Commits for angie
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v289_preview2 to v289_base (2013-09-02 to 2013-09-09) v289
- hgVai can now handle assembly hubs, but if they have no genePred tracks, itcan't really do anything useful so it just suggests that the user choose a different assembly.
fixes #11306
- snp135 got some new rows when it was rebuilt (#11544), so we get some new rows of output.
- src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt - lines changed 3, context: html, text, full: html, text
- In order to detect the overlap of two 0-length (insertion) items, we needto expand at least one of their ranges to the two surrounding bases.
- VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
- src/hg/lib/annoFormatVep.c - lines changed 18, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 3, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 11, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text
- Fixing Mac OS X portability issue.
- src/hg/hgTracks/snakeTrack.c - lines changed 2, context: html, text, full: html, text
- Fixing compiler warning that appears only when compiling with -O.
- src/hg/hgTracks/snakeTrack.c - lines changed 1, context: html, text, full: html, text
- Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
- src/hg/hgGenome/mainPage.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/compositeTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 1, context: html, text, full: html, text
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