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
InstData Import: tcga metadata dies if not library strategy exists when determining target region
InstData Import: add cghub to env path to run cgquery
Merge pull request #79 from nnutter/bam_readcount_ver_clinseq
Remove redundant property declarations.
Move id property into id_by section.
Use canonical names to make Ghosts happy.
Merge pull request #73 from apregier/refactor-with-svr

Refactor with separated value reader/writer
Merge pull request #71 from apregier/warning-message-fix

Fix warning message for undefined entry