CVS changes by file

branch to review (2010-01-05 to 2010-01-12) v223

• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.17 lines changed: 22, context: html, text, full: html, text
    add code to generate tRNA track bed file with links to GtRNAdb for eukaryotes
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.22 lines changed: 1, context: html, text, full: html, text
    add tRNAscan-SE result file as input for draw_trna
  • 1.21 lines changed: 49, context: html, text, full: html, text
    add code to generate tRNA track bed file with links to GtRNAdb for eukaryotes
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.51 lines changed: 2, context: html, text, full: html, text
    add code to generate tRNA track bed file with links to GtRNAdb for eukaryotes
• src/hg/autoSql/autoSql.c
  • 1.39 lines changed: 6, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/doc2.c
  • 1.2 lines changed: 155, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/doc2.h
  • 1.2 lines changed: 48, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/hardTest.c
  • 1.10 lines changed: 49, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/hardTest.h
  • 1.4 lines changed: 16, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/mainTest.c
  • 1.7 lines changed: 171, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/mainTest.h
  • 1.3 lines changed: 48, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/newTest.c
  • 1.9 lines changed: 200, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/newTest.h
  • 1.4 lines changed: 48, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/polyTest.c
  • 1.7 lines changed: 50, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/polyTest.h
  • 1.3 lines changed: 16, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/simpleTest.c
  • 1.5 lines changed: 445, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/autoSql/tests/expected/simpleTest.h
  • 1.2 lines changed: 128, context: html, text, full: html, text
    make tab file load functions for structs of type object
• src/hg/blastToPsl/tests/expected/blastpPsiWrapTest.bscores
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixed parsing where blastp wraps Identity line
• src/hg/blastToPsl/tests/expected/blastpPsiWrapTest.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixed parsing where blastp wraps Identity line
• src/hg/blastToPsl/tests/input/blastpPsiWrap.blast
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixed parsing where blastp wraps Identity line
• src/hg/blastToPsl/tests/makefile
  • 1.21 lines changed: 8, context: html, text, full: html, text
    fixed parsing where blastp wraps Identity line
• src/hg/encode/DAFs/YDHChipSeqInput.daf
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Inputs have replicates
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.22 lines changed: 13, context: html, text, full: html, text
    Create md5sum.txt file
• src/hg/encode/encodePatchTdb/encodePatchTdb.c
  • 1.8 lines changed: 24, context: html, text, full: html, text
    Removing some unused code.
  • 1.7 lines changed: 93, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Getting rid of unused command line options.
  • 1.5 lines changed: 33, context: html, text, full: html, text
    Removing unused routine.
  • 1.4 lines changed: 35, context: html, text, full: html, text
    Implementing mode=replace
• src/hg/encode/encodePatchTdb/makefile
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/expected/add1.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/expected/add3.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/expected/composite.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding another test case.
• src/hg/encode/encodePatchTdb/tests/expected/replace1.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/expected/replace3.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/expected/replace3NoComment.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/in/add1.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/in/add3.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/in/composite.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding another test case.
• src/hg/encode/encodePatchTdb/tests/in/replace1.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/in/replace3.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/test.sh
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adding another test case.
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodePatchTdb/tests/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.181 lines changed: 7, context: html, text, full: html, text
    Added G1 phase for Stam lab
  • 1.180 lines changed: 20, context: html, text, full: html, text
    Change 10 cell lines from provisional to approved
  • 1.179 lines changed: 14, context: html, text, full: html, text
    Missed GM12872 in earlier ci fo cells for Stam
  • 1.178 lines changed: 119, context: html, text, full: html, text
    Added 5 new (provisional) cell lines for Stam and 4 new antibodies for Snyder
  • 1.177 lines changed: 6, context: html, text, full: html, text
    Added Rabbit_IgG for Snyder
  • 1.176 lines changed: 1, context: html, text, full: html, text
    Changed name of treatment
  • 1.175 lines changed: 91, context: html, text, full: html, text
    Added 5 new cells (3 provisional), 1 new antibody and 1 new treatment
  • 1.174 lines changed: 5, context: html, text, full: html, text
    Removed restrictionEnzyme 'None'. This should be done by controlled vocab
  • 1.173 lines changed: 16, context: html, text, full: html, text
    None for restrictionEnzyme. Some new readTypes
  • 1.172 lines changed: 48, context: html, text, full: html, text
    Added 4 antibodies for Snyder lab
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.25 lines changed: 5, context: html, text, full: html, text
    Added phase to ddf
  • 1.24 lines changed: 6, context: html, text, full: html, text
    1. Add new field for versioning comment. 2. Fix typo.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.213 lines changed: 7, context: html, text, full: html, text
    Expand support for versioning. 1. Add V? to metadata column in projects table. 2. Add versioning comment -- newly required field (dataVersionComment) in DAF
  • 1.212 lines changed: 1, context: html, text, full: html, text
    check for table existence using tableExists instead of looking in trackDb
  • 1.211 lines changed: 1, context: html, text, full: html, text
    restrictionEnzyme cv term should support control terms
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.513 lines changed: 10, context: html, text, full: html, text
    In bamUi, add baseColor defaults to tdb if this is a custom track, as we do in hgTracks.c. Otherwise baseColor drop-down doesn't appear for BAM custom tracks.
  • 1.512 lines changed: 5, context: html, text, full: html, text
    Added BAM config help link (if file exists).
• src/hg/hgTracks/altGraphXTrack.c
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Fixing indentation. Removing an unused define/ifdef. Adding braces for readability in a couple of places.
• src/hg/hgTracks/bamTrack.c
  • 1.23 lines changed: 6, context: html, text, full: html, text
    Oops, don't use global var position -- when we zoom, that is not updated and still has the old pos. Use chromName:winStart-winEnd instead (samtools uses 0-based offsets).
• src/hg/hgTracks/config.c
  • 1.88 lines changed: 19, context: html, text, full: html, text
    added configuration option for the width of the label area
• src/hg/hgTracks/cytoBandTrack.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    fixed use on incorrect variable that caused ideogram to be trancated when label width was increased
• src/hg/hgTracks/expRatioTracks.h
  • 1.4 lines changed: 0, context: html, text, full: html, text
    File had weird 775 permissions instead of 664
• src/hg/hgTracks/hgTracks.c
  • 1.1620 lines changed: 0, context: html, text, full: html, text
    fixed broken indentation
  • 1.1619 lines changed: 15, context: html, text, full: html, text
    add longLabel tooltips for links in track controls; change order of css includes in CONTEXT_MENU code
  • 1.1618 lines changed: 41, context: html, text, full: html, text
    Fixing indentation. Removing an unused define/ifdef. Adding braces for readability in a couple of places.
• src/hg/hgTracks/hgTracks.h
  • 1.196 lines changed: 2, context: html, text, full: html, text
    added configuration option for the width of the label area
• src/hg/hgTracks/simpleTracks.c
  • 1.119 lines changed: 15, context: html, text, full: html, text
    added configuration option for the width of the label area
• src/hg/hgc/bamClick.c
  • 1.14 lines changed: 16, context: html, text, full: html, text
    Added read name (wasn't obvious!). Added overall position & size for paired reads.
• src/hg/hgc/encodeClick.c
  • 1.11 lines changed: 5, context: html, text, full: html, text
    list all elements that satisfy the query criteria, not just the first one
• src/hg/hgc/hgc.c
  • 1.1586 lines changed: 58, context: html, text, full: html, text
    Added tRNAs track process per request from Todd Lowe.
  • 1.1585 lines changed: 5, context: html, text, full: html, text
    doHapMapSnpsAllPops: don't warn about differering alleles if one is the empty string -- in older hapmapSnps (phase II) tables, allele2 was empty when homoCount2 and heteroCount were both 0.
• src/hg/hgc/lowelab.c
  • 1.41 lines changed: 7, context: html, text, full: html, text
    add code to display GtRNAdb links for tRNAs track
• src/hg/inc/tRNAs.h
  • 1.2 lines changed: 3, context: html, text, full: html, text
    add fields for GtRNAdb urls
• src/hg/instinct/hgPathways/hgPathwaysFrontend/index.html
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Added save img dialog
• src/hg/instinct/hgPathways/hgPathwaysFrontend/js/hgHeatPath.js
  • 1.17 lines changed: 18, context: html, text, full: html, text
    Added save img dialog
• src/hg/lib/bamFile.c
  • 1.18 lines changed: 15, context: html, text, full: html, text
    Changed some errAborts to warns so BAM track connection troubles don't prevent display of other tracks.
• src/hg/lib/simpleRepeat.as
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixing score description
• src/hg/lib/simpleRepeat.sql
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fixing score description
• src/hg/lib/tRNAs.as
  • 1.4 lines changed: 2, context: html, text, full: html, text
    add fields for GtRNAdb urls
• src/hg/lib/tRNAs.c
  • 1.2 lines changed: 22, context: html, text, full: html, text
    add fields for GtRNAdb urls
• src/hg/lib/tRNAs.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    add fields for GtRNAdb urls
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.42 lines changed: 7, context: html, text, full: html, text
    finishing off tetNig2 and into the pushQ
• src/hg/makeDb/doc/mm8.txt
  • 1.76 lines changed: 4, context: html, text, full: html, text
    Added note about renaming mm8 jaxQTL table to jaxQtl.
• src/hg/makeDb/doc/mm9.txt
  • 1.119 lines changed: 29, context: html, text, full: html, text
    IKMC (komp) update.
• src/hg/makeDb/doc/tetNig2.txt
  • 1.8 lines changed: 45, context: html, text, full: html, text
    finishing off tetNig2 and into the pushQ
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.356 lines changed: 2, context: html, text, full: html, text
    disable tetNig ESTs as there are not any
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.99 lines changed: 1, context: html, text, full: html, text
    added ignored entry
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.86 lines changed: 1, context: html, text, full: html, text
    turned on danRer6
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.60 lines changed: 2, context: html, text, full: html, text
    Rescuing conservation track and others that have "subTrack parentTrack on" rather than just "subTrack parentTrack"
  • 1.59 lines changed: 104, context: html, text, full: html, text
    release alpha/beta was broken. Now that closest-to-home has gone away, it was very easy to implement very-early release pruning, followed later by pruning of orphans with no parent of the correct release. This keeps the code pretty simple which is nice.
  • 1.58 lines changed: 8, context: html, text, full: html, text
    the track hash was not accumulating track names twice when necessary
  • 1.57 lines changed: 13, context: html, text, full: html, text
    Adding some verbose 3 on the pruning business so it can be watched
• src/hg/makeDb/hgTrackDb/makefile
  • 1.34 lines changed: 0, context: html, text, full: html, text
    add clean target
  • 1.33 lines changed: 3, context: html, text, full: html, text
    add clean target
• src/hg/makeDb/schema/all.joiner
  • 1.760 lines changed: 6, context: html, text, full: html, text
    Moved 3 new Illumina SNP array entries from snp129 to snp130.
  • 1.759 lines changed: 3, context: html, text, full: html, text
    Added 3 new Illumina SNP array entries.
  • 1.758 lines changed: 12, context: html, text, full: html, text
    tetNig2 now fully enabled
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    typo (thanks Brooke)
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.18 lines changed: 5, context: html, text, full: html, text
    adding searching for CA Condor track
• src/hg/makeDb/trackDb/human/encodeUcsdChipSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/encodeUtexChipSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/encodeYaleRnaSuper.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • 1.181 lines changed: 3, context: html, text, full: html, text
    Made UT-Austin STAGE track part of encodeUtexChipSuper per Kate.
• src/hg/makeDb/trackDb/human/hg18/encodeUcsdChipSuper.html
  • 1.8 lines changed: 51, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/hg18/encodeUtexChipSuper.html
  • 1.8 lines changed: 45, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleRnaSuper.html
  • 1.9 lines changed: 65, context: html, text, full: html, text
    Moved from hg18 level now that the tracks are superTracks on hg16 and hg17.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.449 lines changed: 10, context: html, text, full: html, text
    dded tRNAs track per request from Todd Lowe.
  • 1.448 lines changed: 3, context: html, text, full: html, text
    shortned the short labels for the three recenlty added snpArray tables because they were more than 16 characters
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.753 lines changed: 58, context: html, text, full: html, text
    a bunch of UW Affy Exon tables, some HepG2 Caltech RNA-seq
  • 1.752 lines changed: 320, context: html, text, full: html, text
    change dimensions back for UwAffyExon
  • 1.751 lines changed: 11, context: html, text, full: html, text
    Uw Exons, change dimensions, add Skmc rep 2
  • 1.750 lines changed: 21, context: html, text, full: html, text
    HAIB methylSeq H1hESC submission 887
  • 1.749 lines changed: 42, context: html, text, full: html, text
    HAIB methyl seq HepG2 and HeLa-S3
  • 1.748 lines changed: 1, context: html, text, full: html, text
    Insignificant change to UMass Uniqueness settings
  • 1.747 lines changed: 1, context: html, text, full: html, text
    remove release alpha from HudsonalphaRnaSeq composite header
  • 1.746 lines changed: 11, context: html, text, full: html, text
    change Caltech signals to use autoScale, per Georgi
  • 1.745 lines changed: 107, context: html, text, full: html, text
    add Myer's lab RNA-seq
  • 1.744 lines changed: 338, context: html, text, full: html, text
    Cleaned up some extra tags in Open Chromatin
  • 1.743 lines changed: 145, context: html, text, full: html, text
    Reorganized Open Chromatin and Duke Affy Exon
  • 1.742 lines changed: 34, context: html, text, full: html, text
    Caltech HepG2 non-directional
  • 1.741 lines changed: 220, context: html, text, full: html, text
    calTech RNA-seq GM12878, K562 two replicates, directional
  • 1.740 lines changed: 3184, context: html, text, full: html, text
    Big change to Open Chromatin, due to adding 77 tracks for Jan 2010 freeze. Made alpha and beta versions of entire composite
  • 1.739 lines changed: 564, context: html, text, full: html, text
    add Duke Affy Exon Array composite
  • 1.738 lines changed: 108, context: html, text, full: html, text
    Added 8 submissions worth for Yale (used new encodePatchTdb)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    add some explanatory text
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.488 lines changed: 16, context: html, text, full: html, text
    Removed alpha/beta block on affyTxnPhase2 that was not doing anything except keeping trackDb from loading correctly on make strict.
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.93 lines changed: 18, context: html, text, full: html, text
    Added cytoBand and cytoBandIdeo to visualize position in chromosome
• src/hg/makeDb/trackDb/makefile
  • 1.282 lines changed: 6, context: html, text, full: html, text
    Add entry for ENCODE reporting
• src/hg/makeDb/trackDb/mouse/komp.html
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Corrections from Katrina.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.179 lines changed: 3, context: html, text, full: html, text
    Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9.
  • 1.178 lines changed: 1, context: html, text, full: html, text
    Oops, copy-paste fix.
  • 1.177 lines changed: 9, context: html, text, full: html, text
    search spec for IKMC (komp): made regex a bit shorter, and inclusive of both old and new names. Added a prefix search so the items with new suffixes can still be found by gene name. Thanks to Katrina for finding that this was broken & fixing it for new names!
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.6 lines changed: 1, context: html, text, full: html, text
    added subGroup7
• src/hg/makeDb/trackDb/tetraodon/gaze.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/tetNig1/gaze.html
  • 1.2 lines changed: 24, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
  • 1.24 lines changed: 16, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • 1.8 lines changed: 5, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.49 lines changed: 16, context: html, text, full: html, text
    fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.33 lines changed: 1, context: html, text, full: html, text
    changed shortLabel for chainNetDanRer6 to o_Organism, as it is the latest and should not use db name
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.579 lines changed: 1, context: html, text, full: html, text
    Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9.
• src/hg/tcga/pBamBam/pBamStats.c
  • 1.3 lines changed: 120, context: html, text, full: html, text
    updated
• src/hg/utils/automation/makePushQSql.pl
  • 1.28 lines changed: 30, context: html, text, full: html, text
    fix up some chain net confusion and beginning to get ready to use composite settings
• src/inc/errabort.h
  • 1.13 lines changed: 5, context: html, text, full: html, text
    added horrible hack so it's possible to distinguish between warning and errors in the warn handler
• src/inc/log.h
  • 1.8 lines changed: 4, context: html, text, full: html, text
    added support for setting minimum priority to log
• src/lib/blastParse.c
  • 1.25 lines changed: 9, context: html, text, full: html, text
    fixed parsing where blastp wraps Identity line
• src/lib/errabort.c
  • 1.16 lines changed: 9, context: html, text, full: html, text
    added horrible hack so it's possible to distinguish between warning and errors in the warn handler
• src/lib/https.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added include of common.c
• src/lib/log.c
  • 1.10 lines changed: 125, context: html, text, full: html, text
    added support for setting minimum priority to log
• src/lib/rudp.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}). Thx Galt for pointing out that the net.c code was dupl'd from this.
• src/lib/udc.c
  • 1.32 lines changed: 2, context: html, text, full: html, text
    In debug message, cast pointer to 32-bit unsigned instead of 64-bit so it doesn't break the 32-bit build.
• src/parasol/broadNode/broadNode.c
  • 1.17 lines changed: 2, context: html, text, full: html, text
    add option to set minimum log level, move some logging to debug
• src/parasol/inc/paraVersion.h
  • 1.11 lines changed: 1, context: html, text, full: html, text
    change version number
• src/parasol/para/para.c
  • 1.109 lines changed: 7, context: html, text, full: html, text
    remove trailing / and /. to fix common problem with -batch option when doing name completion
• src/parasol/paraHub/paraHub.c
  • 1.133 lines changed: 23, context: html, text, full: html, text
    add option to set minimum log level, move some logging to debug
• src/parasol/paraNode/paraNode.c
  • 1.83 lines changed: 12, context: html, text, full: html, text
    add option to set minimum log level, move some logging to debug
• src/parasol/paraNodeStart/paraNodeStart.c
  • 1.16 lines changed: 4, context: html, text, full: html, text
    add option to set minimum log level, move some logging to debug
• src/parasol/version.doc
  • 1.46 lines changed: 12, context: html, text, full: html, text
    added change descriptions
• src/utils/qa/alertBqueue.csh
  • 1.13 lines changed: 4, context: html, text, full: html, text
    changed output text a bit
• src/utils/qa/findLevel.csh
  • 1.17 lines changed: 191, context: html, text, full: html, text
    updated script to use the tdbQuery tool to find the trackDb.ra block(s) in which it is specified
• src/utils/qa/sessionStats.csh
  • 1.7 lines changed: 5, context: html, text, full: html, text
    changed output text a bit
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.95 lines changed: 2, context: html, text, full: html, text
    v223 preview
• src/utils/wigToBedGraph/makefile
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
• src/utils/wigToBedGraph/testFixed.bedGraph
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
• src/utils/wigToBedGraph/testFixed.wig
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
• src/utils/wigToBedGraph/testVar.bedGraph
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
• src/utils/wigToBedGraph/testVar.wig
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
• src/utils/wigToBedGraph/wigToBedGraph.c
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Utility to convert wigs to bedGraphs seems to be working in basic tests at least.

• lines changed: 8591
• files changed: 126