Commits for angie

f9e9dc9fe43953f72b43314aba821045a601ee3c Tue Feb 20 14:16:59 2018 -0800

Add support for PSL with double-sided gaps to pslIntronTooShort and pslNmdTarget. refs #20948
- src/hg/lib/variantProjector.c - lines changed 6, context: html, text, full: html, text

3cdb290e612b39be6cc8073bb17112c6c1385a13 Wed Feb 21 11:28:22 2018 -0800

Yikes, forgetting to update a loop variable caused subsequent chroms' records to be overlooked when restricting to a region. Big VCFs are usually single-chrom, I guess that's why the bug has been under the radar until now.
- src/lib/annoStreamVcf.c - lines changed 2, context: html, text, full: html, text

95be7a6a29674ae32b5f1d8eddb079160054bc86 Thu Feb 22 09:55:32 2018 -0800

genomeTxMismatch was supposed to ignore indels and just find base mismatches, but it wasn't ignoring genomic deletions, so sometimes indel-shifting wasn't performed as expected. This has the effect of reducing the range of no-change in PTV035. refs #20948
- src/hg/lib/variantProjector.c - lines changed 2, context: html, text, full: html, text
- src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab - lines changed 1, context: html, text, full: html, text
- src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf - lines changed 3, context: html, text, full: html, text

11e141539ac33a2571e5422a3723046d49a60644 Fri Feb 23 09:53:40 2018 -0800

Oops, compare shiftR to the block size to the right not left. refs #20948
- src/hg/lib/variantProjector.c - lines changed 1, context: html, text, full: html, text

f073f78c136793c533aa903387ca622b4f2203c6 Fri Feb 23 10:18:29 2018 -0800

Fixing compiler -O warning about uninitialized variables.
- src/hg/hgTracks/interactTrack.c - lines changed 2, context: html, text, full: html, text

b280a09989c0816d3c81c13e284c298b420edc1f Fri Feb 23 15:09:46 2018 -0800

Thanks Jonathan for pointing out that I should update the errAbort message. refs #20988
- src/hg/lib/variantProjector.c - lines changed 1, context: html, text, full: html, text