 7 << 16
};
typedef struct BAMValidateStats BAMValidateStats;
typedef struct BAMValidateStatsRow BAMValidateStatsRow;
struct BAMValidateStatsRow {
uint64_t good;
uint64_t warning;
uint64_t error;
};
struct BAMValidateStats {
uint64_t bamFileSize;
uint64_t bamFilePosition;
uint64_t baiFileSize;
uint64_t baiFilePosition;
BAMValidateStatsRow blockHeaders;
BAMValidateStatsRow blockCompression;
BAMValidateStatsRow blockStructure;
BAMValidateStatsRow recordStructure;
BAMValidateStatsRow extraFields;
BAMValidateStatsRow inOrder;
BAMValidateStatsRow flags[16];
BAMValidateStatsRow CIGAR;
BAMValidateStatsRow bin;
BAMValidateStatsRow quality;
BAMValidateStatsRow hasSequence;
BAMValidateStatsRow hasQuality;
BAMValidateStatsRow indexFileOffset;
BAMValidateStatsRow indexBlockOffset;
BAMValidateStatsRow indexBin;
bool bamHeaderIsGood;
bool bamHeaderIsBad;
bool indexStructureIsGood;
bool indexStructureIsBad;
};
typedef rc_t (CC *BAMValidateCallback)(void *ctx, rc_t result, const BAMValidateStats *stats);
/* Validate
*/
ALIGN_EXTERN rc_t CC BAMValidate ( struct VPath const *bam,
struct VPath const *bai,
BAMValidateOption options,
BAMValidateCallback callback,
void *callbackContext
);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_bam_ */
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