EX-132(kmeng): Jacquard now adjusted for new "Done" message when
warnings thrown.
EX-132(kmeng): Previous version failed all tests because of the way
logger works. This commit fixes that.
EX-107(kmeng): Added tagging of anomalous records. Updated functional
test of tag, and appropriate unit tests.
EX-107(kmeng): "malformed" prefix in tag.py changed to "anomalous".
EX-131 (kmeng): Added and tested code to filter_hc_somatic to exclude
records tagged with "JQ_EXCLUDE". No logging implemented yet.
EX-131(kmeng): filter_hc_somatic now logs debugs and warnings about
filtered records. Tested.
EX-130(kmeng): Added logging in tag.py for the individual file debug
messages and the caller debug messages. Haven't added the total filter
warn message yet.
cgates: fixes to rollup_genes
Merge branch 'develop' of github.com:umich-brcf-bioinf/Jacquard into develop
EX-94 (cgates): Adjust calc and metaheader to reference TIR instead of TAR for Strelka AF calc
EX_94 (cgates): Reformat AF to make code more readable.
EX-131(kmeng): Commit checkpoint.
ex-131/130 (kmeng/jebene): added more tests for logging
EX-126(kmeng): Updating the functional tests to neglect newline
characters.
Merge remote-tracking branch 'origin/develop' into
tag_anomalous_variants

Conflicts:
	test/functional_tests/02_tag/benchmark/tiny_strelka.normalized.jacquardTags.vcf
EX-126(kmeng): Updated functional test for tag.
Ex-126(kmeng): Updated tag functional test.
Merge branch 'develop' of https://github.com/umich-brcf-bioinf/Jacquard
into develop

Conflicts:
	test/functional_tests/02_tag/benchmark/tiny_strelka.normalized.jacquardTags.vcf
cgates: Backed out functional tests breakage
Merge remote-tracking branch 'origin/develop' into
tag_anomalous_variants

Conflicts:
	test/functional_tests/02_tag/benchmark/tiny_strelka.normalized.jacquardTags.vcf