Commits for angie
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v279_base to v280_preview (2013-02-12 to 2013-02-19) v280
- Added setAutoSqlObject method to annoStreamer, to update both asObj andinternal state derived from it. (for #6152)
- src/lib/annoStreamer.c - lines changed 16, context: html, text, full: html, text
- annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
- Added enum annoGratorOverlap and setOverlapRule method to specify
how to treat overlap between primary and internal rows: ignore it,
require it, or forbid it, via integrate method's retRJFilterFailed.
- Added setAutoSqlObject method to update both the outward-facing
(streamer interface) asObj and internal state derived from it.
annoGratorGpVar:
- Added cdsOnly property to keep only variants that change CDS
(via retRJFilterFailed).
- The language of aggvGenRows implies that multiple effect rows may
arise from one {variant x gene}. In case that happens, use slCat
instead of slAddHead to keep all effect rows.
- Added slReverse to make sure output rows are ordered by position.
That required shuffling some lines in an expected-results file.
- Renamed some variables because there are now 3 types of "self":
streamer, grator, gpVar.
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 4, context: html, text, full: html, text
- src/hg/inc/annoGratorGpVar.h - lines changed 4, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 66, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 3, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 47, context: html, text, full: html, text
- Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
- src/hg/altSplice/altSplice/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/hgKnownGeneList/makefile - lines changed 1, context: html, text, full: html, text
- Track #9401 (DGV): Fixed a couple issues found by Brian L. (shortLabel, termRegex)
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 3, context: html, text, full: html, text
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