How to...

This page presents how common operations on BAM file are done with BioD.

For more information, see module/function/method documentation in the source code.

See also examples.

---

• Get all reads in BAM file

import bio.bam.reader;
...
auto bam = new BamReader(filename);
foreach (read; bam.reads)
{
   ...
}

• Get only reads overlapping a region (index must be available)

import bio.bam.reader;
...
auto bam = new BamReader(filename);
foreach (read; bam["chr17"][100000 .. 200000])
{
    ...
}

• Make a pileup and iterate columns

import bio.bam.reader;
import bio.bam.pileup;
...
auto bam = new BamReader(filename);
auto reads = bam["chr11"][500000 .. 600000];
foreach (column; makePileup(reads))
{
    ...
}

• Recover reference bases from read sequence, CIGAR, and MD tag (they start from the first mapped base of the read)

import bio.bam.md.reconstruct;
import std.conv; // optional, to convert the result to a string
...
auto reference_bases = to!string(dna(read));

• Recover reference bases for a whole bunch of reads (they must be sorted by coordinate!)

import bio.bam.md.reconstruct;
import std.conv;
...
auto reference_bases = to!string(dna(bam["chr12"][850000 .. 1850000]));

• Get tag value

  • Preferred way. Throws exception in case of error, does type conversions automatically.

  import std.conv;
  auto value = to!ushort(read["ZF"]); // will check if the value is in 0..65535 range

  • Faster but unsafe way. Exact type of tag must be known.

  auto v = read["ZF"];
  auto value = *cast(int*)(&v);