Merge branch 'release/0.186' into develop
moving test script to the Pipelines dir since it tests a pipeline, not a single step
vrpipe-disk_usage now provides a complete report on all usage across all disks; needs Number::Bytes::Human module from CPAN
new multiple_samples_per_individual option, renamed min_concurrence_ratio option to min_concordance_ratio, and fixed and improved gt_status logic
added support for gt_status now possibly having concordance instead of ratio
new generic r step inheriting from r_script step, for pluritest_plot_gene_expression step to inherit from, also fixing a missing env var problem
new generic r step inheriting from r_script step, for pluritest_plot_gene_expression step to inherit from, also fixing a missing env var problem
always specify the analysis file as an output, even if it already exists
only treat array refs as array refs, leave other refs alone
new/updated test data for genome_studio_import_and_genotype_comparison.t
removed defunct fcr_to_vcf() method; vcf_sample_from_metadata option now supports multi keys and defaults to irods keys; new bcftools_exe option; now records that we output tbi_files
vcf_merge_different_samples_control_aware and hipsci_loh_caller steps now default to irods keys for their options, and the merge now supports forming control_metadata_sample_key from multiple values
external_gzip_file option removed; input gtc files no longer have to exist; reimplemented body_sub to work with irods datasource
new genome_studio_split_and_convert_to_vcf pipeline and redid genome_studio_import_and_genotype_comparison.t to prove irods datasource-based gtc import, vcf merging and loh calling works
updated test expectations following change to metadata in irods
pulling in ym3's new bcftools_cnv_caller pipeline, resolving conflicts in the test script and partially updating the new tests according to new datasource - will need further mods
corrected author to ym3
renamed some options as this is using bcftools, updated default control_metadata_key to the irods key; removed debugging print lines; removed max count on output files, since could be working on more than 1 input VCF
temporarily removing the new bcftools cnv caller pipeline and disabling its tests, since it needs reworking
version bump