CVS changes by file

branch to review (2009-10-27 to 2009-11-03) v219

• src/cdnaAli/cluster/makefile
  • 1.7 lines changed: 3, context: html, text, full: html, text
    allow overriding the location of libpng
• src/fuse/makefile
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Should have finished writing it first.
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Hooking udcFuse into top-level build
• src/fuse/udcFuse/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    First cut, mostly works but performance is not yet satisfactory.
• src/fuse/udcFuse/udcFuse.c
  • 1.1 lines changed: 390, context: html, text, full: html, text
    First cut, mostly works but performance is not yet satisfactory.
• src/hg/archaeStuff/data/Genome-info-meta
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fix seq size and gc for BED
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.38 lines changed: 1, context: html, text, full: html, text
    add code to rsync files to download server - lowelab
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.47 lines changed: 19, context: html, text, full: html, text
    add code to rsync files to download server - lowelab
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.4 lines changed: 130, context: html, text, full: html, text
    Fixed blastx percent length
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.20 lines changed: 1, context: html, text, full: html, text
    fix typo
• src/hg/encode/DAFs/HAIBChIPseq.daf
  • 1.1 lines changed: 38, context: html, text, full: html, text
    New DAF for Rami
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.21 lines changed: 1, context: html, text, full: html, text
    dereference symbolic links
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.51 lines changed: 12, context: html, text, full: html, text
    Added logic to take care "N/A", "N/D", and "" for text mode of Table View.
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3B
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Updated some labels per GSID's request.
• src/hg/hgCustom/hgCustom.c
  • 1.133 lines changed: 2, context: html, text, full: html, text
    Added setUdcCacheDir() as in hgTracks, hgc etc. Without it, files were being initialized in /tmp/udcCache not our locally configured /data/apache/trash/udcCache.
• src/hg/hgTables/makefile
  • 1.54 lines changed: 5, context: html, text, full: html, text
    Add install target to get all.joiner done properly on a make install
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.506 lines changed: 8, context: html, text, full: html, text
    DGV: Change the default filter to include-all instead of exclude-none -- positive logic is more intuitive. (Thx b0b)
• src/hg/hgTracks/bamTrack.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Gordon Robertson request: make gray lighter for unpaired ends.
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/bedTrack.c
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/encode.c
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/hgTracks.c
  • 1.1603 lines changed: 4, context: html, text, full: html, text
    Enabled trackDb setting "nextItemButton on" (actually the setting will work if it's set to "true" or "enabled" as well). This overrides user settings for a specific track when they don't have next-item button navigation turn on.
  • 1.1602 lines changed: 16, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/hgTracks.h
  • 1.188 lines changed: 5, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/simpleTracks.c
  • 1.109 lines changed: 2, context: html, text, full: html, text
    Removed "Sorry, no items found" error.
  • 1.108 lines changed: 20, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgTracks/wikiTrack.c
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/.
• src/hg/hgc/hgc.c
  • 1.1580 lines changed: 7, context: html, text, full: html, text
    Making mrna links in hgGene work in hg19.
• src/hg/js/hui.js
  • 1.42 lines changed: 4, context: html, text, full: html, text
    Fixed bug that left matCB indeterminate though no subtracks match state.
• src/hg/lib/bamFile.c
  • 1.12 lines changed: 71, context: html, text, full: html, text
    If udcFuse.mountPoint is set in hg.conf, translate BAM URLs into filenames underneath that mount point, which mirrors the local udc cacheDir's hierarchy. Open the URL for bam and the associated .bai index file using udc, to make sure that the translated filenames will exist.
• src/hg/lib/customFactory.c
  • 1.107 lines changed: 2, context: html, text, full: html, text
    Better error message in bamLoader.
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
  • 1.6 lines changed: 176, context: html, text, full: html, text
    Kayla noticed too many tables being eliminated and too few files being added.
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.2 lines changed: 177, context: html, text, full: html, text
    Keeping up with the flood
  • 1.1 lines changed: 376, context: html, text, full: html, text
    Initial checking of my clean up of varias issues
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.3 lines changed: 267, context: html, text, full: html, text
    Keeping up with the flood
• src/hg/makeDb/doc/hg19.txt
  • 1.54 lines changed: 153, context: html, text, full: html, text
    started building hgPal downloads
  • 1.53 lines changed: 242, context: html, text, full: html, text
    Done with phastCons and phyloP for 46-way conservation track
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Removing duplicate lines from knownToPfam.tab
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removing duplicate lines from knownToPfam.tab
• src/hg/makeDb/trackDb/README
  • 1.89 lines changed: 3, context: html, text, full: html, text
    Enabled trackDb setting "nextItemButton on" (actually the setting will work if it's set to "true" or "enabled" as well). This overrides user settings for a specific track when they don't have next-item button navigation turn on.
• src/hg/makeDb/trackDb/gorilla/gorGor2/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gorilla/gorGor2/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gorilla/gorGor2/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gorilla/gorGor2/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.638 lines changed: 31, context: html, text, full: html, text
    Added OTTER id search spec for gencode v3c and set gencode freeze to Oct 2009
  • 1.637 lines changed: 8, context: html, text, full: html, text
    add some V2's to the CSHL long RNA-seq K562 cytosol tables
  • 1.636 lines changed: 4, context: html, text, full: html, text
    Getting the url to use the OTT id which is now in the classes table turns out to be easy
  • 1.635 lines changed: 32, context: html, text, full: html, text
    Gencode v3c with new subtrack 2way consensus psuedogenes
  • 1.634 lines changed: 48, context: html, text, full: html, text
    Removed wgEncodeHudsonalphaChipSeqProv provisional composite as its entire contents have been superseded by wgEncodeHudsonalphaChipSeq
  • 1.633 lines changed: 162, context: html, text, full: html, text
    Cut down the Broad ChIP seq long labels to meet the max label length of 65 chars
  • 1.632 lines changed: 414, context: html, text, full: html, text
    Shortened the short track names for UwChIPSeq, to try to bring everything down within 16 chars
  • 1.631 lines changed: 48, context: html, text, full: html, text
    4 more tracks to haibChip and more work to distinguish PCR2x input
  • 1.630 lines changed: 66, context: html, text, full: html, text
    More attempts to straighten out 2 controls fro Gm12878 and K562 on haibChip
  • 1.629 lines changed: 1, context: html, text, full: html, text
    fix sortOrder
  • 1.628 lines changed: 74, context: html, text, full: html, text
    Changed GM12878Taf1 to V2 and made Input(PCR2x) visible for haibChip
  • 1.627 lines changed: 128, context: html, text, full: html, text
    Added labVersion=PCR2x to older GM12989 and K562 experiments for haibChip
  • 1.626 lines changed: 166, context: html, text, full: html, text
    new GIS RNA-seq data
  • 1.625 lines changed: 132, context: html, text, full: html, text
    Renamed some HudsonAlpha tables and cleaned up some metadata
  • 1.624 lines changed: 19, context: html, text, full: html, text
    Limited the number of tracks shown by detault for Broad
  • 1.623 lines changed: 70, context: html, text, full: html, text
    Straightened out GM12878 Taf1 and K562 Taf1 as per Flo's wishes
  • 1.622 lines changed: 2065, context: html, text, full: html, text
    More cleanup of HAIB TFBS
  • 1.621 lines changed: 651, context: html, text, full: html, text
    A lot of work on HudsonAlpha TFSB
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
  • 1.4 lines changed: 8, context: html, text, full: html, text
    add some Release Notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    add some text about the color display
  • 1.1 lines changed: 105, context: html, text, full: html, text
    new Hannon lab short RNA-seq description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.19 lines changed: 8, context: html, text, full: html, text
    Added explanitory note for PCR2x control
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.56 lines changed: 5, context: html, text, full: html, text
    Turning on the 46 way phyloP tracks
• src/hg/makeDb/trackDb/human/omimGene.html
  • 1.21 lines changed: 2, context: html, text, full: html, text
    capitalized Mendelian twice
  • 1.20 lines changed: 1, context: html, text, full: html, text
    changed bars to blocks in describing the BEDdisplay
  • 1.19 lines changed: 19, context: html, text, full: html, text
    changed the way the coloring was described so it matches other places where break it out into a list and highlight the meaning in the actual color. had to pull the link to OMIM out of the Morbid Map text to get it be red
• src/hg/makeDb/trackDb/human/wgEncodeGencode.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    This is Gencode's October 2009 freeze
  • 1.4 lines changed: 31, context: html, text, full: html, text
    New coloring scheme and V3c release
• src/hg/makeDb/trackDb/makefile
  • 1.276 lines changed: 2, context: html, text, full: html, text
    enable gorilla gorGor2 and wallaby macEug1
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.69 lines changed: 1, context: html, text, full: html, text
    correcting matrix for rat and mouse chains
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.42 lines changed: 1, context: html, text, full: html, text
    correcting matrix for rat and mouse chains
• src/hg/pslMap/tests/expected/gapBoth.psl
  • 1.3 lines changed: 1, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslMap/tests/expected/kgProt.psl
  • 1.4 lines changed: 5, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslMap/tests/expected/mrnaMapOver.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslMap/tests/expected/mrnaMrnaMap.psl
  • 1.2 lines changed: 7, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslMap/tests/expected/mrnaMrnaXMap.psl
  • 1.2 lines changed: 17, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslMap/tests/expected/negQChain.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/hg/pslStats/pslStats.c
  • 1.9 lines changed: 6, context: html, text, full: html, text
    fixed bug computing mean query size
• src/hg/pslStats/tests/expected/cdna2cdnaOverallTest.stats
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed bug computing mean query size
• src/hg/pslStats/tests/expected/untransOverallTest.stats
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixed bug computing mean query size
• src/hg/pslStats/tests/expected/untransOverallUnalnTest.stats
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixed bug computing mean query size
• src/hg/pslStats/tests/makefile
  • 1.6 lines changed: 11, context: html, text, full: html, text
    fixed bug computing mean query size
• src/hg/qacAddGapIdx/qacAddGapIdx.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixup crash in mafAddQRows and off-by-one error in qacAddGapIdx
• src/hg/ratStuff/mafAddQRows/mafAddQRows.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixup crash in mafAddQRows and off-by-one error in qacAddQRows
• src/hg/trfBig/trfBig.c
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Allow maybeSystem() to only warn on system errors. trf always exits with an error
• src/hg/utils/automation/Encode.pm
  • 1.49 lines changed: 2, context: html, text, full: html, text
    Sep09 freeze is done!
• src/inc/common.h
  • 1.157 lines changed: 4, context: html, text, full: html, text
    Allow maybeSystem() to only warn on system errors. trf always exits with an error
• src/inc/common.mk
  • 1.73 lines changed: 8, context: html, text, full: html, text
    allow overriding the location of libpng
• src/inc/udc.h
  • 1.11 lines changed: 19, context: html, text, full: html, text
    Support for udcFuse and apps that will read files from it: plug minor memory leaks, use errAbort not assert, make udcFileMayOpen public, make udcParseUrl public so apps can determine path to file in udcFuse, add udcPathToUrl and udcSizeFromCache so that udcFuse can report the correct total file size.
• src/lib/common.c
  • 1.135 lines changed: 12, context: html, text, full: html, text
    Allow maybeSystem() to only warn on system errors. trf always exits with an error
• src/lib/errCatch.c
  • 1.4 lines changed: 25, context: html, text, full: html, text
    Make errCatch POSIX thread (pthread) safe: instead of a single global stack, use per-thread stacks hashed by thread ID.
• src/lib/pngwrite.c
  • 1.3 lines changed: 9, context: html, text, full: html, text
    png portability changes for ubuntu and gcc 4.3.3
• src/lib/pslTransMap.c
  • 1.8 lines changed: 14, context: html, text, full: html, text
    set t/q insert stats in mapped psl
• src/lib/udc.c
  • 1.19 lines changed: 1, context: html, text, full: html, text
    initialize some variables
  • 1.18 lines changed: 102, context: html, text, full: html, text
    Support for udcFuse and apps that will read files from it: plug minor memory leaks, use errAbort not assert, make udcFileMayOpen public, make udcParseUrl public so apps can determine path to file in udcFuse, add udcPathToUrl and udcSizeFromCache so that udcFuse can report the correct total file size.
• src/makefile
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Hooking udcFuse into top-level build
• src/product/README.building.source
  • 1.17 lines changed: 9, context: html, text, full: html, text
    Take care of gif_out_line error out warning situation with newer gcc versions
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.87 lines changed: 2, context: html, text, full: html, text
    v219 preview
  • 1.86 lines changed: 3, context: html, text, full: html, text
    Correct dates for v218 final
• src/utils/qa/weeklybld/doNewBranch.csh
  • 1.32 lines changed: 2, context: html, text, full: html, text
    remove logs before overwriting them to maintain proper ownership

• lines changed: 7011
• files changed: 75