bpbio: a single binary with a collection of sub-commands useful for genomics

• plot-sv-vcf: create a plot that shows the number of large and small variants separated by DEL/DUP/BND/INV for a multi-sample SV VCF. (idea from @ernfrid)

Libraries

• countstats: get median and percentiles for integers in constant space and little time.
• pedfile: ped (fam) file parsing and matching to VCF.
• duko: ergonomic embedded javascript via duktape and duktape-nim
• variexpr: simple expressions for filtering and labeling VCF records e.g.: denovo:kid.alts == 1 && mom.alts == 0 && dad.alts == 0 && kid.DP > 10

Abandoned

• homsv: look for depth changes in self-chains or homologous regions
• homsv-merge: merge output from homsv