dnanexus-rnd / GLnexus / 2075

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travis-ci

add option to trim uncalled alleles (#193)

With genotype revision on, it's possible for an allele to be included in the pVCF site but not actually called in any of the final sample GT genotypes. This is rare and mainly associated with low/marginal quality alleles.

The new command-line option --trim-uncalled-alleles, -a (genotyper_config::trim_uncalled_alleles) adds a postprocessing step to remove such "uncalled" alleles (by invoking htslib's bcf_trim_alleles subroutine).

closes #191

20 of 20 new or added lines in 4 files covered. (100.0%)

4302 of 4606 relevant lines covered (93.4%)

945279.27 hits per line