bioinformatics-toolkit-0.10.0: A collection of bioinformatics tools

Safe Haskell	None
Language	Haskell2010

Bio.Data.Bam

Synopsis

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 ()
bamToBed :: BAMHeader -> BAM -> Maybe BED
bamToFragmentC :: Monad m => BAMHeader -> ConduitT BAM BED m ()
bamToFragment :: BAMHeader -> BAM -> Maybe BED
bamToFastqC :: Monad m => ConduitT BAM Fastq m ()
bamToFastq :: BAM -> Maybe Fastq
sortedBamToBedPE :: Monad m => BAMHeader -> ConduitT BAM (BED, BED) m ()

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 () Source #

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

bamToBed :: BAMHeader -> BAM -> Maybe BED Source #

Convert BAM to BED.

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

Convert pairedend bam to fragment.

bamToFragment :: BAMHeader -> BAM -> Maybe BED Source #

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

Convert bam record to fastq record.

bamToFastq :: BAM -> Maybe Fastq Source #

Convert BAM to Fastq.

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

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.