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);

int tid [@property getter];

int tid [@property setter];

int pos [@property getter];

int pos [@property setter];

ubyte qual [@property getter];

ubyte qual [@property setter];

ushort flag [@property getter];

ushort flag [@property setter];

bool isPaired [@property getter];

bool isReversed [@property getter];

bool isMapped [@property getter];

bool isMateMapped [@property getter];

bool mateReversed [@property getter];

bool isSecondary [@property getter];

bool isSupplementary [@property getter];

char strand [@property getter];

char[] queryName [@property getter];

string queryName [@property setter];

int length [@property getter];

const(char)[] sequence [@property getter];

const(char)[] sequence [@property setter];

const(char)[] qscores();

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

void qscores(ubyte[] seq);

Cigar cigar [@property getter];

Cigar cigar [@property setter];

TagValue opIndex(string val);

void opIndexAssign(T value, string index);

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

int mateTID [@property getter];

int mateTID [@property setter];

int matePos [@property getter];

int matePos [@property setter];

int insertSize [@property getter];

int insertSize [@property setter];

auto getAlignedCoordinates();

auto getAlignedCoordinates(int start, int end);

struct AlignedPair(bool refSeq);

auto getAlignedPairs(int start, int 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

getAlignedCoordinates auto getAlignedCoordinates(): get aligned coordinates per each cigar op
getAlignedCoordinates auto getAlignedCoordinates(int start, int end): get aligned coordinates per each cigar op within range range is 0-based half open using chromosomal coordinates
getAlignedPairs auto getAlignedPairs(int start, int 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
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
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

Properties

cigar Cigar cigar [@property getter]: Create cigar from bam1_t record
cigar Cigar cigar [@property setter]: Assign a cigar string
flag ushort flag [@property getter]
ushort flag [@property setter]: bitwise flag
insertSize int insertSize [@property getter]
int insertSize [@property setter]: 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 [@property getter]: is read mapped?
isMateMapped bool isMateMapped [@property getter]: is read mate mapped?
isPaired bool isPaired [@property getter]: is read paired?
isReversed bool isReversed [@property getter]: is read reversed? bool bam_is_rev(bam1_t *b) { return ( ((*b).core.flag & BAM_FREVERSE) != 0 ); }
isSecondary bool isSecondary [@property getter]: is read secondary?
isSupplementary bool isSupplementary [@property getter]: is read supplementary?
length int length [@property getter]: query (and quality string) length
matePos int matePos [@property getter]
int matePos [@property setter]: 0-based leftmost coordinate of next read in template
mateReversed bool mateReversed [@property getter]: is mate reversed? bool bam_is_mrev(bam1_t *b) { return( ((*b).core.flag & BAM_FMREVERSE) != 0); }
mateTID int mateTID [@property getter]
int mateTID [@property setter]: chromosome ID of next read in template, defined by bam_hdr_t
pos int pos [@property getter]
int pos [@property setter]: 0-based leftmost coordinate
qual ubyte qual [@property getter]
ubyte qual [@property setter]: mapping quality
queryName char[] queryName [@property getter]: auto bam_get_qname(bam1_t *b) { return (cast(char*)(*b).data); }
queryName string queryName [@property setter]: Set query name
sequence const(char)[] sequence [@property getter]: Return char array of the sequence see samtools/sam_view.c: get_read
sequence const(char)[] sequence [@property setter]: Assigns sequence and resets quality score
strand char strand [@property getter]: Return read strand + or - (as char)
tid int tid [@property getter]
int tid [@property setter]: 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 aliases

SAMFile

classes

SAMRecord

enums

SAMWriterTypes

functions

structs