Commits for angie

98fefd88af86752bdad2f436c928cd7e02e59d19 Tue Dec 5 12:38:00 2017 -0800

Adding new vcfToHgvs test case for Personalis variants on patches/alt sequences that are only in hg38. Not adding it to top-level 'make test' because test.2bit is a link to hg19.2bit and reconstructing a 2bit from hg19.2bit and hg38.2bit would be costly in either git repo space or test time, and using hg38 instead of test means that as RefSeq versions increment, the expected result file will get out of date. Still important to capture the test case because it exposed a couple more bugs in github hgvslib example_test_set/hgvs_test_cases_reference.txt.
- src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_patches.tab - lines changed 18, context: html, text, full: html, text
- src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_patches.vcf - lines changed 32, context: html, text, full: html, text
- src/hg/utils/vcfToHgvs/tests/makefile - lines changed 9, context: html, text, full: html, text

e2abb3d38e8bf2296e4be847deff63409bc82d1c Thu Dec 7 12:55:15 2017 -0800

In vpPep, don't distinguish between spansUtrCds and cantPredict. (btw spansUtrCds was only used for 5' UTR/CDS boundary) This should not affect output of anything because they were treated the same anyway.
- src/hg/inc/variantProjector.h - lines changed 1, context: html, text, full: html, text
- src/hg/lib/hgHgvs.c - lines changed 1, context: html, text, full: html, text
- src/hg/lib/variantProjector.c - lines changed 7, context: html, text, full: html, text

57ae0219750957cadcb4a639ad0d83bef11ec24b Mon Dec 11 11:24:20 2017 -0800

Yet another case of bigDataUrl-only track running into old hgTables assumption that everything is in mysql. refs #19638 note-136
- src/hg/hgTables/filterFields.c - lines changed 4, context: html, text, full: html, text