Bio.SamTools.BamIndex

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.

Documentation

data IdxHandle

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

idxFilename :: IdxHandle -> FilePath

Filename of sorted, indexed BAM file

idxHeader :: IdxHandle -> Header

Target sequences

open :: FilePath -> IO IdxHandle

Open a sorted, indexed BAM file.

close :: IdxHandle -> IO ()

withIndex :: FilePath -> (IdxHandle -> IO a) -> IO a

data Query

qyHandle :: Query -> IdxHandle

query :: IdxHandle -> Int -> (Int64, Int64) -> IO Query

next :: Query -> IO (Maybe Bam1)

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

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