genome/genome — pull request #347 by davidlmorton (2014-12-18 20:46:31+00:00)
Title: Header labels

This makes headers (for the full/acmg/docm reports) that look like:

Discovery(H_KA-174556-1309245)_ref_count
Discovery(H_KA-174556-1309245)_vaf
Discovery(H_KA-174556-1309245)_var_count
Followup(H_KA-174556-1309237)_ref_count
Followup(H_KA-174556-1309237)_vaf
Followup(H_KA-174556-1309237)_var_count
Normal(H_KA-174556-1309246)_ref_count
Normal(H_KA-174556-1309246)_vaf
Normal(H_KA-174556-1309246)_var_count
min_coverage_observed
max_normal_vaf_observed
max_tumor_vaf_observed
variant_callers
variant_caller_count
Discovery-Library2(H_KA-174556-1309245-lg3-lib1)_ref_count
Discovery-Library2(H_KA-174556-1309245-lg3-lib1)_vaf
Discovery-Library2(H_KA-174556-1309245-lg3-lib1)_var_count
Discovery-Library4(H_KA-174556-1309245-lg5-lib1)_ref_count
Discovery-Library4(H_KA-174556-1309245-lg5-lib1)_vaf
Discovery-Library4(H_KA-174556-1309245-lg5-lib1)_var_count
Followup-Library2(H_KA-174556-1309237-lg3-lib1)_ref_count
...
Normal-Library2(H_KA-174556-1309246-lg2-lib1)_ref_count
...

The order is not quite what was asked for, but will be consistently (discovery, followup, normal). The Library# is determined based on all of the libraries for the given samples, so the counter doesn't always start at 1 (in the case that some libraries for a given sample are not associated with the builds used to make the reports). Since this number is arbitrary, I wasn't considered important to enforce it starting at 1.