SAMRecord

Encapsulates a SAM/BAM/CRAM record, using the bam1_t type for memory efficiency, and the htslib helper functions for speed.

class SAMRecord {

this(bam1_t* b);

void tid(int tid);

void pos(long pos);

ubyte qual();

void qual(ubyte q);

int l_qname();

int l_extranul();

ushort flag();

void flag(ushort fl);

bool isPaired();

bool isReversed();

bool isMapped();

bool isMateMapped();

bool mateReversed();

bool isSecondary();

bool isSupplementary();

char strand();

char[] queryName();

void queryName(string qname);

int length();

const(char)[] sequence();

void sequence(const(char)[] seq);

const(char)[] qscores();

void q_scores(const(char)[] seq);

void qscores(ubyte[] seq);

Cigar cigar();

void cigar(Cigar cigar);

TagValue opIndex(string val);

void opIndexAssign(T value, string index);

void opIndexAssign(T[] value, string index);

int mateTID();

void mateTID(int mtid);

long matePos();

void matePos(long mpos);

long insertSize();

void insertSize(long isize);

auto getAlignedCoordinates();

auto getAlignedCoordinates(long start, long end);

struct AlignedPair(bool refSeq);

auto getAlignedPairs(long start, long end);

auto getAlignedPairs();

}

Constructors

this this(): Construct blank SAMRecord with empty backing bam1_t
this this(bam1_t* b): Construct SAMRecord from supplied bam1_t

Destructor

~this ~this(): Undocumented in source.

Members

Functions

cigar Cigar cigar(): Create cigar from bam1_t record
cigar void cigar(Cigar cigar): Assign a cigar string
flag ushort flag()
void flag(ushort fl): bitwise flag
getAlignedCoordinates auto getAlignedCoordinates(): get aligned coordinates per each cigar op
getAlignedCoordinates auto getAlignedCoordinates(long start, long end): get aligned coordinates per each cigar op within range range is 0-based half open using chromosomal coordinates
getAlignedPairs auto getAlignedPairs(long start, long end): get a range of aligned read and reference positions this is meant to recreate functionality from pysam: https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.get_aligned_pairs range is 0-based half open using chromosomal coordinates
getAlignedPairs auto getAlignedPairs(): get a range of aligned read and reference positions this is meant to recreate functionality from pysam: https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.get_aligned_pairs
insertSize long insertSize()
void insertSize(long isize): Presumably Insert size, but is undocumented. Per samtools source, is measured 5' to 5' https://github.com/samtools/samtools/blob/bd1a409aa750d25d70a093405d174db8709a3f2c/bam_mate.c#L320
isMapped bool isMapped(): is read mapped?
isMateMapped bool isMateMapped(): is read mate mapped?
isPaired bool isPaired(): is read paired?
isReversed bool isReversed(): is read reversed? bool bam_is_rev(bam1_t *b) { return ( ((*b).core.flag & BAM_FREVERSE) != 0 ); }
isSecondary bool isSecondary(): is read secondary?
isSupplementary bool isSupplementary(): is read supplementary?
l_extranul int l_extranul(): number of EXTRA trailing \0 in qname; 0 <= l_extranul <= 3, see l_qname. Never set directly.
l_qname int l_qname(): length of query name. Terminated by 1-4 \0, see l_extranul. Never set directly.
length int length(): query (and quality string) length
matePos long matePos()
void matePos(long mpos): 0-based leftmost coordinate of next read in template
mateReversed bool mateReversed(): is mate reversed? bool bam_is_mrev(bam1_t *b) { return( ((*b).core.flag & BAM_FMREVERSE) != 0); }
mateTID int mateTID()
void mateTID(int mtid): chromosome ID of next read in template, defined by bam_hdr_t
opIndex TagValue opIndex(string val): Get aux tag from bam1_t record and return a TagValue
opIndexAssign void opIndexAssign(T value, string index): Assign a tag key value pair
opIndexAssign void opIndexAssign(T[] value, string index): Assign a tag key array pair
pos long pos()
void pos(long pos): 0-based leftmost coordinate
q_scores void q_scores(const(char)[] seq): Add qscore sequence given that it is the same length as the bam sequence
qscores const(char)[] qscores(): Return char array of the qscores see samtools/sam_view.c: get_quality
qscores void qscores(ubyte[] seq): Add qscore sequence given that it is the same length as the bam sequence
qual ubyte qual()
void qual(ubyte q): mapping quality
queryName char[] queryName(): auto bam_get_qname(bam1_t *b) { return (cast(char*)(*b).data); }
queryName void queryName(string qname): Set query name
sequence const(char)[] sequence(): Return char array of the sequence see samtools/sam_view.c: get_read
sequence void sequence(const(char)[] seq): Assigns sequence and resets quality score
strand char strand(): Return read strand + or - (as char)
tid int tid()
void tid(int tid): chromosome ID, defined by bam_hdr_t

Structs

AlignedPair struct AlignedPair(bool refSeq): Undocumented in source.

Variables

b bam1_t* b;

Meta

Source

See Implementation

dhtslib sam modules

header

aliases

SAMFile

classes

SAMRecord

enums

SAMWriterTypes

functions

structs