samtools- Binding to the C samtools library

Safe HaskellNone



This module provides an interface to sorted, indexed BAM alignment files, which allow rapid extraction of alignments that lie within one specific region of one sequence.



data IdxHandle Source #

Handle for fetching alignments by region from a sorted, indexed BAM file.

idxFilename :: IdxHandle -> FilePath Source #

Filename of sorted, indexed BAM file

idxHeader :: IdxHandle -> Header Source #

Target sequences

open :: FilePath -> IO IdxHandle Source #

Open a sorted, indexed BAM file.

readBamRegion :: IdxHandle -> Int -> (Int64, Int64) -> IO [Bam1] Source #

Use a BAM index file to extract Bam1 records aligned to a specific target sequence (chromosome) number and region.