Merge branch 'release/0.187' into develop
simplying pluritest pipeline steps slightly by getting rid of merge_tag_id metadata and changing steps to only cope with one set of input files for the same individual
new mapping_sample_from_metadata option to choose how the sample name appearing in plots will be formed
vcf_sample_from_metadata option of sequenom_csv_to_vcf step now supports multiple keys and defaults to public_name+sample
new combined_metadata() method in StepRole, used by vcf_merge_different_samples_control_aware step to keep all the metadata of input vcfs on the output merged vcf
make the expected sample fudge occur when the ratio is 1.00, not 1.000
check the return value of unlink and report if files could not be deleted
vcf_merge_different_samples* steps now throw if try and get them to output the wrong type, since they are type-specific, and estimate memory requirements better based on number of input vcfs
now asks if files created by more than 1 setup should be deleted, instead of silently skipping them
no longer includes out file in cmd line, for compatability with latest samtools
fixed datasource on second setup, but test failing due to python/stampy install issues right now
new bcftools base module, and various bcftools-using steps updated to use it, allowing them to work with both old and new bcftools
new bcftools base module, and various bcftools-using steps updated to use it, allowing them to work with both old and new bcftools
new genotype_analysis step that htscmd_genotype_analysis inherits from, and updated test expectations for different versions of bcftools/htscmd
new _bcftools_site_files_option method in bcftools step to set the sites file option correctly in old and new bcftools
now inherits from bcftools step
new vrtrack_auto_qc_with_genotype_checking pipeline which runs new bcftools genotype checking steps prior to auto qc
version bump
Merge branch 'release/0.188'