Commits for angie

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
  • src/inc/asParse.h - lines changed 4, context: html, text, full: html, text
  • src/lib/asParse.c - lines changed 12, context: html, text, full: html, text
• When freeing annoRows created by internal source, pass in internal source not self. (#6152)
  • src/lib/annoGrator.c - lines changed 1, context: html, text, full: html, text
• Removed outdated comment.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.
  • src/lib/annoRow.c - lines changed 1, context: html, text, full: html, text
• 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/inc/gpFx.h - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/soTerm.h - lines changed 82, context: html, text, full: html, text
  • src/hg/inc/soterm.h - lines changed 74, 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/gpFx.c - lines changed 174, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/soTerm.c - lines changed 43, 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
  • src/hg/lib/variant.c - lines changed 7, 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.
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
• 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