Commits for angie
switch to files view, user index
v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297
- Fixed a typo that caused hgTracks to ignore settings for coloringSNPs by exceptions. Thanks Brian L!
fixes #12793
- src/hg/hgTracks/variation.c - lines changed 1, context: html, text, full: html, text
- Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
not too big it will work OK. This means adding a new track type
vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
hgc, hgTables and hgVai. (and others I've forgotten?)
refs #12416
- src/hg/hgTables/bedList.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 12, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 11, context: html, text, full: html, text
- src/hg/hgTables/hgTables.h - lines changed 12, context: html, text, full: html, text
- src/hg/hgTables/identifiers.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTables/intersect.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/joining.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTables/mainPage.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/schema.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 7, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 6, context: html, text, full: html, text
- src/hg/hgTracks/vcfTrack.c - lines changed 95, context: html, text, full: html, text
- src/hg/hgVai/libifyMe.c - lines changed 5, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 155, context: html, text, full: html, text
- src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text
- Added a few tests for 0-length (insertion) variants, to avoid errAbortwhen trying to fetch sequence for empty region.
- Handle blank line(s) preceding header lines that specify format.
- src/hg/lib/customFactory.c - lines changed 4, context: html, text, full: html, text
- In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
are any. I've seen multiple cases of user VCF with indels that
have inflated size due to including right flanking bases; when
trying to determine functional consequences, it's misleading to
have an indel sized larger than it has to be.
- src/hg/hgTracks/vcfTrack.c - lines changed 12, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 17, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 28, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTests.mk - lines changed 5, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt - lines changed 82, context: html, text, full: html, text
- src/hg/lib/tests/input/annoGrator/indelTrim.vcf - lines changed 17, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text
- Fixing an incomplete renaming of a variable that caused a compile errorfor a mirror admin using USE_BAM w/samtools but not using KNETFILE_HOOKS.
refs #12827
- Fixing compiler warning for stricter format checkers (don't use variable in place of format argument).
- src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text
- hgSession/makefile had an override of HG_WARN that prevented compilewarning from halting the build -- oops!
- src/hg/hgSession/makefile - lines changed 2, context: html, text, full: html, text
switch to files view, user index