SAMHeader

Constructors

this

this(bam_hdr_t* h)

Construct from existing pointer

Members

Functions

addLine

auto addLine(RecordType type, T kvargs)

Add a single line to an existing header

addLines

auto addLines(const(char)[][] lines)

add multiple \n-terminated full SAM header records, eg "@SQ\tSN:foo\tLN:100" (single line or last of multiple does not require terminal \n)

dup

auto dup()

Copy a SAMHeader

isNull

bool isNull()

Undocumented in source. Be warned that the author may not have intended to support it.

lineById

const(char)[] lineById(RecordType type, string id_key, string id_val)

Return a complete line of formatted text for a given type and ID, or if no ID, first line matching type.

numRecords

size_t numRecords(RecordType rt)

number of records (lines) of type e.g. SQ, RG, etc.

opBinaryRight

bool opBinaryRight(RecordType lhs)

'in' membership operator. usage: RecordType.SQ in hdr; => <bool>

opIndex

const(char)[] opIndex(RecordType rt, size_t pos, const(char)[] key)

For position-based lookups of key, e.g. a sample-name lookup in Pysam is ["RG"][0]["SM"] , while in dhtslib: [RecordType.RG, 0, "SN"]

targetId

int targetId(string name)

reference contig name to integer id

targetLength

uint targetLength(int target)

length of specific reference sequence by number (tid)

targetName

const(char)[] targetName(int tid)

reference contig name to integer id

valueByPos

const(char)[] valueByPos(RecordType type, size_t pos, const(char)[] key)

/ //// int sam_hdr_find_tag_id(sam_hdr_t *h, const char *type, const char *ID_key, const char *ID_value, const char *key, kstring_t *ks); Return the value associated with a key for a header line identified by position

Properties

nTargets

int nTargets [@property getter]

number of reference sequences; from bam_hdr_t

targetLengths

uint[] targetLengths [@property getter]

lengths of the reference sequences

targetNames

string[] targetNames [@property getter]

names of the reference sequences

Variables

h

BamHdr h;

rc bam_hdr_t * wrapper

import std;

auto h = sam_hdr_init();
auto hdr = SAMHeader(h);

assert(!(RecordType.RG in hdr));

//sam_hdr_add_line(h, RecordType.RG.ptr, "ID".ptr, "001".ptr, "SM".ptr, "sample1".ptr, null);
hdr.addLine(RecordType.RG, "ID", "001", "SM", "sample1");

assert(RecordType.RG in hdr);

auto line = hdr.lineById(RecordType.RG, "ID", "001");
assert(line == "@RG	ID:001	SM:sample1");

auto val = hdr.valueByPos(RecordType.RG, 0, "SM");
assert(val == "sample1");
assert(hdr[RecordType.RG, 0, "SM"] == "sample1");
assert(hdr[RecordType.RG, 0, "XX"] == "");

• RecordType

• SAMHeader