Fixed a bug in phased haplotype output
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Speed up of fill-aa: removed unnecessary stat call and faidx exec for positions beyond the ancestral fasta file
run-chunkify: Check for close() error
Moved run-filter into run-som-filter
run-mpileup: Updated for use with the new samtools/bcftools with htslib callers
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
runner: Fixed a rare issue when is_job_array_running returns undefined job status. Added a system cmd() to Runner, as this is present in virtually all pipelines. Check return of lsadmin and retry repeatedly if it fails, which it does often.
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop