Safe Haskell | None |
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- enumInHandle :: MonadIO m => InHandle -> Enumerator Bam1 m a
- enumTam :: FilePath -> Enumerator Bam1 IO a
- enumTamWithIndex :: FilePath -> FilePath -> Enumerator Bam1 IO a
- enumBam :: FilePath -> Enumerator Bam1 IO a
- enumQuery :: Query -> Enumerator Bam1 IO a
- enumIndexRegion :: IdxHandle -> Int -> (Int64, Int64) -> Enumerator Bam1 IO a
- enumBamRegion :: FilePath -> ByteString -> (Int64, Int64) -> Enumerator Bam1 IO a
- iterHandle :: OutHandle -> Iteratee Bam1 IO ()
Documentation
BAM/SAM enumeration
enumInHandle :: MonadIO m => InHandle -> Enumerator Bam1 m aSource
Enumerate over the contents of a BAM/SAM alignment input handle
enumTam :: FilePath -> Enumerator Bam1 IO aSource
Enumerate over the contents of a TAM (tab-delimited text) alignment file
enumTamWithIndex :: FilePath -> FilePath -> Enumerator Bam1 IO aSource
Enumerate over the contents of a TAM file with a separate target sequence index
enumBam :: FilePath -> Enumerator Bam1 IO aSource
Enumerate over the contents of a BAM (binary) alignment file
Indexed BAM region enumeration
enumQuery :: Query -> Enumerator Bam1 IO aSource
Enumerate over the results of a query into a sorted, indexed BAM file
enumIndexRegion :: IdxHandle -> Int -> (Int64, Int64) -> Enumerator Bam1 IO aSource
Enumerate over the reads in a region from an indexed BAM file input handle
enumBamRegion :: FilePath -> ByteString -> (Int64, Int64) -> Enumerator Bam1 IO aSource
Enumerate over the reads in a region from a sorted, indexed BAM file
BAM/SAM iteration