CVS changes by file

branch to review (2009-08-18 to 2009-08-25) v213

• src/ameme/ameme.c
  • 1.15 lines changed: 1, 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/amemeFloat.c
  • 1.3 lines changed: 1, 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/fixpAmeme.c
  • 1.2 lines changed: 1, 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/hg/das/das.c
  • 1.45 lines changed: 14, context: html, text, full: html, text
    DAS wants 0 for unspecified strand
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.126 lines changed: 28, context: html, text, full: html, text
    Added two for Duke/UTA
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    makeg
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Sort of terms should ignore case
• src/hg/encode/validateFiles/validateFiles.c
  • 1.26 lines changed: 15, context: html, text, full: html, text
    add matchFirst argument
• src/hg/gsid/pbGsid/pbGsid.c
  • 1.11 lines changed: 1, 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/hg/hgCustom/hgCustom.c
  • 1.131 lines changed: 13, 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/hgGene/altSplice.c
  • 1.13 lines changed: 1, 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/hg/hgGeneRing/hgGeneRing.c
  • 1.8 lines changed: 1, 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/hg/hgGenome/mainPage.c
  • 1.27 lines changed: 1, 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/hg/hgTables/correlatePlot.c
  • 1.16 lines changed: 5, 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/hg/hgTracks/bamTrack.c
  • 1.7 lines changed: 3, 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.
  • 1.6 lines changed: 26, context: html, text, full: html, text
    Removed the hardcoded BAM_MAX_ZOOM -- using trackDb setting maxWindowToDraw now.
• src/hg/hgTracks/hgTracks.c
  • 1.1594 lines changed: 23, 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).
  • 1.1593 lines changed: 1, context: html, text, full: html, text
    Use trackDbSettingClosestToHome (not just trackDbSetting) in getMaxWindowToDraw, so subtracks will display the correct size threshold.
  • 1.1592 lines changed: 11, context: html, text, full: html, text
    Handle composite tracks in maxWindowSizeExceeded. (Individual subtracks of a composite track still not supported.)
  • 1.1591 lines changed: 2, 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.
  • 1.1590 lines changed: 5, context: html, text, full: html, text
    When winEnd-winStart > trackDb setting maxWindowToDraw, inhibit the toggle-link over the message because toggling vis doesn't affect the image.
• src/hg/hgTracks/mafTrack.h
  • 1.8 lines changed: 1, context: html, text, full: html, text
    change summary view to start after 50K rather than 1mb.
• src/hg/hgTracks/oneTrack.c
  • 1.3 lines changed: 1, 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/hg/hgTracks/wigMafTrack.c
  • 1.144 lines changed: 3, context: html, text, full: html, text
    Avoid thousands of describe tables on wigMaf summary tables on large chrom views
• src/hg/hgc/bamClick.c
  • 1.7 lines changed: 38, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.6 lines changed: 26, context: html, text, full: html, text
    Added search for paired ends outside window, +- trackDb setting pairSearchRange.
  • 1.5 lines changed: 47, context: html, text, full: html, text
    Added pairing for easy cases (both ends in hgTracks window).
  • 1.4 lines changed: 7, 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.
  • 1.3 lines changed: 15, context: html, text, full: html, text
    Use the new bamToFfAli and the old ffShAliPart to display aligned bases.
• src/hg/hgc/hgc.c
  • 1.1566 lines changed: 1, 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/hg/inc/bamFile.h
  • 1.7 lines changed: 14, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Added bamToFfAli (for using fuzzyShow display).
• src/hg/inc/cart.h
  • 1.46 lines changed: 15, context: html, text, full: html, text
    fixed bogus return of value that compiler didn't detected; correct non-kentian indentation
• src/hg/inc/hvGfx.h
  • 1.5 lines changed: 11, 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/hg/instinct/hgHeatmap/mainPage.c
  • 1.71 lines changed: 3, 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/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.70 lines changed: 12, 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.
  • 1.69 lines changed: 27, context: html, text, full: html, text
    fix bug find to draw overlaping probes not just within probes when drawing heatmap, summary view
• src/hg/instinct/hgHeatmap2/hgAnnotations.c
  • 1.11 lines changed: 4, 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/hg/instinct/hgHeatmap2/hgCircleMaps.c
  • 1.12 lines changed: 1, 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/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.77 lines changed: 9, context: html, text, full: html, text
    add patient id to tooltip
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.49 lines changed: 2, context: html, text, full: html, text
    add patient id to tooltip
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb.instinct.ra
  • 1.1 lines changed: 1023, context: html, text, full: html, text
    add columnDb.instinct.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb.ra
  • 1.6 lines changed: 1019, context: html, text, full: html, text
    remove columnDb.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_grayCellLines.ra
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Added neve classification type to columndb
  • 1.1 lines changed: 787, context: html, text, full: html, text
    Added new gray cell line clinical data columndb
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenGBMBio.ra
  • 1.3 lines changed: 851, context: html, text, full: html, text
    Updated clinical features
  • 1.2 lines changed: 178, context: html, text, full: html, text
    clean up GBM columnDB ra file
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.2 lines changed: 27, context: html, text, full: html, text
    clean up intgenMinOVBio.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.9 lines changed: 14, context: html, text, full: html, text
    fix bug/typo in columnDB_intgenOVBio.ra
  • 1.8 lines changed: 297, context: html, text, full: html, text
    New drug features
  • 1.7 lines changed: 138, context: html, text, full: html, text
    modify ovarian columnDB ra file
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_lajos.ra
  • 1.4 lines changed: 10, context: html, text, full: html, text
    modify columnDB_lajos.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    add downsample table for segmented CGH data
  • 1.15 lines changed: 23, context: html, text, full: html, text
    add Broad Affy U133A Tumor vs. Normal set
  • 1.14 lines changed: 558, context: html, text, full: html, text
    clean up TCGA dataset.ra file
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.instinct.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    add columnDb.instinct.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.14 lines changed: 70, context: html, text, full: html, text
    Added gray data to dataset.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.73 lines changed: 2, context: html, text, full: html, text
    add patient id to tooltip
• src/hg/instinct/hgHeatmap2/hgToolTip.c
  • 1.9 lines changed: 26, context: html, text, full: html, text
    add patient id to tooltip
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.61 lines changed: 19, context: html, text, full: html, text
    fix bug find all overlaping probes not just within probes to draw heatmap, summary view
• src/hg/instinct/lib/sortFeatures.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    updated max NULL val
• src/hg/js/hgTracks.js
  • 1.36 lines changed: 16, context: html, text, full: html, text
    move map manipulation code into contextMenu block
  • 1.35 lines changed: 460, context: html, text, full: html, text
    add contextMenu support (currently dead code if jquery.contextmenu.js hasn't been loaded by hgTracks.c)
  • 1.34 lines changed: 1, context: html, text, full: html, text
    Fixed bug in my jquery code that threw exception
• src/hg/js/hui.js
  • 1.30 lines changed: 25, context: html, text, full: html, text
    Now composites are automatically made vis=full only when they are vis=hide and a multi-view is made visible.
• src/hg/js/utils.js
  • 1.24 lines changed: 28, context: html, text, full: html, text
    add Rectangle class support
  • 1.23 lines changed: 5, context: html, text, full: html, text
    Toggling metadata didn't work on MSIE. Converting contents to comment was the problem.
• src/hg/lib/bamFile.c
  • 1.6 lines changed: 89, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.5 lines changed: 15, context: html, text, full: html, text
    Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
  • 1.4 lines changed: 49, context: html, text, full: html, text
    Added bamToFfAli (for using fuzzyShow display).
• src/hg/lib/bioCycPathways.sql
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Number of names has increased to 70
• src/hg/lib/customFactory.c
  • 1.102 lines changed: 14, context: html, text, full: html, text
    fixing htmlUrl to handle net.c errAbort using errCatch
  • 1.101 lines changed: 3, context: html, text, full: html, text
    better err handling for URL redirect
• src/hg/lib/hdb.c
  • 1.410 lines changed: 17, context: html, text, full: html, text
    avoid N^2 list scan in hasTrackDbAlready by using a loaded hash
• src/hg/lib/hui.c
  • 1.232 lines changed: 1, context: html, text, full: html, text
    Missing 'else' caused Gencode level filter to duplicate entries.
  • 1.231 lines changed: 4, context: html, text, full: html, text
    cgi encode controlled vocabulary terms
• src/hg/lib/hvGfx.c
  • 1.5 lines changed: 4, 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/hg/lib/jksql.c
  • 1.132 lines changed: 6, context: html, text, full: html, text
    support showTableCache config in sqlListTables
  • 1.131 lines changed: 25, context: html, text, full: html, text
    use tableList table (if available) instead of show tables in sqlListTables
• src/hg/lib/wiggleUtils.c
  • 1.54 lines changed: 1, context: html, text, full: html, text
    add comment
  • 1.53 lines changed: 23, context: html, text, full: html, text
    take out slow query to find all spans and replace with code to look for first span
  • 1.52 lines changed: 2, context: html, text, full: html, text
    take out "first" change cuz I stupid
  • 1.51 lines changed: 4, context: html, text, full: html, text
    if no spanList is specified in trackDb, build list by choosing first span in the table rather than trying to find all the spans. This is the same behavior as adding "spanList first" to the trackDb for over 500 tables.
• src/hg/makeDb/doc/hg18.txt
  • 1.378 lines changed: 41, context: html, text, full: html, text
    Documented adding new code to handle Vega Genes track and loaded a vegaGtp table.
  • 1.377 lines changed: 29, context: html, text, full: html, text
    Updated snp130 with corrected functional annotations from dbSNP.
• src/hg/makeDb/doc/mm9.txt
  • 1.106 lines changed: 36, context: html, text, full: html, text
    Documented adding new code to handle Vega Genes track and loaded a vegaGtp table.
  • 1.105 lines changed: 86, context: html, text, full: html, text
    Updates for MGI: RepTranscript, Allele, Phenotype, and IKMC.
• src/hg/makeDb/doc/panTro2.txt
  • 1.16 lines changed: 25, context: html, text, full: html, text
    re-annotate/reload unrelease maf to fix bug
• src/hg/makeDb/doc/uniProt/sp090821.txt
  • 1.1 lines changed: 50, context: html, text, full: html, text
    Creating sp090821 database.
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.116 lines changed: 2, context: html, text, full: html, text
    added to-do
  • 1.115 lines changed: 3, context: html, text, full: html, text
    fix problem missing syntentic clones in mgc
  • 1.114 lines changed: 2, context: html, text, full: html, text
    added to-do item
• src/hg/makeDb/genbank/etc/build-genbank
  • 1.8 lines changed: 3, context: html, text, full: html, text
    removed ulimits
• src/hg/makeDb/genbank/etc/build-mgc
  • 1.3 lines changed: 3, context: html, text, full: html, text
    removed ulimits
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • 1.24 lines changed: 19, context: html, text, full: html, text
    fix problem missing syntentic clones in mgc
• src/hg/makeDb/genbank/src/process/keyFields.doc
  • 1.11 lines changed: 2, context: html, text, full: html, text
    fix problem missing syntentic clones in mgc
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.85 lines changed: 1, context: html, text, full: html, text
    Fixed caps issue on one label
  • 1.84 lines changed: 12, context: html, text, full: html, text
    Added gray Exon data
  • 1.83 lines changed: 11, context: html, text, full: html, text
    Fixed incorrectly named cell lines, added most recent list of gray snp data
  • 1.82 lines changed: 4, context: html, text, full: html, text
    update microArray ra file for Broad Affy U133A Tumor vs. Normal
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.413 lines changed: 1, context: html, text, full: html, text
    removed maxWindowToDraw 500000 from snpArray for now
  • 1.412 lines changed: 1, context: html, text, full: html, text
    Added maxWindowToDraw 500000 to the snpArray track
  • 1.411 lines changed: 3, context: html, text, full: html, text
    added spanList to uwNunOcc tracks
  • 1.410 lines changed: 1, 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.wgEncode.ra
  • 1.497 lines changed: 2, context: html, text, full: html, text
    make min and max on HA CNV track integers
  • 1.496 lines changed: 1, context: html, text, full: html, text
    add noScoreFilter to CNV tracks
  • 1.495 lines changed: 2, context: html, text, full: html, text
    set minLimit and maxLimit
  • 1.494 lines changed: 1, context: html, text, full: html, text
    change back HA CNV to bed 9 to get back colors and labels (D'oh!)
  • 1.493 lines changed: 1, context: html, text, full: html, text
    change HudsonalphaCnv top level to bed3 to disable score filtering
  • 1.492 lines changed: 33, context: html, text, full: html, text
    testing some things
  • 1.491 lines changed: 1, context: html, text, full: html, text
    Fixed typo in the longLabel
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    a little text that Katrina wanted
  • 1.9 lines changed: 6, context: html, text, full: html, text
    added link to cell line information and cell culture procedures
  • 1.8 lines changed: 15, context: html, text, full: html, text
    some fix-ups requested by Katrina
  • 1.7 lines changed: 30, context: html, text, full: html, text
    Added Display Conventions and Configuration section
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Made minor edits and fixed a reference format
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Made minor edits and fixed a reference format
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Made minor edits and fixed a reference format
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • 1.5 lines changed: 91, context: html, text, full: html, text
    Updated and revised out of date description page
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.46 lines changed: 2, context: html, text, full: html, text
    grouped fish in proper near-neighbor order
• src/hg/makeDb/trackDb/mouse/jaxAllele.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Added link to file referenced in Methods.
• src/hg/makeDb/trackDb/mouse/jaxPhenotype.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Added link to file referenced in Methods.
• src/hg/makeDb/trackDb/oreganno.html
  • 1.15 lines changed: 4, context: html, text, full: html, text
    reinstated reference to ORegAnno links since the site and links are now working
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.526 lines changed: 1, context: html, text, full: html, text
    don't display repeat masker when > 10000000 bases window
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/phyloGif/phyloGif.c
  • 1.22 lines changed: 1, 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/hg/protein/lib/doTracks.c
  • 1.22 lines changed: 1, 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/hg/protein/pbGlobal/pbGlobal.c
  • 1.47 lines changed: 1, 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/hg/protein/pbTracks/pbTracks.c
  • 1.59 lines changed: 1, 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/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Coping with addition of sp| at start of fasta protein name in varSplice section of SwissProt.
• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    remove commented code
  • 1.25 lines changed: 1, context: html, text, full: html, text
    bug in filtering alignments
  • 1.24 lines changed: 3, context: html, text, full: html, text
    fix counter
  • 1.23 lines changed: 46, context: html, text, full: html, text
    fix bug with non pass thru mode. alignments are now removed if there are multiple hits that are less than minDiff cutoff. removed commented code and tweaked logging messages.
• src/hg/stsMarkers/fixPrimersQueryGaps.pl
  • 1.2 lines changed: 30, context: html, text, full: html, text
    Cleaned code and working better May 6th 2009
• src/hg/tutorial/cgiPicture/cgiPicture.c
  • 1.4 lines changed: 1, 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/hg/txCds/makefile
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add txCdsEvFromBed to the build
• src/hg/updateStsInfo/updateStsInfo.c
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Take care of faAcc strings being (null)
• src/hg/wikiPlot/wikiPlot.c
  • 1.8 lines changed: 1, 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/inc/fuzzyFind.h
  • 1.20 lines changed: 8, context: html, text, full: html, text
    Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
• src/inc/memgfx.h
  • 1.26 lines changed: 14, 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/inc/seqOut.h
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Added bafFlushLineNoHr for more compact side-by-side alignment display.
• src/inc/vGfx.h
  • 1.15 lines changed: 7, 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/jkOwnLib/fuzzyFind.c
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Initializing a field to zero which otherwise would be garbage.
• src/lib/fuzzyShow.c
  • 1.25 lines changed: 150, context: html, text, full: html, text
    Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
• src/lib/gifLabel.c
  • 1.10 lines changed: 1, 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/lib/gifwrite.c
  • 1.8 lines changed: 29, 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/lib/htmshell.c
  • 1.63 lines changed: 44, context: html, text, full: html, text
    Fixed warnBox to go to prev page when page halted by errorAbort. Restored multiple message suppoprt. Still supports selectAll not selecting empty warnBox.
• src/lib/net.c
  • 1.71 lines changed: 3, context: html, text, full: html, text
    add https support for redirect
• src/lib/pngwrite.c
  • 1.2 lines changed: 10, 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/seqOut.c
  • 1.28 lines changed: 10, context: html, text, full: html, text
    Added bafFlushLineNoHr for more compact side-by-side alignment display.
• src/lib/vGif.c
  • 1.5 lines changed: 4, 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/lib/vPng.c
  • 1.2 lines changed: 5, 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.
• src/test/test.c
  • 1.4 lines changed: 1, 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/tracks/tracks.c
  • 1.9 lines changed: 1, 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/utils/bedToBigBed/bedToBigBed.c
  • 1.8 lines changed: 521, context: html, text, full: html, text
    Changing to a multi-pass design to conserve memory.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.74 lines changed: 1, context: html, text, full: html, text
    moving the bogus preview to a real preview
  • 1.73 lines changed: 3, context: html, text, full: html, text
    v214 preview
• src/weblet/counter/counter.c
  • 1.5 lines changed: 1, 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.

• lines changed: 7718
• files changed: 104