Bio.Data.Bam

Documentation

data BAM

getBamHeader :: FilePath -> IO BAMHeader

streamBam :: forall (m :: Type -> Type) i. MonadResource m => FilePath -> ConduitT i BAM m ()

sinkBam :: forall (m :: Type -> Type) o. MonadResource m => FilePath -> BAMHeader -> ConduitT BAM o m ()

bamToBedC :: MonadIO m => BAMHeader -> ConduitT BAM BED m ()

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

bamToBed :: BAMHeader -> BAM -> Maybe BED

Convert BAM to BED.

bamToFragmentC :: Monad m => BAMHeader -> ConduitT BAM BED m ()

Convert pairedend bam to fragment.

bamToFragment :: BAMHeader -> BAM -> Maybe BED

bamToFastqC :: Monad m => ConduitT BAM Fastq m ()

Convert bam record to fastq record.

bamToFastq :: BAM -> Maybe Fastq

Convert BAM to Fastq.

sortedBamToBedPE :: Monad m => BAMHeader -> ConduitT BAM (BED, BED) m ()

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.