CVS changes by file

branch to review (2009-06-23 to 2009-06-30) v209

• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.33 lines changed: 20, context: html, text, full: html, text
    add lowelab server
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.35 lines changed: 44, context: html, text, full: html, text
    if no feature list html is found, table cell will not be created in desc html
  • 1.34 lines changed: 42, context: html, text, full: html, text
    add code to filter out private tracks when making desc html
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.42 lines changed: 6, context: html, text, full: html, text
    add lowelab server
• src/hg/encode/DAFs/CshlRnaSeq.daf
  • 1.4 lines changed: 8, context: html, text, full: html, text
    temporary new version until we get CSHL working with bigBed tagAlign
• src/hg/encode/DAFs/GisRnaSeq.daf
  • 1.4 lines changed: 17, context: html, text, full: html, text
    added split tags, and raw data for Solexa
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Fix perms
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Add execute bit to enable SSI
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.118 lines changed: 32, context: html, text, full: html, text
    Four more antibodies for Yale
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.185 lines changed: 6, context: html, text, full: html, text
    fix filename in fileDb.ra so it handles types with spaces
• src/hg/hgCustom/hgCustom.c
  • 1.129 lines changed: 4, context: html, text, full: html, text
    Add bigBed and bigWig help doc pointers
• src/hg/hgGateway/hgGateway.c
  • 1.112 lines changed: 2, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/hgGene/mrnaDescriptions.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Talk to the all_mrna table after testing for its existence, not the chr*_mrna table.
• src/hg/hgGeneList/hgGeneList.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/hgNotAvail/hgNotAvail.c
  • 1.2 lines changed: 3, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/hgNotYet/hgNotYet.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/hgTracks/bamTrack.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Oops, reverse-complement BAM query sequence when on - strand.
  • 1.1 lines changed: 156, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
• src/hg/hgTracks/bedTrack.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/bigWigTrack.c
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/cds.c
  • 1.102 lines changed: 6, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
  • 1.101 lines changed: 1, context: html, text, full: html, text
    bugfix: when using sf->qStart as mrnaS in drawCdsDiffBaseTickmarksOnly, correct for adjustment to target start.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.15 lines changed: 12, context: html, text, full: html, text
    Inital checkin of imageV2, but ifdef'd out.
• src/hg/hgTracks/config.c
  • 1.81 lines changed: 5, context: html, text, full: html, text
    fix dragZoomingConfig so it works when hgTracks is called from command line
• src/hg/hgTracks/expRatioTracks.c
  • 1.41 lines changed: 24, context: html, text, full: html, text
    Inital checkin of imageV2, but ifdef'd out.
• src/hg/hgTracks/hgTracks.c
  • 1.1579 lines changed: 3, context: html, text, full: html, text
    imageV2 should now work with reverse.
  • 1.1578 lines changed: 31, context: html, text, full: html, text
    Drag reorder should now be persistent
  • 1.1577 lines changed: 175, context: html, text, full: html, text
    Inital checkin of imageV2, but ifdef'd out.
  • 1.1576 lines changed: 19, context: html, text, full: html, text
    Added logic to check user authentication for the GISAID server. For other servers, a dummy/empty validation function is called, which just pass thru.
  • 1.1575 lines changed: 2, context: html, text, full: html, text
    removed outdated mgc code
  • 1.1574 lines changed: 1, context: html, text, full: html, text
    Make a CGI parameter for measureTiming (not just hardcoded), for convenience and so we don't risk accidentally checking in measureTiming=TRUE.
• src/hg/hgTracks/hgTracks.h
  • 1.185 lines changed: 5, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
  • 1.184 lines changed: 3, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/imageV2.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    imageV2 should now work with reverse.
  • 1.2 lines changed: 87, context: html, text, full: html, text
    Drag reorder should now be persistent
  • 1.1 lines changed: 1020, context: html, text, full: html, text
    Initial check-in of new image V2.0 which will allow drag-reorder and drag-scroll. This is a work in progress and ifdef'd out of the build.
• src/hg/hgTracks/imageV2.h
  • 1.2 lines changed: 13, context: html, text, full: html, text
    Drag reorder should now be persistent
  • 1.1 lines changed: 305, context: html, text, full: html, text
    Initial check-in of new image V2.0 which will allow drag-reorder and drag-scroll. This is a work in progress and ifdef'd out of the build.
• src/hg/hgTracks/makefile
  • 1.85 lines changed: 2, context: html, text, full: html, text
    Adding imageV2.c into build.
  • 1.84 lines changed: 4, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
• src/hg/hgTracks/simpleTracks.c
  • 1.88 lines changed: 40, context: html, text, full: html, text
    Inital checkin of imageV2, but ifdef'd out.
  • 1.87 lines changed: 5, context: html, text, full: html, text
    In linkedFeaturesDrawAt's hairy if() that decides whether to call baseColorDrawItem, !psl no longer cuts it as a test for whether we are drawing codons.
  • 1.86 lines changed: 6, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
  • 1.85 lines changed: 2, context: html, text, full: html, text
    Make a CGI parameter for measureTiming (not just hardcoded), for convenience and so we don't risk accidentally checking in measureTiming=TRUE.
• src/hg/hgTracks/variation.c
  • 1.142 lines changed: 38, context: html, text, full: html, text
    Inital checkin of imageV2, but ifdef'd out.
• src/hg/hgc/hgc.c
  • 1.1558 lines changed: 5, context: html, text, full: html, text
    Added logic to validate GISAID user if the server is a GISAID server.
• src/hg/inc/hCommon.h
  • 1.24 lines changed: 2, context: html, text, full: html, text
    Added validateGisaidUser() to be used ONLY on the GISAID server. This will be a dummy blank function for other servers.
• src/hg/inc/hui.h
  • 1.132 lines changed: 3, context: html, text, full: html, text
    added suppot for downloadsServer variable in html
• src/hg/inc/web.h
  • 1.44 lines changed: 2, context: html, text, full: html, text
    Added validateGisaidUser() declaration.
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.43 lines changed: 6, context: html, text, full: html, text
    Small mod for coded features
  • 1.42 lines changed: 42, context: html, text, full: html, text
    Updated UI to use dynamic ranges on clinical features
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.23 lines changed: 4, context: html, text, full: html, text
    fixed bug with cohort_id
• src/hg/js/hgTracks.js
  • 1.29 lines changed: 25, context: html, text, full: html, text
    Tweeks to get post on click to work in IE
  • 1.28 lines changed: 28, context: html, text, full: html, text
    Some adjustments to make sure dragZoom still works with imageV2
  • 1.27 lines changed: 18, context: html, text, full: html, text
    First baby steps for imageV2
• src/hg/lib/hCommon.c
  • 1.38 lines changed: 15, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/lib/hVarSubst.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    added suppot for downloadsServer variable in html
• src/hg/lib/hui.c
  • 1.217 lines changed: 4, context: html, text, full: html, text
    removed outdated mgc code
  • 1.216 lines changed: 7, context: html, text, full: html, text
    added suppot for downloadsServer variable in html
  • 1.215 lines changed: 3, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
  • 1.214 lines changed: 5, context: html, text, full: html, text
    Fix for matrix 'right buttons' being parially triggered by empty columns
• src/hg/lib/makefile
  • 1.390 lines changed: 1, context: html, text, full: html, text
    Added validateGisaid.o.
• src/hg/lib/validateGisaid.c
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Dummy/empty validateGisaidUser() for non-GISAID servers. The real validateGisaidUser() for GISAID server is confidential and is kept elsewhere.
• src/hg/lib/validateGisaid.dummy
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Created validateGisaid.dummy, which should be used as validateGisaid.c for non-GISAID servers.
• src/hg/makeDb/doc/dm1.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    typo
• src/hg/makeDb/doc/hg18.txt
  • 1.366 lines changed: 240, context: html, text, full: html, text
    Added instructions for making the (35-mer) uniqueness track data
• src/hg/makeDb/doc/hg19.txt
  • 1.28 lines changed: 21, context: html, text, full: html, text
    added n-scan track
• src/hg/makeDb/doc/mm9.txt
  • 1.100 lines changed: 16, context: html, text, full: html, text
    Updated MGI (jax%) tracks.
• src/hg/makeDb/doc/monDom5.txt
  • 1.10 lines changed: 24, context: html, text, full: html, text
    loaded monDom5 nscan
• src/hg/makeDb/doc/sacCer2.txt
  • 1.8 lines changed: 3, context: html, text, full: html, text
    changed from CREATE new table to RENAME
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh
  • 1.3 lines changed: 44, context: html, text, full: html, text
    Ready to start loading the database
• src/hg/makeDb/genbank/etc/dbload
  • 1.28 lines changed: 1, context: html, text, full: html, text
    moved grepIndex to /gbdb/genbank/grepIndex
  • 1.27 lines changed: 9, context: html, text, full: html, text
    relocate grepIndex on hgnfs1
  • 1.26 lines changed: 1, context: html, text, full: html, text
    switch hgsqlrr load host to hgnfs1
  • 1.25 lines changed: 1, context: html, text, full: html, text
    move hgsqlrr update to hgw2 to aboid poltergeist
• src/hg/makeDb/genbank/etc/hgnfs1.crontab
  • 1.6 lines changed: 15, context: html, text, full: html, text
    switch hgsqlrr load host to hgnfs1
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • 1.16 lines changed: 5, context: html, text, full: html, text
    just leave ccds database download as nightly
• src/hg/makeDb/genbank/etc/rr-dbload
  • 1.34 lines changed: 6, context: html, text, full: html, text
    
• src/hg/makeDb/genbank/makefile
  • 1.15 lines changed: 5, context: html, text, full: html, text
    running load on hgnfs1 requires a copy of hgsql
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • 1.49 lines changed: 15, context: html, text, full: html, text
    allow override of grepIndex location
  • 1.48 lines changed: 3, context: html, text, full: html, text
    don't try to build grepIndex on hgnfs1
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.46 lines changed: 1, context: html, text, full: html, text
    switch hgsqlrr load host to hgnfs1
  • 1.45 lines changed: 1, context: html, text, full: html, text
    move hgsqlrr update to hgw2 to aboid poltergeist
• src/hg/makeDb/genbank/src/lib/gbDefs.c
  • 1.12 lines changed: 2, context: html, text, full: html, text
    disabled poltergeist hack
  • 1.11 lines changed: 3, context: html, text, full: html, text
    output more info when molType corruption is detected
  • 1.10 lines changed: 13, context: html, text, full: html, text
    attempt to correct very strange corruption reading gbidx files on RR
  • 1.9 lines changed: 4, context: html, text, full: html, text
    added dumpStack call in attempt to understand intermitent bug
• src/hg/makeDb/genbank/src/lib/gbProcessed.c
  • 1.9 lines changed: 11, context: html, text, full: html, text
    output more info when molType corruption is detected
• src/hg/makeDb/makefile
  • 1.41 lines changed: 1, context: html, text, full: html, text
    don't build genbank as part of standard build, causes grief to mirrors who don't needed it
• src/hg/makeDb/schema/all.joiner
  • 1.721 lines changed: 2, context: html, text, full: html, text
    added sgdToPfam to all.joiner and removed it from the tables ignored
• src/hg/makeDb/trackDb/README
  • 1.81 lines changed: 2, context: html, text, full: html, text
    added suppot for downloadsServer variable in html
  • 1.80 lines changed: 1, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
• src/hg/makeDb/trackDb/chainPanTro2.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    fixed some tiny problems in the references
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.401 lines changed: 4, context: html, text, full: html, text
    Added baseColor settings to bamNA12878.
  • 1.400 lines changed: 2, context: html, text, full: html, text
    Ahem, forgot to fix default visibility before checking in.
  • 1.399 lines changed: 22, context: html, text, full: html, text
    Adding experimental tracks with a spot of 1000Genomes data for HapMap individual NA12878 on chr22.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.386 lines changed: 2, context: html, text, full: html, text
    Two typos
  • 1.385 lines changed: 46, context: html, text, full: html, text
    Broad alpha tracks had default hide for raw signals which made the matrix checkbox normalize code do strange things
  • 1.384 lines changed: 234, context: html, text, full: html, text
    loading CSHL bigbed tagAligns
  • 1.383 lines changed: 2, context: html, text, full: html, text
    Updates to the UW Affy Exon track description including track configuration.
  • 1.382 lines changed: 1, context: html, text, full: html, text
    Try raising scoreMin to darken the transfrags
  • 1.381 lines changed: 6, context: html, text, full: html, text
    made entry show more clearly what will change when converted to real track - using comments
  • 1.380 lines changed: 1, context: html, text, full: html, text
    tweak to UI
  • 1.379 lines changed: 42, context: html, text, full: html, text
    moved two subtracks into a new track to test provisional release idea
  • 1.378 lines changed: 29, context: html, text, full: html, text
    add missing metadata for HA MethylSeq
  • 1.377 lines changed: 7, context: html, text, full: html, text
    metadata for wgEncodeHudsonalphaMethyl27
  • 1.376 lines changed: 298, context: html, text, full: html, text
    Added 5 new experiments to Yale alpha, changed tags to ensure sort order, removed empty NT2-D1 cell line from yale beta
  • 1.375 lines changed: 13, context: html, text, full: html, text
    GIS RnaSeq base coloring
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.23 lines changed: 8, context: html, text, full: html, text
    Fixed up instructions for editing this file when Mapability is available.
  • 1.22 lines changed: 14, context: html, text, full: html, text
    Clarify views section
  • 1.21 lines changed: 3, context: html, text, full: html, text
    Added a link to downloads.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • 1.4 lines changed: 9, context: html, text, full: html, text
    added data-release policy dna-pet doco
  • 1.3 lines changed: 78, context: html, text, full: html, text
    updated version of dna-pet doco
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.6 lines changed: 74, context: html, text, full: html, text
    new clone-free method for GIS RNA-PET
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.2 lines changed: 7, context: html, text, full: html, text
    format tweak
  • 1.1 lines changed: 102, context: html, text, full: html, text
    Track documentation for GIS RNA-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.6 lines changed: 24, context: html, text, full: html, text
    credits
  • 1.5 lines changed: 10, context: html, text, full: html, text
    minor edits
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriNre.html
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Touch ups getting ready for the pushQ 'D'
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
  • 1.2 lines changed: 41, context: html, text, full: html, text
    Updates to the UW Affy Exon track description including track configuration.
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.10 lines changed: 4, context: html, text, full: html, text
    add comments for species info and feature lists table cells
• src/hg/makeDb/trackDb/makefile
  • 1.270 lines changed: 1, context: html, text, full: html, text
    Added danRer6 to DBS.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.51 lines changed: 12, context: html, text, full: html, text
    Oops, backing out inadvertently added debugging track.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.6 lines changed: 2, context: html, text, full: html, text
    loaded monDom5 nscan
• src/hg/makeDb/trackDb/phastConsElements.html
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Added italics.
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Added italics and formatting.
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • 1.1 lines changed: 223, context: html, text, full: html, text
    Initial file, with bits of hg18 44-way discussion brought over
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Use new multiz7way.html file for the conservation details page
• src/hg/makeDb/trackDb/snp128.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    changed nucleotoide to nucleotide
• src/hg/makeDb/trackDb/snp129.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    changed nucleotoide to nucleotide
• src/hg/makeDb/trackDb/snp130.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changed nucleotoide to nucleotide
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • 1.2 lines changed: 20, context: html, text, full: html, text
    Touch ups getting ready for the pushQ
• src/hg/phyloGif/phyloGif.c
  • 1.21 lines changed: 3, context: html, text, full: html, text
    making more senseful error messages
  • 1.20 lines changed: 11, context: html, text, full: html, text
    MSIE is not able to handle long urls in GET forms, so detect and MSIE will just have to miss out on the copy-the-url to generate a tree feature
  • 1.19 lines changed: 8, context: html, text, full: html, text
    make sure leafs have labels
• src/hg/protein/pbGateway/pbGateway.c
  • 1.10 lines changed: 4, context: html, text, full: html, text
    removed outdated mgc code
• src/hg/ratStuff/mafFrags/mafFrags.c
  • 1.10 lines changed: 12, context: html, text, full: html, text
    The meFirst stuff was broken when the input maf does not have the separator
• src/inc/common.h
  • 1.153 lines changed: 1, context: html, text, full: html, text
    Removing not ready for prime time code (debugMsg) which I accidentally checked in
  • 1.152 lines changed: 5, context: html, text, full: html, text
    Added strSwapStrs like replaceChrs but swaps in place.
• src/inc/common.mk
  • 1.61 lines changed: 11, context: html, text, full: html, text
    Added support for samtools/libbam, disabled by default.
• src/inc/linefile.h
  • 1.36 lines changed: 3, context: html, text, full: html, text
    Adding lineFileRewind.
• src/lib/basicBed.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Changing reserved field to a string so it can handle the various color morphs.
• src/lib/common.c
  • 1.131 lines changed: 21, context: html, text, full: html, text
    Added strSwapStrs like replaceChrs but swaps in place.
• src/lib/htmshell.c
  • 1.55 lines changed: 5, context: html, text, full: html, text
    Pass a file pointer to htmlWarnBoxSetup, so when we are creating trash/ html files for a frameset, the script is printed to the files not stdout.
  • 1.54 lines changed: 2, context: html, text, full: html, text
    Newling also breaks the warnBox code. sway '\n' with '<BR>'.
  • 1.53 lines changed: 3, context: html, text, full: html, text
    In warnBox sheild ' with HTML specil char is possible.
  • 1.52 lines changed: 42, context: html, text, full: html, text
    Reworked the html warning one more time. Fan complained about lack of html inside warnings and inability to copy/paste from an IE abort box, so I have created a warnBox embedded into the page. Again, no jQuery
• src/lib/linefile.c
  • 1.60 lines changed: 7, context: html, text, full: html, text
    Adding lineFileRewind.
• src/lib/phyloTree.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    making more senseful error messages
  • 1.10 lines changed: 7, context: html, text, full: html, text
    adding more error checking to phyloTree, especially for case of missing subtree (A,);
• src/makefile
  • 1.61 lines changed: 1, context: html, text, full: html, text
    adding hg libs for user apps
• src/utils/makefile
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Adding bedGraphToBigWig
• src/utils/qa/checkWigFiles.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Changed the error and usage message so that it does not appear that something is assumed about the location of the file specified.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.65 lines changed: 2, context: html, text, full: html, text
    v210 preview
• src/utils/qa/weeklybld/doHgDownloadUtils.csh
  • 1.5 lines changed: 16, context: html, text, full: html, text
    new process for copying userApps binaries (not just liftOver now)
• src/utils/qa/weeklybld/makeLiftOver.csh
  • 1.2 lines changed: 141, context: html, text, full: html, text
    liftover is part of larger suite of user apps now
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.2 lines changed: 20, context: html, text, full: html, text
    new process for copying userApps binaries (not just liftOver now)
  • 1.1 lines changed: 47, context: html, text, full: html, text
    liftover is part of larger suite of user apps now

• lines changed: 4569
• files changed: 100