Giraffe integration for haplotype sampling #4053
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Changelog Entry
To be copied to the draft changelog by merger:
vg giraffecommand line help; full list of options is still available with-h.Description
vg girafferuns haplotype sampling with the default options and--include-referenceif it is given a GBZ graph, the corresponding haplotype information (with--haplotype-name) and kmer counts for the reads (with--kff-name). Names for the sample-specific graph/index files are based on the name of the input graph and basename of the KFF file. This can be overridden with options--index-basenameand-N/--sample.There is also a better kmer coverage estimation heuristic. If the most common kmer count above 1 is below median, the secondary peak close to 2x that will be used as the estimate.
I also changed the
vg giraffecommand line help to show only the most important options by default. The full help with all options is still available with-h.