bio.bam.reference

Each BAM file contains reads aligned to different reference sequences.

These sequences have unique identifiers in BAM file, starting from 0. Unmapped reads are associated with id = -1.

If BAI file is available, fast region queries are available, that is, getting all reads that overlap given region. This is achieved via opSlice method.

Public Imports

bio.bam.referenceinfo public import bio.bam.referenceinfo;: Undocumented in source.

Members

Structs

ReferenceSequence struct ReferenceSequence

Examples

import bio.bam.reader, std.stdio;
...
auto bam = new BamReader("file.bam");
auto refseq = bam["chr17"];
writeln(refseq.name, " - length ", refseq.length);
foreach (read; refseq[1234 .. 5678])
    if (read.cigar.length > 1)
        writeln(read.name, " ", read.cigarString());

bio.bam.reference

Public Imports

Members

Structs

Examples

Meta

Source