Bio.SamTools.Enumerator

Documentation

BAM/SAM enumeration

enumInHandle :: MonadIO m => InHandle -> Enumerator Bam1 m a

Enumerate over the contents of a BAM/SAM alignment input handle

enumTam :: FilePath -> Enumerator Bam1 IO a

Enumerate over the contents of a TAM (tab-delimited text) alignment file

enumTamWithIndex :: FilePath -> FilePath -> Enumerator Bam1 IO a

Enumerate over the contents of a TAM file with a separate target sequence index

enumBam :: FilePath -> Enumerator Bam1 IO a

Enumerate over the contents of a BAM (binary) alignment file

Indexed BAM region enumeration

enumQuery :: Query -> Enumerator Bam1 IO a

Enumerate over the results of a query into a sorted, indexed BAM file

enumIndexRegion :: IdxHandle -> Int -> (Int64, Int64) -> Enumerator Bam1 IO a

Enumerate over the reads in a region from an indexed BAM file input handle

enumBamRegion :: FilePath -> ByteString -> (Int64, Int64) -> Enumerator Bam1 IO a

Enumerate over the reads in a region from a sorted, indexed BAM file

BAM/SAM iteration

iterHandle :: OutHandle -> Iteratee Bam1 IO ()