Bio.SamTools.Conduit

Documentation

sourceHandle :: MonadIO m => InHandle -> Producer m Bam1

Streams the alignments read from a InHandle

sourceBamInFile :: MonadResource m => FilePath -> Producer m Bam1

Streams the alignments read from a BAM format (binary) file

sourceTamInFile :: MonadResource m => FilePath -> Producer m Bam1

Streams the alignments read from a TAM format (tab-delimited text) file

sourceQuery :: MonadIO m => Query -> Producer m Bam1

Streams the alignments read from a Query set of query results

sinkHandle :: MonadIO m => OutHandle -> Consumer Bam1 m ()

Stream incoming alignments into a OutHandle

sinkBamOutFileWithHeader :: MonadResource m => FilePath -> Header -> Consumer Bam1 m ()

Stream incoming alignments into a BAM-format output file with header specified

sinkBamOutFile :: MonadResource m => FilePath -> Consumer Bam1 m ()

Stream incoming alignments into a BAM-format output file using the target sequence headers from the first Bam1 alignment.

sinkTamOutFileWithHeader :: MonadResource m => FilePath -> Header -> Consumer Bam1 m ()

Stream incoming alignments into a TAM-format output file with header specified

sinkTamOutFile :: MonadResource m => FilePath -> Consumer Bam1 m ()

Stream incoming alignments into a TAM-format output file using the target sequence headers from the first Bam1 alignment.