Bio.Data.Bam

Documentation

type Bam = ForeignPtr Bam'

type HeaderState = ResourceT (ReaderT * FileHeader IO)

withBamFile :: FilePath -> (BamFileHandle -> HeaderState a) -> IO a

readBam :: BamFileHandle -> ConduitT () Bam HeaderState ()

writeBam :: FilePath -> ConduitT Bam o HeaderState ()

bamToBed :: ConduitT Bam BED HeaderState ()

Convert bam record to bed record. Unmapped reads will be discarded.

sortedBamToBedPE :: ConduitT Bam (BED, BED) HeaderState ()

Convert pairedend bam file to bed. the bam file must be sorted by names, e.g., using "samtools sort -n". This condition is checked from Bam header.