Utility

Documentation

findWithError :: (Eq a, Ord a, Show a) => a -> Map a b -> b

Return a specific error when the text key is not found.

bamToFasta :: Maybe AccessionMap -> Maybe MatchMap -> Text -> Maybe Headers -> BamRow -> [Text]

Convert a line in a bam file to a fasta format for duplication input. Uses values from the maps if Assembly.

appendHeader :: Maybe Headers -> Line -> Line

Append a header to the end of the header line in a fasta row.

fastaToMap :: Char -> [FastaSequence] -> AccessionMap

Create a mapping from accession number to sequence. Trinity outputs ' ' as a separator.

getMatchMap :: [BamRow] -> MatchMap

Get a mapping from accession to if the cigar has all matching.

nub' :: (Eq a, Ord a) => [a] -> [a]

Better nub.

decodeSAMFlag :: Int -> String

Decode a SAM flag into the bit representation (as a string).