Safe Haskell | None |
---|---|
Language | Haskell98 |
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
- 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)
- readBamRegion :: IdxHandle -> Int -> (Int64, Int64) -> IO [Bam1]
Documentation
idxFilename :: IdxHandle -> FilePath Source
Filename of sorted, indexed BAM file