CVS changes by file

branch to review (2009-02-24 to 2009-03-03) v201

• src/hg/encode/DAFs/HelicosRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Helicos platform doesnt make quality scores
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.78 lines changed: 1, context: html, text, full: html, text
    Changed SREBP1 to SREBP1A as per Mike Willson's request
  • 1.77 lines changed: 32, context: html, text, full: html, text
    Added GATA-1, JunD, SREBP1 and SREBP2 antibodies
  • 1.76 lines changed: 1, context: html, text, full: html, text
    Sanitize out slash from cell type name (w/ agreement of Peggy Farnham)
  • 1.75 lines changed: 8, context: html, text, full: html, text
    Added TCF4 for Snyder's lab
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.12 lines changed: 6, context: html, text, full: html, text
    fixing perm problems
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.18 lines changed: 14, context: html, text, full: html, text
    1. Add links to cell protocol files 2. Add option to set background color
• src/hg/hgGenome/upload.c
  • 1.35 lines changed: 1, context: html, text, full: html, text
    adding snpArrayIllumina1M table
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.474 lines changed: 151, context: html, text, full: html, text
    Updated hapmapSnpsUi to handle HapMap phase III (11 populations).
• src/hg/hgTracks/encode.c
  • 1.18 lines changed: 34, context: html, text, full: html, text
    Changed encodePeak support for individual filters: qValue, pValue, signalValue and score
• src/hg/hgTracks/hgTracks.c
  • 1.1556 lines changed: 8, context: html, text, full: html, text
    Fixup Ensembl link for 2-micron genome referenc
  • 1.1555 lines changed: 3, context: html, text, full: html, text
    User+local request: show the primer boundaries in hgPcr results.
• src/hg/hgc/hgc.c
  • 1.1512 lines changed: 247, context: html, text, full: html, text
    Refactored hapmapSnps code to support both phase II (4 populations) and phase III (11 populations) SNPs.
  • 1.1511 lines changed: 7, context: html, text, full: html, text
    Made dbIsFound a global so there's no need to set it again after doMiddle sets it.
  • 1.1510 lines changed: 1, context: html, text, full: html, text
    changed strstr() to startsWtih() per Hiram's suggestion.
• src/hg/inc/chromGraphFactory.h
  • 1.8 lines changed: 1, context: html, text, full: html, text
    adding snpArrayIllumina1M table
• src/hg/inc/hapmapSnps.h
  • 1.6 lines changed: 31, context: html, text, full: html, text
    Added some new #defines for the HapMap Phase III updates to hgc, hgTrackUi and hgTracks.
• src/hg/inc/hui.h
  • 1.119 lines changed: 19, context: html, text, full: html, text
    Added dyAddFilterAsInt and dyAddFilterAsDouble for encodePeak support
• src/hg/inc/jksql.h
  • 1.81 lines changed: 3, context: html, text, full: html, text
    Added sqlSetParanoid; complain about failed MayConnect only if paranoidness is on (the only time we really should complain is when trying to get to the central database.
• src/hg/instinct/hgHeatmap2/hgCircleMaps.c
  • 1.10 lines changed: 27, context: html, text, full: html, text
    updated text color for dark median backgrounds
  • 1.9 lines changed: 22, context: html, text, full: html, text
    fixed bug with summary rings and subgrouping
  • 1.8 lines changed: 17, context: html, text, full: html, text
    updated code
  • 1.7 lines changed: 174, context: html, text, full: html, text
    updated hgcirclemaps
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    accidentally included
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed bug with summary rings and subgrouping
• src/hg/js/hgTracks.js
  • 1.19 lines changed: 7, context: html, text, full: html, text
    fix bug in updatePosition that caused negative chrom positions when user was at/near beginning of the the chrom
• src/hg/js/hui.js
  • 1.20 lines changed: 39, context: html, text, full: html, text
    Fixed some less efficient jQuery calls.
• src/hg/lib/chromGraphFactory.c
  • 1.17 lines changed: 15, context: html, text, full: html, text
    adding snpArrayIllumina1M table
• src/hg/lib/hapmapSnps.c
  • 1.4 lines changed: 5, context: html, text, full: html, text
    Added global vars: lists of population codes and ortho-species for HapMap Phase II and III.
• src/hg/lib/hdb.c
  • 1.396 lines changed: 2, context: html, text, full: html, text
    Use the new sqlSetParanoid to enable extra stderr message if we fail to connect to the central database.
• src/hg/lib/hgFind.c
  • 1.218 lines changed: 1, context: html, text, full: html, text
    Make canonicalRangeExp accept negative start coord -- hgTracks will clip to 0.
• src/hg/lib/hgSeq.c
  • 1.39 lines changed: 20, context: html, text, full: html, text
    Made hgSeqChromSize more concise, and took out a redundant call to it (chromSize is passed down instead).
• src/hg/lib/hui.c
  • 1.162 lines changed: 18, context: html, text, full: html, text
    Support for Min Gray level in multi-view and for min but not max score filter.
  • 1.161 lines changed: 2, context: html, text, full: html, text
    Cosmetic change to views section (no italics, and lowercase wording) for consistency
  • 1.160 lines changed: 181, context: html, text, full: html, text
    Changed encodePeak support for individual filters: qValue, pValue, signalValue and score
  • 1.159 lines changed: 86, context: html, text, full: html, text
    Change contolled vocab link to use trackDb setting, Also change to support javascript multi-view droip downs
• src/hg/lib/jksql.c
  • 1.128 lines changed: 9, context: html, text, full: html, text
    Added sqlSetParanoid; complain about failed MayConnect only if paranoidness is on (the only time we really should complain is when trying to get to the central database.
• src/hg/makeDb/doc/hg18.txt
  • 1.352 lines changed: 27, context: html, text, full: html, text
    Rebuilt omimGene.
• src/hg/makeDb/doc/hivA244.txt
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Added posSelection for vax004 section.
• src/hg/makeDb/doc/hivGne8v2.txt
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Added posSelection for vax004 section.
• src/hg/makeDb/doc/hivMn2.txt
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Added posSelection for vax004 section.
• src/hg/makeDb/doc/hivVax003Vax004.txt
  • 1.8 lines changed: 176, context: html, text, full: html, text
    Checked in the section of the posSelection tracks build for vax004.
• src/hg/makeDb/doc/sacCer2.txt
  • 1.5 lines changed: 326, context: html, text, full: html, text
    Finished with sacCer2
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.94 lines changed: 1, context: html, text, full: html, text
    Added sacCer2 - S. cerevisiae
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.99 lines changed: 1, context: html, text, full: html, text
    Added sacCer2 - S. cerevisiae
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.50 lines changed: 1, context: html, text, full: html, text
    Too many soring messages.
• src/hg/makeDb/schema/all.joiner
  • 1.697 lines changed: 2, context: html, text, full: html, text
    two more tables to ignore in sacCer2
  • 1.696 lines changed: 12, context: html, text, full: html, text
    sacCer2 looking pretty good, some tables out in the cold for sacCer1
• src/hg/makeDb/trackDb/human/hg16/description.html
  • 1.21 lines changed: 2, context: html, text, full: html, text
    restored the 15-pixel spacing around the image
  • 1.20 lines changed: 4, context: html, text, full: html, text
    Replacing Darwin's picture with the CBSE human picture.
• src/hg/makeDb/trackDb/human/hg17/description.html
  • 1.26 lines changed: 2, context: html, text, full: html, text
    restored the 15-pixel spacing around the image
  • 1.25 lines changed: 4, context: html, text, full: html, text
    Replacing Darwin's picture with the CBSE human picture.
• src/hg/makeDb/trackDb/human/hg18/description.html
  • 1.19 lines changed: 2, context: html, text, full: html, text
    restored the 15-pixel spacing around the image
  • 1.18 lines changed: 1, context: html, text, full: html, text
    one stragler!
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Replacing Darwin's picture with the CBSE human picture.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.378 lines changed: 68, context: html, text, full: html, text
    removed beta block for snpArray track
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.173 lines changed: 74, context: html, text, full: html, text
    fixes to html description and to make long labels nad tags consistent and readable
  • 1.172 lines changed: 684, context: html, text, full: html, text
    Added Feb freeze tracks for Duke and Yale
  • 1.171 lines changed: 14, context: html, text, full: html, text
    Replaced filterPvalQval with pValueFilter=0.0,qValueFilter=0.0 making filters individually supportable
  • 1.170 lines changed: 30, context: html, text, full: html, text
    Prune short labels
  • 1.169 lines changed: 223, context: html, text, full: html, text
    Shorten short labels to approved length
  • 1.168 lines changed: 164, context: html, text, full: html, text
    Remove individual configurability of subtracks until performance improves
  • 1.167 lines changed: 0, context: html, text, full: html, text
    Adjust whitespace to conventional
  • 1.166 lines changed: 295, context: html, text, full: html, text
    More regeneration of Duke/UNC/UTA peaks and signals
  • 1.165 lines changed: 498, context: html, text, full: html, text
    Added for Yale, updated Chromatin, change to controlledVocab setting
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.3 lines changed: 14, context: html, text, full: html, text
    fixes to html description and to make long labels nad tags consistent and readable
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.12 lines changed: 12, context: html, text, full: html, text
    Changed 1st to 3rd person in methods section.
  • 1.11 lines changed: 14, context: html, text, full: html, text
    More edits to conform to our usual style.
  • 1.10 lines changed: 24, context: html, text, full: html, text
    Took out some titles, tweaked links, added credits.
  • 1.9 lines changed: 76, context: html, text, full: html, text
    Whitespace changes.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.11 lines changed: 6, context: html, text, full: html, text
    starting to remove a lot of the detail in Methods. will link to protocol when available
  • 1.10 lines changed: 19, context: html, text, full: html, text
    cleaned up links and added TARGET for the contributing labs' info
  • 1.9 lines changed: 4, context: html, text, full: html, text
    changed refs to include 10 names before the et al.
  • 1.8 lines changed: 80, context: html, text, full: html, text
    cleaned up html, mostly. made outlinks use TARGET _BLANK and shortened lines to conform to 80-limit where possible. cosmetic. real changes follow, but did want them to get lost in the noise
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Correction from Joe Pickrell.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.440 lines changed: 7, context: html, text, full: html, text
    Fixed hgdpHzy subtrack priorities (forgot they're int not float).
  • 1.439 lines changed: 69, context: html, text, full: html, text
    Added hgdpHzyBantu and changed 'Africa' to 'Bantu' in hgdpIhs and hgdpXpehh. Added hapmapSnps* for 7 new populations in HapMap Phase III.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.153 lines changed: 16, context: html, text, full: html, text
    Removed release beta in preparation for release of komp track
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • 1.1 lines changed: 252, context: html, text, full: html, text
    Added multiz9way description.
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • 1.16 lines changed: 1, context: html, text, full: html, text
    added a bit more shitespace around images
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    corrected downloads link
  • 1.4 lines changed: 1, context: html, text, full: html, text
    corrected credits link
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added a bit more shitespace around images
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixup treeImage name
• src/hg/qa/apacheMonitor.c
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Some fields can be null -- added checks.
  • 1.13 lines changed: 57, context: html, text, full: html, text
    Use sqlConnectRemote instead of hAllocConn (host was being ignored). Reuse one conn instead of realloc'ing in every function. Bump up the verbosity level of most messages, to make the error counts stand out.
• src/inc/net.h
  • 1.33 lines changed: 1, context: html, text, full: html, text
    fixing need for cgiDecode of user and password in url
• src/lib/blastOut.c
  • 1.28 lines changed: 5, context: html, text, full: html, text
    don't go past end of string if code checked out with -kk
• src/lib/bwgQuery.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Removing some debug statements.
• src/lib/cheapcgi.c
  • 1.110 lines changed: 2, context: html, text, full: html, text
    class needed quotations.
• src/lib/net.c
  • 1.69 lines changed: 4, context: html, text, full: html, text
    fixing need for cgiDecode of user and password in url
• src/utils/qa/alertBqueue.csh
  • 1.6 lines changed: 4, context: html, text, full: html, text
    rest counter to reflect the fact that ting had been dropped from list
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.49 lines changed: 2, context: html, text, full: html, text
    v202 preview

• lines changed: 4529
• files changed: 59