File Changes for angie

v280_base to v281_preview (2013-03-05 to 2013-03-12) v281

• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 49, 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/inc/annoFormatVep.h
  • lines changed 43, 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/annoGratorGpVar.h
  • lines changed 4, 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/gpFx.h
  • lines changed 7, 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/soTerm.h
  • lines changed 82, 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/soterm.h
  • lines changed 74, 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/lib/annoFormatVep.c
  • lines changed 405, 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.
    
  • lines changed 1, context: html, text, full: html, text
    Fixing strict-gcc warning: non-literal format argument.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 127, 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/lib/annoStreamDb.c
  • lines changed 12, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/hg/lib/gpFx.c
  • lines changed 174, 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/lib/makefile
  • lines changed 3, 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/lib/soTerm.c
  • lines changed 43, 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/lib/tests/annoGratorTester.c
  • lines changed 56, 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/lib/tests/annoGratorTests.mk
  • lines changed 6, 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/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 46, 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/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 17, 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/lib/tests/input/annoGrator/vepSample.pgSnp.tab
  • lines changed 2, 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/lib/variant.c
  • lines changed 7, 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/inc/asParse.h
  • lines changed 4, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/inc/common.mk
  • 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/lib/annoFormatTab.c
  • lines changed 1, context: html, text, full: html, text
    bugfix: if some word is NULL, print out empty string.
• src/lib/annoGrator.c
  • lines changed 1, context: html, text, full: html, text
    When freeing annoRows created by internal source, pass in internal source not self. (#6152)
• src/lib/annoRow.c
  • lines changed 1, context: html, text, full: html, text
    bugfix: forgot to null out *pList in a FreeList function.
• src/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    Removed outdated comment.
• src/lib/asParse.c
  • lines changed 12, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/utils/qa/weeklybld/summaryEmail.sh
  • lines changed 2, context: html, text, full: html, text
    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.