Bio.SamTools.BamIndex

Description

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.

Synopsis

data IdxHandle
idxFilename :: IdxHandle -> FilePath
idxHeader :: IdxHandle -> Header
open :: FilePath -> IO IdxHandle
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)

Documentation

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.

close :: IdxHandle -> IO () Source

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

data Query Source

qyHandle :: Query -> IdxHandle Source

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

next :: Query -> IO (Maybe Bam1)Source