start of work on new genome_studio_fcr_to_vcf step for the genome_studio_import_genotype_files pipeline
Merge branch 'release/0.173' into develop
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/hipsci_pipelines
completed implementation of and tests for fcr->vcf step
genome_studio_fcr_to_vcf step now sorts the output VCF, and we now test the pipeline with more samples for 2 individuals
point out the result is a sorted VCF in the description
improved descriptions to clarify that these use vcf-isec, and the implications of that
fixed so that vcf_isec_options are actually used, and a cmd_summary is generated
new vcf merge step that uses bcftools merge
new vcf merge step that uses bcftools merge
now bgzips the output VCF
now adds genotype_maximum_deviation metadata to output files
new vcf_merge_and_compare_genotypes pipeline and tests
renamed module to match pipeline name
corrected class name to match module name
corrected POD
dedicated simple test script for the new vcf_merge_different_samples step
Merge branch 'feature/hipsci_pipelines' into develop
renamed test to better reflect what it does
no longer exits on failure to move a file, just skips it instead