bioinformatics-toolkit-0.9.0: A collection of bioinformatics tools

Safe HaskellNone
LanguageHaskell2010

Bio.Data.Bam

Synopsis

Documentation

data BAM #

getBamHeader :: FilePath -> IO BAMHeader #

sinkBam :: 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.