Commits for angie
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v285_preview2 to v285_base (2013-06-11 to 2013-06-18) v285
- Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
- src/hg/hgCustom/hgCustom.c - lines changed 11, context: html, text, full: html, text
- src/hg/htdocs/inc/globalNavBar.inc - lines changed 1, context: html, text, full: html, text
- src/hg/lib/annoStreamDb.c - lines changed 17, context: html, text, full: html, text
- Fixing code review bugs -- Tim noticed I was not using lm when I meant to, and pointed out a contradiction in the way I was using nextChunkStart. refs #11034
- src/hg/lib/annoStreamDb.c - lines changed 9, context: html, text, full: html, text
- Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
hyphens to determine effects on genes, use the genePred information directly
to determine the variant's offset in CDS, and how many CDS bases are
added/deleted. This solves two problems: 1) the reference was never padded,
so the method didn't work for insertions because string comparison could not
pick up the trail of identical bases again; 2) the hyphens were messing up
protein translation.
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 13, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 1, context: html, text, full: html, text
- Bugfix: forgot to pass through an argument, so all sections started up closed by default. refs #6152
- Fix corner case (deletion falls across exon boundary; normally we wantto trim the part of the allele that falls outside, but for the deletion
the allele is "").
- Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 15, context: html, text, full: html, text
- oops, one more thing that Tim caught. refs #11034
- src/hg/lib/annoStreamDb.c - lines changed 1, context: html, text, full: html, text
- Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
for frameshifts) refs #6152
- src/hg/lib/annoFormatVep.c - lines changed 23, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 1, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 2, context: html, text, full: html, text
- More bugfixing after testing with artificially low ASD_CHUNK_SIZE.
- src/hg/lib/annoStreamDb.c - lines changed 17, context: html, text, full: html, text
- Added cgiExitTime to main.
- Adding HTML version of VEP output format. refs #6152
- src/hg/inc/annoFormatVep.h - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 251, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 2, context: html, text, full: html, text
- As Jonathan pointed out, to be consistent with VEP we should uppercase only the varying bases in the codon change column. refs #6152
- src/hg/lib/annoFormatVep.c - lines changed 22, context: html, text, full: html, text
- Oops, catching up VEP output test cases with that last commit.
- src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 6, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 2, context: html, text, full: html, text
- As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
refs #6152
- src/hg/lib/annoGratorGpVar.c - lines changed 8, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 13, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 13, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 13, context: html, text, full: html, text
- Fixing bug w/interaction of merge state and chrom-skipping queries.
- src/hg/lib/annoStreamDb.c - lines changed 7, context: html, text, full: html, text
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