angie: changes by commit
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branch to review (2009-08-18 to 2009-08-25) v213
- When winEnd-winStart > trackDb setting maxWindowToDraw, inhibit the toggle-link over the message because toggling vis doesn't affect the image.
- src/hg/hgTracks/hgTracks.c 1.1590 - lines changed: 5, context: html, text, full: html, text
- Updated snp130 with corrected functional annotations from dbSNP.
- src/hg/makeDb/doc/hg18.txt 1.377 - lines changed: 29, context: html, text, full: html, text
- Added maxWindowToDraw setting to bamNA12878 so we don't have to rely on hardcoded max in bamTrack.c.
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.410 - lines changed: 1, context: html, text, full: html, text
- Removed the hardcoded BAM_MAX_ZOOM -- using trackDb setting maxWindowToDraw now.
- src/hg/hgTracks/bamTrack.c 1.6 - lines changed: 26, context: html, text, full: html, text
- Added errCatch around customTracksParseCartDetailed (similar to that around customTrackUpdateFromConfig) because bad URL in doc input was causing abort.
- src/hg/hgCustom/hgCustom.c 1.131 - lines changed: 13, context: html, text, full: html, text
- Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
- src/ameme/ameme.c 1.15 - lines changed: 1, context: html, text, full: html, text
- src/ameme/amemeFloat.c 1.3 - lines changed: 1, context: html, text, full: html, text
- src/ameme/fixpAmeme.c 1.2 - lines changed: 1, context: html, text, full: html, text
- src/hg/gsid/pbGsid/pbGsid.c 1.11 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgGene/altSplice.c 1.13 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgGeneRing/hgGeneRing.c 1.8 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgGenome/mainPage.c 1.27 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgTables/correlatePlot.c 1.16 - lines changed: 5, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c 1.1591 - lines changed: 2, context: html, text, full: html, text
- src/hg/hgTracks/oneTrack.c 1.3 - lines changed: 1, context: html, text, full: html, text
- src/hg/hgc/hgc.c 1.1566 - lines changed: 1, context: html, text, full: html, text
- src/hg/inc/hvGfx.h 1.5 - lines changed: 11, context: html, text, full: html, text
- src/hg/instinct/hgHeatmap/mainPage.c 1.71 - lines changed: 3, context: html, text, full: html, text
- src/hg/instinct/hgHeatmap2/drawingCode.c 1.70 - lines changed: 12, context: html, text, full: html, text
- src/hg/instinct/hgHeatmap2/hgAnnotations.c 1.11 - lines changed: 4, context: html, text, full: html, text
- src/hg/instinct/hgHeatmap2/hgCircleMaps.c 1.12 - lines changed: 1, context: html, text, full: html, text
- src/hg/lib/hvGfx.c 1.5 - lines changed: 4, context: html, text, full: html, text
- src/hg/phyloGif/phyloGif.c 1.22 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/lib/doTracks.c 1.22 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/pbGlobal/pbGlobal.c 1.47 - lines changed: 1, context: html, text, full: html, text
- src/hg/protein/pbTracks/pbTracks.c 1.59 - lines changed: 1, context: html, text, full: html, text
- src/hg/tutorial/cgiPicture/cgiPicture.c 1.4 - lines changed: 1, context: html, text, full: html, text
- src/hg/wikiPlot/wikiPlot.c 1.8 - lines changed: 1, context: html, text, full: html, text
- src/inc/memgfx.h 1.26 - lines changed: 14, context: html, text, full: html, text
- src/inc/vGfx.h 1.15 - lines changed: 7, context: html, text, full: html, text
- src/lib/gifLabel.c 1.10 - lines changed: 1, context: html, text, full: html, text
- src/lib/gifwrite.c 1.8 - lines changed: 29, context: html, text, full: html, text
- src/lib/vGif.c 1.5 - lines changed: 4, context: html, text, full: html, text
- src/test/test.c 1.4 - lines changed: 1, context: html, text, full: html, text
- src/tracks/tracks.c 1.9 - lines changed: 1, context: html, text, full: html, text
- src/weblet/counter/counter.c 1.5 - lines changed: 1, context: html, text, full: html, text
- Handle composite tracks in maxWindowSizeExceeded. (Individual subtracks of a composite track still not supported.)
- src/hg/hgTracks/hgTracks.c 1.1592 - lines changed: 11, context: html, text, full: html, text
- Use trackDbSettingClosestToHome (not just trackDbSetting) in getMaxWindowToDraw, so subtracks will display the correct size threshold.
- src/hg/hgTracks/hgTracks.c 1.1593 - lines changed: 1, context: html, text, full: html, text
- Used more civilized language in comment & errAbort per Larry's code review feedback. Also corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency.
- src/lib/pngwrite.c 1.2 - lines changed: 10, context: html, text, full: html, text
- Corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency.
- Added link to file referenced in Methods.
- src/hg/makeDb/trackDb/mouse/jaxAllele.html 1.3 - lines changed: 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/jaxPhenotype.html 1.4 - lines changed: 3, context: html, text, full: html, text
- Updates for MGI: RepTranscript, Allele, Phenotype, and IKMC.
- src/hg/makeDb/doc/mm9.txt 1.105 - lines changed: 86, context: html, text, full: html, text
- Added bamToFfAli (for using fuzzyShow display).
- src/hg/inc/bamFile.h 1.5 - lines changed: 3, context: html, text, full: html, text
- src/hg/lib/bamFile.c 1.4 - lines changed: 49, context: html, text, full: html, text
- Use the new bamToFfAli and the old ffShAliPart to display aligned bases.
- src/hg/hgc/bamClick.c 1.3 - lines changed: 15, context: html, text, full: html, text
- Added bafFlushLineNoHr for more compact side-by-side alignment display.
- Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
- src/inc/fuzzyFind.h 1.20 - lines changed: 8, context: html, text, full: html, text
- src/lib/fuzzyShow.c 1.25 - lines changed: 150, context: html, text, full: html, text
- Use the new ffShowSideBySide to display just the side-by-side read alignments, instead of ffShAliPart which expects to fill a page.
- src/hg/hgc/bamClick.c 1.4 - lines changed: 7, context: html, text, full: html, text
- Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
- src/hg/inc/bamFile.h 1.6 - lines changed: 3, context: html, text, full: html, text
- src/hg/lib/bamFile.c 1.5 - lines changed: 15, context: html, text, full: html, text
- Added pairing for easy cases (both ends in hgTracks window).
- src/hg/hgc/bamClick.c 1.5 - lines changed: 47, context: html, text, full: html, text
- Added search for paired ends outside window, +- trackDb setting pairSearchRange.
- src/hg/hgc/bamClick.c 1.6 - lines changed: 26, context: html, text, full: html, text
- Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
- src/hg/hgc/bamClick.c 1.7 - lines changed: 38, context: html, text, full: html, text
- src/hg/inc/bamFile.h 1.7 - lines changed: 14, context: html, text, full: html, text
- src/hg/lib/bamFile.c 1.6 - lines changed: 89, context: html, text, full: html, text
- Fixed maxWindowToDraw-handling to support the setting at both composite track and subtrack level. Unfortunately, view-level does not yet work because limitedVisFromComposite overrides the dense limitedVis, so if view default vis is pack then the message is not displayed (clipped, 0 items = 0 height).
- src/hg/hgTracks/hgTracks.c 1.1594 - lines changed: 23, context: html, text, full: html, text
- Ignore strand -- seems to always be + and BAM inherently adjusts sequence and CIGAR to the positive strand when the alignment was -. Probably should test for inversion cases and make those appear minus strand.
- src/hg/hgTracks/bamTrack.c 1.7 - lines changed: 3, context: html, text, full: html, text
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