changing instance of patient out for the more generally applicable individual, this may break some analyst scripts that I will attempt to discover
changes to get tests passing after patient to individual naming change in genome sample
Fix warning message for undefined entry
multiple changes to views, reports, ClinSeq to support the change from patient_common_name to individual_common_name
replacing patient_name with individual_name
batch of updates to get some ClinSeq and Export commands to pass
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
changed 4 ClinSeq scripts that were used by 4 ClinSeq converge tests to not use the patient accessor on Sample
InstData Import: rm prematurely pushed tcga load metadata module
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.
reverting inadvertent changes to variable names in a ClinSeq module
InstData Import: add ref name and version & update target region in tcga metadata
InstData Import: tcga bam uses metadata module
Merge pull request #65 from jeldred/master