feature requests for output VCF

[zeeev]

Hello,

A few requests regarding the output VCF.

1. It would be really useful if the REF/ALT alleles could be populated via the graph traversal. Most users won't know how to walk the graph to extract the alleles.
2. Replacing genotype separator to | or /, rather than :.
3. It appears that the sample names on the final step is ignored, the VCF samples still has the samples as {sample}_{hap1/2} rather than {sample} which is what is encoded in sample_names.txt

./k8 mgutils-es6.js merge2vcf -r0 merged_sv_calls_labeled.bed -s sample_names.txt

[lh3]

1. Will add later
2. Minigraph only outputs haplotype and thus GT only has one number. : is not for separating haplotypes; it separates GT and GT0.
3. Could you show an example?