Fix warning message for undefined entry
Use SeparatedValueReader
Refactor to use SeparatedValue{Reader,Writer}

instead of implementing our own column order logic
Refactor split_file to use SeparatedValue{Reader,Writer}
Refactor to use SeparatedValueReader
pass b-r-c version to clinseq steps
Merge 4d9c0df4e0fef85199c463e8f9eb2f358e38abac into 618c9e8a7bd3194ae89fa9d345be4056f3637128
InstData Import: add tcga metadata module
hard-code secondary bam-readcount version

The last passing builds ClinSeq was using 0.4 in "Run clonality analysis
and produce clonality plots" while using 0.6 in "Produce a report using
DOCM" and "Generate SnvIndel Report".  This change preserves that
behavior while not just using a default value.
InstData Import: add ref name and version & update target region in tcga metadata
InstData Import: tcga bam uses metadata module
changing gmt htseq count to use the new individual attribut of genome sample
Use the build directory to decide which result is the correct one.

If the indel_detection_strategy contains an unfiltered detector that
also detects snvs, the previous logic would get confused about which
result is the correct one.  The final result symlinked in the variants
directory knows the one true result.

(In SomVal a different label is set on the SR::User--this would be a
better solution, but it isn't backwards-compatible.)
Use List::Util::first instead of a homespun version.
Allow export of our new function.
InstData Import: tcga metadata dies if not library strategy exists when determining target region
Check if we got an allocation and an owner.
InstData Import: add cghub to env path to run cgquery
missing comma
update mutspec file accessors