Commits for angie
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v282_base to v283_preview (2013-04-16 to 2013-04-23) v283
- Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 22, context: html, text, full: html, text
- src/hg/inc/annoGrateWigDb.h - lines changed 2, context: html, text, full: html, text
- src/hg/inc/annoStreamDb.h - lines changed 2, context: html, text, full: html, text
- src/hg/inc/annoStreamWig.h - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 50, context: html, text, full: html, text
- src/hg/lib/annoGrateWigDb.c - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoStreamDb.c - lines changed 4, context: html, text, full: html, text
- src/hg/lib/annoStreamWig.c - lines changed 13, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 79, context: html, text, full: html, text
- src/inc/annoAssembly.h - lines changed 24, context: html, text, full: html, text
- src/inc/annoFormatter.h - lines changed 19, context: html, text, full: html, text
- src/inc/annoGratorQuery.h - lines changed 19, context: html, text, full: html, text
- src/inc/annoStreamBigBed.h - lines changed 1, context: html, text, full: html, text
- src/inc/annoStreamBigWig.h - lines changed 1, context: html, text, full: html, text
- src/inc/annoStreamTab.h - lines changed 2, context: html, text, full: html, text
- src/inc/annoStreamVcf.h - lines changed 2, context: html, text, full: html, text
- src/inc/annoStreamer.h - lines changed 28, context: html, text, full: html, text
- src/lib/annoAssembly.c - lines changed 33, context: html, text, full: html, text
- src/lib/annoFormatTab.c - lines changed 22, context: html, text, full: html, text
- src/lib/annoFormatter.c - lines changed 13, context: html, text, full: html, text
- src/lib/annoGratorQuery.c - lines changed 81, context: html, text, full: html, text
- src/lib/annoStreamBigBed.c - lines changed 2, context: html, text, full: html, text
- src/lib/annoStreamBigWig.c - lines changed 2, context: html, text, full: html, text
- src/lib/annoStreamTab.c - lines changed 3, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 3, context: html, text, full: html, text
- src/lib/annoStreamer.c - lines changed 10, context: html, text, full: html, text
- Patching up one more mem leak for #6152.
- src/hg/inc/annoGratorGpVar.h - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 27, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 17, context: html, text, full: html, text
- Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- src/inc/annoStreamer.h - lines changed 12, context: html, text, full: html, text
- src/lib/annoFormatTab.c - lines changed 9, context: html, text, full: html, text
- src/lib/annoStreamer.c - lines changed 18, context: html, text, full: html, text
- Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/hg/lib/annoFormatVep.c - lines changed 6, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 3, context: html, text, full: html, text
- src/hg/lib/annoStreamDb.c - lines changed 6, context: html, text, full: html, text
- src/hg/lib/annoStreamWig.c - lines changed 7, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 1, context: html, text, full: html, text
- src/lib/annoFormatTab.c - lines changed 2, context: html, text, full: html, text
- src/lib/annoStreamBigBed.c - lines changed 3, context: html, text, full: html, text
- src/lib/annoStreamBigWig.c - lines changed 8, context: html, text, full: html, text
- src/lib/annoStreamTab.c - lines changed 1, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 5, context: html, text, full: html, text
- Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 44, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 17, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 5, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 7, context: html, text, full: html, text
- src/lib/annoFormatTab.c - lines changed 1, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text
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