pmelsted/bifrost: v1.3.5

New querying options

• -Q, --files-as-queries: It is now possible to use a file containing one or multiple sequences as one query.
• -E, --min-nb-colors: Requires that a query occurs in a user-provided minimum number of colors to report the query as present in the graph

Bug fixes

• Fix bug with incorrect read positions in input files causing suboptimal construction time
• Fix bug with the resizing of MinimizerIndex and KmerHashtable causing program hanging for very small input data

Refactor

• Querying works a little differently from previous versions. Default behavior for previous versions was to report presence/absence of each query. New behavior is to report the number of k-mers from each query shared with the graph or with its colors, unless parameter -e is used explicitly in which case presence/absence is reported. Parameter -p will make the querying report a ratio of found k-mers (with respect to the number of k-mers in each query) rather than a number
• README updated: New "Benchmarking" section provides guidelines on how to properly compare other tools to Bifrost, use cases updated, citation updated, installation description simplified, etc.