Commits for angie
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v280_base to v281_preview (2013-03-05 to 2013-03-12) v281
- Added --stat to the git log command that reminds us what we changed inthe branch, so it will also remind us which files changed with each commit.
- src/utils/qa/weeklybld/summaryEmail.sh - lines changed 2, context: html, text, full: html, text
- Libified asColumnFindIx. (#6152)
- src/hg/lib/annoStreamDb.c - lines changed 12, context: html, text, full: html, text
- When freeing annoRows created by internal source, pass in internal source not self. (#6152)
- Removed outdated comment.
- src/lib/annoStreamVcf.c - lines changed 2, context: html, text, full: html, text
- bugfix: if some word is NULL, print out empty string.
- src/lib/annoFormatTab.c - lines changed 1, context: html, text, full: html, text
- bugfix: forgot to null out *pList in a FreeList function.
- Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
- src/hg/inc/annoFormatVep.h - lines changed 43, context: html, text, full: html, text
- src/hg/inc/annoGratorGpVar.h - lines changed 4, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 405, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 127, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 56, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTests.mk - lines changed 6, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 46, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 17, context: html, text, full: html, text
- src/hg/lib/tests/input/annoGrator/vepSample.pgSnp.tab - lines changed 2, context: html, text, full: html, text
- Fixing strict-gcc warning: non-literal format argument.
- src/hg/lib/annoFormatVep.c - lines changed 1, context: html, text, full: html, text
- Added -Wformat-security to hgwdev's HG_WARN so that a common stricter-gcc warning is detected during development.
- Feature #6152 (varAnnogrator): fixing bugs uncovered by switching todifferent organisms and assemblies when the cart has a queryConfig
that includes sources available in some assemblies but not others.
Tests for NULLs, propagate changes to default from group to track,
etc. Also found that mouse's Phenotype group has a slightly different
name from human's, so check for both.
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 49, context: html, text, full: html, text
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