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
new scripts for hipsci update and gs file reformatting
correcting hash bang line
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
More informative messages with +verbose showing the location of checkpoint files.
Module for single-pass quantile estimation.
Mann-Whitney U-test implementation.
team page for new vm, plus updated ViewUtil module
disk usage and hipsci viewer tools for new vm
sample mapping, map view and pending view tools for new vm
qc grind tool for new vm
fixed module path for new vm symlinks
correcting lib path for new vm checkout