heatitup-complete-0.5.3.3: Find and annotate ITDs with assembly or read pair joining.

Safe Haskell	None
Language	Haskell2010

Merge

Synopsis

mergeAbundance :: FrequencyMap -> DuplicationRow -> DuplicationRow
mergeMates :: Fill -> [BamRow] -> [BamRow]
bamToFasta :: Maybe AccessionMap -> Maybe MatchMap -> Text -> Maybe Headers -> BamRow -> [Text]

Documentation

mergeAbundance :: FrequencyMap -> DuplicationRow -> DuplicationRow Source #

mergeMates :: Fill -> [BamRow] -> [BamRow] Source #

Merge all mate pairs. Assumes that the lines are sorted by mate pair already (samtools sort -n).

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

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