CVS changes by file

branch to review (2009-10-13 to 2009-10-20) v218

• src/ai/paraFlow/runtime/fileLib.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    keep http request together
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.91 lines changed: 16, context: html, text, full: html, text
    add Name_chg to haloSali1
  • 1.90 lines changed: 1, context: html, text, full: html, text
    change to use Hvo-genome.fa for haloVolc1_1
  • 1.89 lines changed: 1, context: html, text, full: html, text
    change blat port id again
  • 1.88 lines changed: 1, context: html, text, full: html, text
    fix blat port for haloVolc1_1
  • 1.87 lines changed: 21, context: html, text, full: html, text
    add Public_phylo for halophiles
• src/hg/archaeStuff/data/private-genomes.tab
  • 1.6 lines changed: 2, context: html, text, full: html, text
    replace spaces with tab
  • 1.5 lines changed: 5, context: html, text, full: html, text
    add schiPomb1 as private genome
  • 1.4 lines changed: 25, context: html, text, full: html, text
    add ynpyoung browser and nympLake_PGA2009 metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/AlignmentCompare.pm
  • 1.5 lines changed: 65, context: html, text, full: html, text
    read annotRev cds.gp instead of genePred.tab if available for igenics and alignInfo
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.21 lines changed: 4, context: html, text, full: html, text
    read annotRev cds.gp instead of genePred.tab if available for igenics and alignInfo
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.16 lines changed: 7, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.10 lines changed: 4, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.10 lines changed: 8, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
  • 1.3 lines changed: 7, context: html, text, full: html, text
    remove snoRNA hits from alignInfo for public browser
• src/hg/archaeStuff/scripts/archaeBrowser/arCOGs.pm
  • 1.1 lines changed: 121, context: html, text, full: html, text
    Archaeal COGs
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Added arCOG code
  • 1.2 lines changed: 65, context: html, text, full: html, text
    Added arCOGs
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.137 lines changed: 14, context: html, text, full: html, text
    Don't you know I am just trying to up my total modified lines in cvs-reports.
  • 1.136 lines changed: 20, context: html, text, full: html, text
    Type HA-E2F1 not H1-E2F1
  • 1.135 lines changed: 4, context: html, text, full: html, text
    Altered E2F1 to HA-E2F1 at Farnham's request
• src/hg/encode/validateFiles/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Must use DESTDIR with BINDIR to be sane
• src/hg/gsid/gsidSubj/gsidSubjData/section.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updated a section title per GSID request.
• src/hg/gsid/gsidSubj3/vaccine.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Added logic for special processing of sequencing day.
• src/hg/gsid/gsidTable/advFilter.c
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Disable danSeqs and aaSeqs as options to filter.
• src/hg/gsid/gsidTable/configure.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed a typo.
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Reversed the previous change, which was done in error.
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Disable DNA Sequences and Protein Sequences options per GSID request.
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Updated the text of a long label.
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3B
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Updated the text of a long label.
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • 1.2 lines changed: 10, context: html, text, full: html, text
    make display of hgPal link dependent on multiz46way on hg19
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.505 lines changed: 2, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
  • 1.504 lines changed: 60, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/hgTracks/bamTrack.c
  • 1.12 lines changed: 136, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
  • 1.11 lines changed: 177, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/hgTracks/hgTracks.h
  • 1.187 lines changed: 11, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/hgc/lowelab.c
  • 1.39 lines changed: 102, context: html, text, full: html, text
    Added arCOG code
  • 1.38 lines changed: 101, context: html, text, full: html, text
    add support to annotRev tracks; use annotRev instead of genepred if available for blastp tracks detail page
• src/hg/hgc/virusClick.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    keep http request together
• src/hg/inc/arCOGs.h
  • 1.1 lines changed: 67, context: html, text, full: html, text
    adding arcog table
• src/hg/inc/arcogdesc.h
  • 1.1 lines changed: 63, context: html, text, full: html, text
    adding arcog table
• src/hg/inc/bamFile.h
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
• src/hg/inc/hui.h
  • 1.140 lines changed: 23, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/inc/jksql.h
  • 1.86 lines changed: 3, context: html, text, full: html, text
    adding warnings to jksql new for mysql5
• src/hg/instinct/flatfileToBED15/flatfileToBED15.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Fixed negative values being reported for positions because of int rather than unsigned printing type
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.29 lines changed: 1, context: html, text, full: html, text
    changed TCGA include line
• src/hg/js/hgTracks.js
  • 1.44 lines changed: 15, context: html, text, full: html, text
    ignore drag activity in gray tab and track title column; fixes "jumping coordinates" bug found by ann
• src/hg/js/hui.js
  • 1.38 lines changed: 459, context: html, text, full: html, text
    Major changes to support the matrix 3-way CBs. Also some cleanup of old code.
• src/hg/lib/arCOGs.as
  • 1.1 lines changed: 11, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/arCOGs.c
  • 1.1 lines changed: 154, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/arCOGs.sql
  • 1.1 lines changed: 17, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/arcogdesc.as
  • 1.1 lines changed: 7, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/arcogdesc.c
  • 1.1 lines changed: 131, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/arcogdesc.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    adding arcog table
• src/hg/lib/bamFile.c
  • 1.11 lines changed: 50, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
• src/hg/lib/hui.c
  • 1.241 lines changed: 44, context: html, text, full: html, text
    Changes to support the matrix 3-way CBs. Requires hui.js to be uptodate as well.
• src/hg/lib/jksql.c
  • 1.138 lines changed: 1, context: html, text, full: html, text
    deleted forgotten debug
  • 1.137 lines changed: 23, context: html, text, full: html, text
    adding warnings to jksql new for mysql5
• src/hg/lib/makefile
  • 1.398 lines changed: 1, context: html, text, full: html, text
    Added arcog targets
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.7 lines changed: 390, context: html, text, full: html, text
    Getting things ready for Release2
  • 1.6 lines changed: 48, context: html, text, full: html, text
    Keeping up to date
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
  • 1.4 lines changed: 304, context: html, text, full: html, text
    Minor edits - no change of table/file lists
  • 1.3 lines changed: 364, context: html, text, full: html, text
    cleaned up: moved the raw seq files into the deleted files section. In the replaced files section, listed the files that have been replaced.
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Minor edit
  • 1.1 lines changed: 816, context: html, text, full: html, text
    Created an update log for the Broad Chip Seq tracks
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • 1.8 lines changed: 438, context: html, text, full: html, text
    Keeping up to date
• src/hg/makeDb/doc/encodeDccHg18/uwDgfStamm.notes.txt
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Update notes for the wgEncodeUwDgf composite track
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.2 lines changed: 102, context: html, text, full: html, text
    Keeping up to date
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.9 lines changed: 74, context: html, text, full: html, text
    Release 2 is out the door.
  • 1.8 lines changed: 692, context: html, text, full: html, text
    Keeping up to date
• src/hg/makeDb/doc/encodeDccHg18/yaleUpdate9-30.notes.txt
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Removed 3 tables erroneously listed as new. Thanks Ann
• src/hg/makeDb/doc/hg18.txt
  • 1.385 lines changed: 10, context: html, text, full: html, text
    Updating omimGene
• src/hg/makeDb/doc/hg19.txt
  • 1.48 lines changed: 1, context: html, text, full: html, text
    Fixed glitch in knownToHprd table build instructions.
  • 1.47 lines changed: 8, context: html, text, full: html, text
    updating visiGene for hg19
  • 1.46 lines changed: 1, context: html, text, full: html, text
    Getting rid of _1 from hprd ID's.
  • 1.45 lines changed: 60, context: html, text, full: html, text
    Creating knownToHprd column.
  • 1.44 lines changed: 88, context: html, text, full: html, text
    Adding omimGene
  • 1.43 lines changed: 53, context: html, text, full: html, text
    Creating nibbImageProbes table.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.7 lines changed: 68, context: html, text, full: html, text
    Creating knownToHprd column.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.2 lines changed: 113, context: html, text, full: html, text
    Creating knownToHprd column.
• src/hg/makeDb/doc/visiGene.txt
  • 1.12 lines changed: 40, context: html, text, full: html, text
    updating visiGene for hg19
  • 1.11 lines changed: 5, context: html, text, full: html, text
    adjustments for mysql5 blob string comparisons
  • 1.10 lines changed: 5, context: html, text, full: html, text
    Creating knownToHprd column.
• src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    backed out previous change, as it was incorrect. Instead improve a more informative diagnostic message
• src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    backed out previous change, as it was incorrect. Instead improve a more informative diagnostic message
  • 1.6 lines changed: 3, context: html, text, full: html, text
    don't skip validate non-coding RNAs
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • 1.16 lines changed: 16, context: html, text, full: html, text
    don't generate warnings on invalid dates; error not if warns occur, also added -drop option
• src/hg/makeDb/schema/all.joiner
  • 1.741 lines changed: 1, context: html, text, full: html, text
    Relaxing the minCheck on omimMorbidMap a little.
• src/hg/makeDb/trackDb/drosophila/dm1/flyreg.html
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Updated link to Dan Pollard's matrices and email (thx Brooke).
• src/hg/makeDb/trackDb/drosophila/dm2/flyreg2.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Updated link to Dan Pollard's matrices and email (thx Brooke).
• src/hg/makeDb/trackDb/elephant/loxAfr3/gold.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Add note about chrM being type F finished
• src/hg/makeDb/trackDb/genscan.html
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to Burge lab.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixing another broken link.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.421 lines changed: 1, context: html, text, full: html, text
    Added dimensionZchecked for supporting the new 3-way dimension checkboxes
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.595 lines changed: 10, context: html, text, full: html, text
    Added dimensionZchecked for supporting the new 3-way dimension checkboxes
  • 1.594 lines changed: 29, context: html, text, full: html, text
    Temporarily commented out the UW DGF footprints subtracks
  • 1.593 lines changed: 3, context: html, text, full: html, text
    Fixed a typo in the visibilityViewDefaults entry for the visibilityViewDefaults entry for wgEncodeUwDgf (Foorprints -> Footprints). Replaced the longLabel with a more descriptive label
  • 1.592 lines changed: 6, context: html, text, full: html, text
    bedGraph 4 cannot handle viewLimits on same line
  • 1.591 lines changed: 4, context: html, text, full: html, text
    Changed UwDGF signals settings as per Stam lab.
  • 1.590 lines changed: 5, context: html, text, full: html, text
    Fixed Broad metadata, 5 cases of H3K04me1 which should have been H3K4me1
  • 1.589 lines changed: 1, context: html, text, full: html, text
    Correct typo in lab name
  • 1.588 lines changed: 1, context: html, text, full: html, text
    Metatdata typo
  • 1.587 lines changed: 14, context: html, text, full: html, text
    No sooner is Yale publicly released than errors are found that need correction. HA to HA-E2F1 and make GM12989 and K562 tracks on by default
  • 1.586 lines changed: 87, context: html, text, full: html, text
    Added one last submission for Terry. Fixed some DNCT view limits and colors
  • 1.585 lines changed: 193, context: html, text, full: html, text
    Cleaned up commented out and replaced tracks
  • 1.584 lines changed: 1, context: html, text, full: html, text
    Put back changes on the UwDGF settings under viewLimitsMax
  • 1.583 lines changed: 1, context: html, text, full: html, text
    Added html page for DGF
  • 1.582 lines changed: 2, context: html, text, full: html, text
    Correct a minor setting error (track with table had parentTable setting which is used for downloadables only)
  • 1.581 lines changed: 1, context: html, text, full: html, text
    Remove Tier in cell type labels until there can be some review
  • 1.580 lines changed: 39, context: html, text, full: html, text
    fixed color of HeLa cell line for Yale TFBS tracks
  • 1.579 lines changed: 6, context: html, text, full: html, text
    added mocked up submission dir 685 to methyl27 tracks
  • 1.578 lines changed: 6, context: html, text, full: html, text
    add submission id for HudsonAlpha CNV
  • 1.577 lines changed: 300, context: html, text, full: html, text
    Nine more UwChIP submissions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.19 lines changed: 32, context: html, text, full: html, text
    Cleaned up the release notes a little and removed references to Raw Signals
  • 1.18 lines changed: 4, context: html, text, full: html, text
    Revised the release notes
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Cleaned up the Release Notes sections.
  • 1.16 lines changed: 23, context: html, text, full: html, text
    Added a Release Notes section.
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Changed Broad link by request of Charles Epstein
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Cleaned up the Release Notes sections.
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Fixed a few miscolored font lines
  • 1.1 lines changed: 144, context: html, text, full: html, text
    Added html page for DGF
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.47 lines changed: 2, context: html, text, full: html, text
    last fixes
  • 1.46 lines changed: 2, context: html, text, full: html, text
    prettier
  • 1.45 lines changed: 130, context: html, text, full: html, text
    Streamline & clarify the Release Notes section
  • 1.44 lines changed: 1, context: html, text, full: html, text
    hard link to download server
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • 1.1 lines changed: 134, context: html, text, full: html, text
    Copied hg18 knownGene.html to hg19 so that hg19 description is more up to date. The top level has an old description from hg17 and that is what hg19 UCSC Genes was displaying
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.54 lines changed: 3, context: html, text, full: html, text
    Now with frames, irows and phastCons46way all bigWig
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloUtah1/trackDb.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Update multiz track
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/multizHalophiles.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra
  • 1.7 lines changed: 17, context: html, text, full: html, text
    Update multiz track
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Update ultraConserved track
  • 1.5 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/ultraConserved.html
  • 1.1 lines changed: 3, context: html, text, full: html, text
    New ultraConserved track
• src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/privateTracks.ra
  • 1.22 lines changed: 8, context: html, text, full: html, text
    add restricted tracks to ynpyoung browser
  • 1.21 lines changed: 12, context: html, text, full: html, text
    add haloferax private tracks
• src/hg/makeDb/trackDb/lowelab/pyrAby1/trackDb.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyrHor1/trackDb.ra
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.536 lines changed: 2, context: html, text, full: html, text
    removing release alpha from chainNetEquCab2
• src/hg/near/hgNear/hgNearData/Human/hg19/columnDb.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding hg19 columns.
• src/hg/near/hgNear/hgNearData/Human/hg19/orderDb.ra
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Adding hg19 columns.
• src/hg/near/hprdXmlToTab/hprd.c
  • 1.1 lines changed: 2172, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/hprd.h
  • 1.1 lines changed: 627, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/hprdXmlToTab.c
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/makefile
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/out.atree
  • 1.1 lines changed: 71, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/out.dtd
  • 1.1 lines changed: 100, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/out.stats
  • 1.1 lines changed: 110, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/hprdXmlToTab/out.tree
  • 1.1 lines changed: 71, context: html, text, full: html, text
    Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
• src/hg/near/makeNear.doc
  • 1.42 lines changed: 45, context: html, text, full: html, text
    Adding update procedure for hg19 P2P tracks.
  • 1.41 lines changed: 1, context: html, text, full: html, text
    tiny update
• src/hg/pslCDnaFilter/makefile
  • 1.13 lines changed: 1, context: html, text, full: html, text
    binary result to DESTDIR
• src/hg/ratStuff/mafsInRegion/makefile
  • 1.4 lines changed: 5, context: html, text, full: html, text
    result properly honoring DESTDIR
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed syntax error in case of multiple previous logfiles.
• src/hg/visiGene/vgProbeTrack/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    making adjustments for mysql5 blob string compare behavior
• src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
  • 1.16 lines changed: 3, context: html, text, full: html, text
    making adjustments for mysql5 blob string compare behavior
  • 1.15 lines changed: 12, context: html, text, full: html, text
    handle 2bit as well as nib
• src/inc/common.h
  • 1.156 lines changed: 4, context: html, text, full: html, text
    Added dyStringCreate which will create a new dyString from printf style content.
• src/inc/common.mk
  • 1.72 lines changed: 1, context: html, text, full: html, text
    STRINGIFY needs to look in DESTDIR
• src/inc/dystring.h
  • 1.19 lines changed: 3, context: html, text, full: html, text
    Added dyStringCreate which will create a new dyString from printf style content.
• src/inc/net.h
  • 1.34 lines changed: 9, context: html, text, full: html, text
    keep http request together
• src/lib/cheapcgi.c
  • 1.125 lines changed: 1, context: html, text, full: html, text
    Added halfVis class to support 3-way matrix CBs
• src/lib/common.c
  • 1.134 lines changed: 33, context: html, text, full: html, text
    Added findWordByDemiliter which allows searching a string for a word, but the word must be set off by a delimiter.
• src/lib/dystring.c
  • 1.24 lines changed: 12, context: html, text, full: html, text
    Added dyStringCreate which will create a new dyString from printf style content.
• src/lib/htmlPage.c
  • 1.39 lines changed: 9, context: html, text, full: html, text
    keep http request together
• src/lib/net.c
  • 1.75 lines changed: 27, context: html, text, full: html, text
    keep http request together
  • 1.74 lines changed: 9, context: html, text, full: html, text
    adding some better error messages
• src/makefile
  • 1.68 lines changed: 3, context: html, text, full: html, text
    adding stringify encode/validateFiles ratStuff/mafsInRegion and pslCDnaFilter to the userApps build
  • 1.67 lines changed: 1, context: html, text, full: html, text
    liftOver out of place on lists, there were duplicates
  • 1.66 lines changed: 4, context: html, text, full: html, text
    fixup the userApps list of build items
• src/utils/bedClip/makefile
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Properly create the destination directory before making a binary there
• src/utils/jkUniq/jkUniq.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    added warning that it overwrite input; fixed bug in count
• src/utils/qa/doGenbankTests
  • 1.16 lines changed: 4, context: html, text, full: html, text
    Fixed bug that was causing intronEst to be printed in the list of tracks when no such table exists (thanks, pauline).
• src/utils/qa/knownGene.csh
  • 1.15 lines changed: 1, context: html, text, full: html, text
    added kgTableAll
  • 1.14 lines changed: 3, context: html, text, full: html, text
    updated some of the script output
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.84 lines changed: 2, context: html, text, full: html, text
    v218 preview
• src/utils/stringify/makefile
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Properly send output to DESTDIR BINDIR

• lines changed: 10832
• files changed: 118