CVS changes by file

branch to review (2009-05-26 to 2009-06-02) v207

• java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java
  • 1.13 lines changed: 4, context: html, text, full: html, text
    disable JavaScript on the rest of the pages
• java/src/edu/ucsc/genome/qa/lib/HgTracks.java
  • 1.17 lines changed: 9, context: html, text, full: html, text
    disable JavaScript on the rest of the pages
• src/hg/archaeStuff/data/Genome-info-meta
  • 1.6 lines changed: 9, context: html, text, full: html, text
    add multiz genomes for monaGeys and cistSpri
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fix site number of cistSpri
  • 1.4 lines changed: 84, context: html, text, full: html, text
    add YNP sites 3, 4, 19
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.33 lines changed: 1, context: html, text, full: html, text
    fix bug in calculating startpos of scaffolds
  • 1.32 lines changed: 29, context: html, text, full: html, text
    fix problem when parsing YNP assemblies
  • 1.31 lines changed: 14, context: html, text, full: html, text
    change joinassembly to load YNP sites 3,4,19
• src/hg/encode/DAFs/AffyRnaChip.daf
  • 1.5 lines changed: 2, context: html, text, full: html, text
    shortened view names
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.65 lines changed: 16, context: html, text, full: html, text
    Load should now make the RawSignals files but put them in 'raw' subdir. Fixed some typos.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.102 lines changed: 1, context: html, text, full: html, text
    One protocol had a broken link
  • 1.101 lines changed: 11, context: html, text, full: html, text
    Added some cell line protocols which had not been checked in before
  • 1.100 lines changed: 189, context: html, text, full: html, text
    Approved cell lines for Myers: BG02ES,H9ES, HAL, HFL11W and HFL24W
• src/hg/hgTables/joining.c
  • 1.55 lines changed: 1, context: html, text, full: html, text
    no, we do not, the type of a track is its type no need to consult parent
• src/hg/hgTables/wiggle.c
  • 1.74 lines changed: 1, context: html, text, full: html, text
    no, we do not, the type of a track is its type no need to consult parent
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.491 lines changed: 3, context: html, text, full: html, text
    changed to ChIP-chip to match elsewhere
• src/hg/hgTracks/bedTrack.c
  • 1.13 lines changed: 33, context: html, text, full: html, text
    make colorByStrand work for ordinary beds (item is a bed) and for sequences where basecoloring is done (item is a linkedFeature)
  • 1.12 lines changed: 4, context: html, text, full: html, text
    make colorByStrand independent of baseColor
• src/hg/hgTracks/cds.c
  • 1.99 lines changed: 8, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.98 lines changed: 12, context: html, text, full: html, text
    choose a contrasting color for tick marks when drawgin differnt bases
  • 1.97 lines changed: 1, context: html, text, full: html, text
    Fixing recently introduced bug -- missing left side & assignment.
• src/hg/hgTracks/config.c
  • 1.79 lines changed: 2, context: html, text, full: html, text
    Show database
• src/hg/hgTracks/hgTracks.c
  • 1.1568 lines changed: 2, context: html, text, full: html, text
    added assembly name to header
  • 1.1567 lines changed: 13, context: html, text, full: html, text
    Do not allow ruler chrom name to spill over into buttons on left, truncate chrom name until it fits properly
• src/hg/hgTracks/simpleTracks.c
  • 1.82 lines changed: 18, context: html, text, full: html, text
    added cache to avoid repeated databases queries for organism name for xeno items, 4.28x speedup
• src/hg/hgc/bigBedClick.c
  • 1.5 lines changed: 13, context: html, text, full: html, text
    show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign. This is not very nice way to deal with it, asking Jim for other suggestion.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    dont print the full record if all the fields are already nicely formatted above
• src/hg/hgc/hgc.c
  • 1.1547 lines changed: 4, context: html, text, full: html, text
    show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign
• src/hg/hgc/regMotif.c
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Added score to the transRegCode hgc
• src/hg/instinct/bioInt2/bioController.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    forced order by id in analyses
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.22 lines changed: 13, context: html, text, full: html, text
    fixed bug
  • 1.21 lines changed: 4, context: html, text, full: html, text
    fixed factor graph bug
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.instinct.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    updated probe table for new affy dataset
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.72 lines changed: 1, context: html, text, full: html, text
    Added link to stats help page
  • 1.71 lines changed: 15, context: html, text, full: html, text
    update the text around the slider while it's changing
• src/hg/lib/hui.c
  • 1.207 lines changed: 25, context: html, text, full: html, text
    Minor changes to UI links. Ensure two cfg boxes are not opened at the same time
  • 1.206 lines changed: 47, context: html, text, full: html, text
    Fixup chainCfgUi to honor a normScore option from the trackDb composite bucket
  • 1.205 lines changed: 26, context: html, text, full: html, text
    Support for composite level controls to update view and subtrack level. Support for blocking view level controls. Fix for single dimension matrix.
• src/hg/makeDb/doc/aplCal1.txt
  • 1.5 lines changed: 99, context: html, text, full: html, text
    aplCal1 sea hare progress: genbank blat downloads
  • 1.4 lines changed: 133, context: html, text, full: html, text
    more work on sea hare
• src/hg/makeDb/doc/hg18.txt
  • 1.363 lines changed: 484, context: html, text, full: html, text
    Added snp130 basic tables.
• src/hg/makeDb/doc/hg19.txt
  • 1.21 lines changed: 282, context: html, text, full: html, text
    lastz run updates, now running the last two, and many are finished
  • 1.20 lines changed: 103, context: html, text, full: html, text
    Running Elephant and Tenrec lastz
  • 1.19 lines changed: 382, context: html, text, full: html, text
    Update to the lastz run status, many going at this point
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.96 lines changed: 1, context: html, text, full: html, text
    Added aplCal1
• src/hg/makeDb/genbank/etc/dbload
  • 1.24 lines changed: 4, context: html, text, full: html, text
    fixed for hgsqlrr
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.337 lines changed: 1, context: html, text, full: html, text
    Added aplCal1.
  • 1.336 lines changed: 20, context: html, text, full: html, text
    Added aplCal1.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.101 lines changed: 1, context: html, text, full: html, text
    Added aplCal1
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.44 lines changed: 1, context: html, text, full: html, text
    fixed for hgsqlrr
  • 1.43 lines changed: 8, context: html, text, full: html, text
    enable using hgsqlrr for hgw1
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.71 lines changed: 2, context: html, text, full: html, text
    adding aplCal
• src/hg/makeDb/schema/all.joiner
  • 1.716 lines changed: 16, context: html, text, full: html, text
    Added snp130.
• src/hg/makeDb/trackDb/README
  • 1.75 lines changed: 6, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.74 lines changed: 5, context: html, text, full: html, text
    choose a contrasting color for tick marks when drawgin differnt bases
• src/hg/makeDb/trackDb/cgapSage.html
  • 1.21 lines changed: 3, context: html, text, full: html, text
    Removed broken link to transcriptomes.org, which has not worked for several months.
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.35 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Removed broken link to Release 3.2 heterochromatic sequence.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.78 lines changed: 7, context: html, text, full: html, text
    More tricks from Tim: use noInherit on and settingsByView so hgTracks doesn't get misled by the composite type of bed3.
  • 1.77 lines changed: 1, context: html, text, full: html, text
    Changing bdntpChipper composite type back to wig instead of bed 3, which caused all subtracks to be drawn as bed3 not wig despite the wig subtrack types.
  • 1.76 lines changed: 153, context: html, text, full: html, text
    Several more suggestions from Tim: get rid of dimZ FDR subgroup (redundant w/view), add sortOrder and dragAndDrop, and move type wig declaration from composite down into subtracks, so the composite-level controls will not be shown and view-level controls will work. Also broke down classes Anterior-posterior early and Dorsal-ventral into more detailed subclasses for proper sort ordering.
  • 1.75 lines changed: 1, context: html, text, full: html, text
    Added boxedCfg on to bdtnpChipper (thanks Tim!).
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed broken Exogean link.
• src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed broken Exogean link.
• src/hg/makeDb/trackDb/human/hg16/encodeGisRnaPet.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Bioinformatics Institute of Singapore.
• src/hg/makeDb/trackDb/human/hg17/dukeDnaseCd4Signal.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg17/dukeDnaseCd4Sites.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg17/dukeDnaseHsCd4Pval.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg17/dukeDnaseHsCd4Sites.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg17/dukeDnaseSuper.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg17/encodeGisRnaPet.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Bioinformatics Institute of Singapore.
• src/hg/makeDb/trackDb/human/hg17/encodeNhgriDnaseHsChipRaw.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to Nature Methods, which was causing an html error 404
• src/hg/makeDb/trackDb/human/hg18/encodeEgaspSuper.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed broken Exogean link.
• src/hg/makeDb/trackDb/human/hg18/encodeGisRnaPet.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Bioinformatics Institute of Singapore.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • 1.23 lines changed: 0, context: html, text, full: html, text
    Next ENCODE data freeze has been set for July 2009 (guessed wrong on May)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.328 lines changed: 183, context: html, text, full: html, text
    Edit labels for consistency (need to update DAF files)
  • 1.327 lines changed: 1, context: html, text, full: html, text
    Moved mapability track to map group
  • 1.326 lines changed: 6, context: html, text, full: html, text
    Changed some Elnitski labels
  • 1.325 lines changed: 1, context: html, text, full: html, text
    Make signal height consistent for Riken
  • 1.324 lines changed: 23, context: html, text, full: html, text
    Added searching for geneId on ENCODE Gencode tables
  • 1.323 lines changed: 20, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.322 lines changed: 168, context: html, text, full: html, text
    Set colors on Riken to indicate strand
  • 1.321 lines changed: 590, context: html, text, full: html, text
    adding 4 new AffyRnaChip submissions, removing old duplicated metadata settings, adding a missing metadata line
  • 1.320 lines changed: 24, context: html, text, full: html, text
    Added searching to ENCODE Gencode and 1D matrix to mapability
  • 1.319 lines changed: 48, context: html, text, full: html, text
    fix up FilteredRawSignal View name to be shorter FiltRawSignal for mysql table names
  • 1.318 lines changed: 47, context: html, text, full: html, text
    rename view to FiltTransfrags to ensure MySQL tablenames shorter than 65
  • 1.317 lines changed: 381, context: html, text, full: html, text
    Redo cellular localization labels so enforce order requested by Carrie Davis, CSHL
  • 1.316 lines changed: 232, context: html, text, full: html, text
    Next ENCODE data freeze has been set for July 2009 (guessed wrong on May)
  • 1.315 lines changed: 1, context: html, text, full: html, text
    Turn on individual subtrack configurability for Open Chromatin, by request of Terry Furey. Will turn off before release
  • 1.314 lines changed: 24, context: html, text, full: html, text
    ShortLable needs to be short
  • 1.313 lines changed: 1445, context: html, text, full: html, text
    Broad's Raw Signals were updated
  • 1.312 lines changed: 4, context: html, text, full: html, text
    turn off the base display until we have a better visualization
  • 1.311 lines changed: 5, context: html, text, full: html, text
    showing diffBases for Helicos until we can find an alignment format
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.6 lines changed: 76, context: html, text, full: html, text
    Terry Furey's latest take on this. Not doubt it will be parred down.
  • 1.5 lines changed: 9, context: html, text, full: html, text
    Added description of Base Overlap Signal
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaPet.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Bioinformatics Institute of Singapore.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisSuper.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Bioinformatics Institute of Singapore.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriBip.html
  • 1.3 lines changed: 79, context: html, text, full: html, text
    Moved this description page to the root directory because it is needed for hg18, mm9, rn4, panTro2, rheMac2, canFam2 and bosTau4
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriNre.html
  • 1.3 lines changed: 36, context: html, text, full: html, text
    Reformatting. No wording changes, except adding contact
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Adding Carrie Davis of CSHL to credits
  • 1.12 lines changed: 17, context: html, text, full: html, text
    Finally got mapping parameters from Timo
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.12 lines changed: 7, context: html, text, full: html, text
    added range query syntax to searches now that we have STS Markers up
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.25 lines changed: 54, context: html, text, full: html, text
    Now with all tracks individually configurable, and species order on Vertebrate group
  • 1.24 lines changed: 206, context: html, text, full: html, text
    Put in the species order list for the Placental chain net composite track
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Indicate chain norm score available for the MHC composite of chains and nets
  • 1.22 lines changed: 33, context: html, text, full: html, text
    allow the Primates chain and net tracks to sort by specified order
  • 1.21 lines changed: 612, context: html, text, full: html, text
    Adding placental and vertebrate Chain/Net composite tracks
  • 1.20 lines changed: 162, context: html, text, full: html, text
    Add Primates Chain/Net composite track as an 'alpha' release configuration
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.457 lines changed: 1, context: html, text, full: html, text
    Moved the uniqueness track from expression to varRep, to be consistent with the mapability track
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.45 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/opossum/monDom5/phastConsElements9way.html
  • 1.1 lines changed: 2, context: html, text, full: html, text
    dummy page to silence error during build
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.34 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.40 lines changed: 1, context: html, text, full: html, text
    Added 'NHGRI' to long label of ENCODE BiP track
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.37 lines changed: 2, context: html, text, full: html, text
    Changed the scoreFilter and scoreFilterLimits for transRegCode
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.508 lines changed: 2, context: html, text, full: html, text
    No species dimension in the venter chain net composite
  • 1.507 lines changed: 45, context: html, text, full: html, text
    Put Venter chain and net together into a composite
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • 1.1 lines changed: 92, context: html, text, full: html, text
    Moved this description page to the root directory because it is needed for hg18, mm9, rn4, panTro2, rheMac2, canFam2 and bosTau4
• src/hg/makeDb/trackDb/worm/ce4/description.html
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/hg/makeDb/trackDb/worm/ce4/gap.html
  • 1.4 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/hg/makeDb/trackDb/worm/ce4/gold.html
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/hg/makeDb/trackDb/worm/ce5/description.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/hg/makeDb/trackDb/worm/ce5/gap.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/hg/makeDb/trackDb/worm/ce5/gold.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Changed links to specific worm data freezes to generic wormbase links, at least temporarily.
• src/lib/htmshell.c
  • 1.49 lines changed: 3, context: html, text, full: html, text
    Kayla didn't like the prev button repeat errors
• src/lib/psl.c
  • 1.81 lines changed: 83, context: html, text, full: html, text
    don't modify input sequences when converting alignments
• src/utils/qa/countPerChrom.csh
  • 1.10 lines changed: 7, context: html, text, full: html, text
    added error-checking for case where 4th parameter is no good. thanks katrina
• src/utils/qa/doGenbankTests
  • 1.13 lines changed: 7, context: html, text, full: html, text
    Simplified getting intronEst table names even further (and logic was backwards in last commit).
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Simplified some if statements.
  • 1.11 lines changed: 35, context: html, text, full: html, text
    Added special handling for intronEst in split form. Also changed a variable name.
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Removed unused variable, changed date format slightly.
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.22 lines changed: 1, context: html, text, full: html, text
    removign /cluster/hive even from comment in case it causes confusion
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.61 lines changed: 2, context: html, text, full: html, text
    v208 preview

• lines changed: 7174
• files changed: 82