Giraffe integration for haplotype sampling

[jltsiren]

Changelog Entry

To be copied to the draft changelog by merger:

• Giraffe can do haplotype sampling automatically if sufficient inputs are provided.
• Simplified vg giraffe command line help; full list of options is still available with -h.

Description

vg giraffe runs haplotype sampling with the default options and --include-reference if 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-basename and -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 giraffe command line help to show only the most important options by default. The full help with all options is still available with -h.