bam

Documentation

Overview

Package bam provides support for parsing BAM files.

Index

• func GetReferenceID(bam io.Reader, reference string) (int32, error)
• func Read(bai io.Reader, region genomics.Region) ([]*bgzf.Chunk, error)

Functions

func GetReferenceID

func GetReferenceID(bam io.Reader, reference string) (int32, error)

GetReferenceID attempts to determine the ID for the named genomic reference by reading BAM header data from bam.

func Read

func Read(bai io.Reader, region genomics.Region) ([]*bgzf.Chunk, error)

Read reads index data from bai and returns a set of BGZF chunks covering the header and all mapped reads that fall inside the specified region. The first chunk is always the BAM header.