CVS changes by file

branch to review (2009-02-09 to 2009-02-17) v200

• src/blat/blat.c
  • 1.113 lines changed: 2, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/blat/version.doc
  • 1.73 lines changed: 1, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/hg/encode/DAFs/GisDnaPet.daf
  • 1.3 lines changed: 38, context: html, text, full: html, text
    draft including discordant tag alignments
• src/hg/encode/DAFs/HelicosRnaSeq.daf
  • 1.1 lines changed: 48, context: html, text, full: html, text
    first version of helicos rna seq daf
• src/hg/encode/DAFs/WoldRnaSeq.daf
  • 1.2 lines changed: 30, context: html, text, full: html, text
    version of D?F that was successfully loaded
• src/hg/encode/DAFs/WoldRnaSeq.ex.ddf
  • 1.3 lines changed: 33, context: html, text, full: html, text
    version of D?F that was successfully loaded
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.56 lines changed: 1, context: html, text, full: html, text
    allow 12-column beds for Wold
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.72 lines changed: 4, context: html, text, full: html, text
    shortening names for sake of 64 char table name limit in mysql
  • 1.71 lines changed: 2, context: html, text, full: html, text
    shortening for table name limit of 64 chars for Wold
  • 1.70 lines changed: 4, context: html, text, full: html, text
    no algorithm applicable for some data like download only sequences
  • 1.69 lines changed: 10, context: html, text, full: html, text
    new tag map algorithms for Wold
  • 1.68 lines changed: 8, context: html, text, full: html, text
    Added ZNF263 antibody for Yale.
  • 1.67 lines changed: 41, context: html, text, full: html, text
    new cell lines from Rami (they are not yet approved and we still need more details)
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.154 lines changed: 2, context: html, text, full: html, text
    test for table name too long
  • 1.153 lines changed: 17, context: html, text, full: html, text
    fixed mismatched duplicates of downloadOnly logic by moving to a function
  • 1.152 lines changed: 7, context: html, text, full: html, text
    forgot a <tab>
  • 1.151 lines changed: 1, context: html, text, full: html, text
    forgot a <tab>
  • 1.150 lines changed: 6, context: html, text, full: html, text
    fixes to first 21 ccolumns of psl format (commas at end of last 3)
  • 1.149 lines changed: 2, context: html, text, full: html, text
    assuming last column is optional as missing from some data
  • 1.148 lines changed: 3, context: html, text, full: html, text
    allow commas
  • 1.147 lines changed: 1, context: html, text, full: html, text
    allow dots in there
  • 1.146 lines changed: 6, context: html, text, full: html, text
    allow pipes in the name in bowtie
  • 1.145 lines changed: 3, context: html, text, full: html, text
    allowing gene name to comprise any char but <tab>
  • 1.144 lines changed: 3, context: html, text, full: html, text
    RawData3 and RawData4 types are for Wold lab
  • 1.143 lines changed: 85, context: html, text, full: html, text
    validation rules for new Wold download types
  • 1.142 lines changed: 48, context: html, text, full: html, text
    added null validators for rpkm, fasta, bowtie, psl formats
• src/hg/hgGene/ctd.c
  • 1.9 lines changed: 2, context: html, text, full: html, text
    fixed some invalid html
• src/hg/hgGene/hgGene.c
  • 1.113 lines changed: 4, context: html, text, full: html, text
    fixed some invalid html
• src/hg/hgGene/otherOrgs.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    fixed some invalid html
• src/hg/hgGene/rnaStructure.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixed some invalid html
• src/hg/hgTracks/bedTrack.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Improving comment.
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/hgTracks/encode.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Error fixed for trackDbSetting thinking trackDb is NULL in the peaks tracks.
• src/hg/hgTracks/hgTracks.c
  • 1.1554 lines changed: 3, context: html, text, full: html, text
    Straighten out business with fr2ScaffoldEnsemblLink()
  • 1.1553 lines changed: 19, context: html, text, full: html, text
    Creating bigBed type custom tracks.
  • 1.1552 lines changed: 2, context: html, text, full: html, text
    turn on dragZooming by default
• src/hg/hgc/bigBedClick.c
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/hgc/hgc.c
  • 1.1508 lines changed: 33, context: html, text, full: html, text
    Added support for db.table.column=title setting in compareGenomeLinks
  • 1.1507 lines changed: 1, context: html, text, full: html, text
    Remove '_' in title
  • 1.1506 lines changed: 63, context: html, text, full: html, text
    added printCompareGenomeLinks for Elnitski's BiP tracks
  • 1.1505 lines changed: 2, context: html, text, full: html, text
    Creating bigBed type custom tracks.
  • 1.1504 lines changed: 2, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/hgc/hgc.h
  • 1.45 lines changed: 3, context: html, text, full: html, text
    Creating bigBed type custom tracks.
  • 1.44 lines changed: 3, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/hgc/hgcData/links.ra
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Updated UniProtSearch link to use new URL, UniProtVar link still uses the old links internally at UniProtKB, so left that one as is.
• src/hg/hgc/hgdpClick.c
  • 1.5 lines changed: 45, context: html, text, full: html, text
    Use hg.conf settings to determine GMT executable paths and enable/disable images, instead of hIsPrivateHost.
• src/hg/hgc/wiggleClick.c
  • 1.31 lines changed: 25, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/inc/web.h
  • 1.41 lines changed: 3, context: html, text, full: html, text
    fixed some invalid html
• src/hg/instinct/bioIntegrator/bioIntDb.as
  • 1.4 lines changed: 2, context: html, text, full: html, text
    updated -- add script to help populate db
  • 1.3 lines changed: 22, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 12, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDb.c
  • 1.4 lines changed: 7, context: html, text, full: html, text
    updated -- add script to help populate db
  • 1.3 lines changed: 498, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 255, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDb.h
  • 1.4 lines changed: 2, context: html, text, full: html, text
    updated -- add script to help populate db
  • 1.3 lines changed: 229, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 121, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDb.sql
  • 1.1 lines changed: 141, context: html, text, full: html, text
    added sql file for database
• src/hg/instinct/bioIntegrator/bioIntDriver.c
  • 1.8 lines changed: 140, context: html, text, full: html, text
    updated
  • 1.7 lines changed: 207, context: html, text, full: html, text
    updated
  • 1.6 lines changed: 52, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 95, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 276, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 449, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 263, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDriver.h
  • 1.8 lines changed: 24, context: html, text, full: html, text
    updated
  • 1.7 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.6 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 20, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 73, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 16, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntegrator.c
  • 1.12 lines changed: 197, context: html, text, full: html, text
    updated
  • 1.11 lines changed: 13, context: html, text, full: html, text
    updated
  • 1.10 lines changed: 39, context: html, text, full: html, text
    updated
  • 1.9 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.8 lines changed: 105, context: html, text, full: html, text
    updated
  • 1.7 lines changed: 32, context: html, text, full: html, text
    updated
  • 1.6 lines changed: 39, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/makefile
  • 1.4 lines changed: 20, context: html, text, full: html, text
    updated -- add script to help populate db
• src/hg/instinct/bioIntegrator/populateDb.c
  • 1.1 lines changed: 797, context: html, text, full: html, text
    updated -- add script to help populate db
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_maser2007.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    New .ra file for updated Maser conglomerated sets.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.instinct.ra
  • 1.2 lines changed: 44, context: html, text, full: html, text
    added two ispy datasets
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.5 lines changed: 33, context: html, text, full: html, text
    Merged Maser sets and added mouse sets.
• src/hg/instinct/segmentBed/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    initial commit
• src/hg/instinct/segmentBed/microarrayGroups.ra
  • 1.1 lines changed: 944, context: html, text, full: html, text
    initial commit
• src/hg/instinct/segmentBed/segmentBed.c
  • 1.1 lines changed: 241, context: html, text, full: html, text
    initial commit
• src/hg/lib/chromGraphFactory.c
  • 1.16 lines changed: 7, context: html, text, full: html, text
    fixed memory allocation error
• src/hg/lib/customFactory.c
  • 1.96 lines changed: 34, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/lib/customTrack.c
  • 1.175 lines changed: 13, context: html, text, full: html, text
    fix for customTrack when numbers appear in the middle of the track name
• src/hg/lib/genePred.c
  • 1.102 lines changed: 57, context: html, text, full: html, text
    ignore non-GTF features, as specified by the spec
• src/hg/lib/hVarSubst.c
  • 1.3 lines changed: 13, context: html, text, full: html, text
    correctly handle $$ escape in variable subtituion
• src/hg/lib/hui.c
  • 1.157 lines changed: 5, context: html, text, full: html, text
    Obscur change to allow filterBy Dropdowns to load properly in ms ie
• src/hg/lib/joiner.c
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Performance fix for tableExists: use sqlTableWildExists only when table name has a wildcard, because in large dbs like hg18, sqlTableWildExists is ~100x slower than sqlTableExists (0.090s --> 0.000s). When joining through gbCdnaInfo, we may call tableExists 255 times to find a path to tissue.name.
• src/hg/lib/trackDbCustom.c
  • 1.58 lines changed: 3, context: html, text, full: html, text
    Added gappedPeak as an approved multi-view type because Mike asked really nice.
• src/hg/lib/web.c
  • 1.158 lines changed: 9, context: html, text, full: html, text
    fixed some invalid html
• src/hg/makeDb/doc/hg18.txt
  • 1.345 lines changed: 48, context: html, text, full: html, text
    Add primate and glire lineage specific phyloP
• src/hg/makeDb/doc/hgFixed.txt
  • 1.16 lines changed: 12, context: html, text, full: html, text
    REBASE update.
• src/hg/makeDb/doc/hgdpGeo.txt
  • 1.1 lines changed: 127, context: html, text, full: html, text
    Per-SNP geographic map data and scripts from Human Genome Diversity Project.
• src/hg/makeDb/doc/rn4.txt
  • 1.32 lines changed: 9, context: html, text, full: html, text
    Ran liftOver to rn5 back in December
• src/hg/makeDb/doc/sacCer1.txt
  • 1.7 lines changed: 27, context: html, text, full: html, text
    Ran the liftOver to sacCer2
• src/hg/makeDb/doc/sacCer2.txt
  • 1.4 lines changed: 289, context: html, text, full: html, text
    Finished 7-way conservation business
  • 1.3 lines changed: 165, context: html, text, full: html, text
    Human proteins done by Brian, and multiple alignment in progress, genbank done
  • 1.2 lines changed: 164, context: html, text, full: html, text
    added Human Proteins
  • 1.1 lines changed: 312, context: html, text, full: html, text
    Initial work has genome up and running, sgdGene tracks functioning, running genbank
• src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
  • 1.17 lines changed: 13, context: html, text, full: html, text
    Updating worm link
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.328 lines changed: 16, context: html, text, full: html, text
    Added sacCer2.
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.64 lines changed: 15, context: html, text, full: html, text
    added two ispy datasets
  • 1.63 lines changed: 20, context: html, text, full: html, text
    Merged maser sets and added mouse set
• src/hg/makeDb/hgCutters/hgCutters.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Compile-error fix. Library code changed years ago and this one didn't get updated then for some reason.
• src/hg/makeDb/makefile
  • 1.40 lines changed: 1, context: html, text, full: html, text
    Adding hgBbiDbLink.
• src/hg/makeDb/outside/yeast/hgSgdGff3/sgdGffToGtf.pl
  • 1.4 lines changed: 1, context: html, text, full: html, text
    If we translate the type five_prime_UTR_intron to 5utr and use the -gtf option to ldHgGene then it seems to work OK.
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • 1.13 lines changed: 17, context: html, text, full: html, text
    Allowing remote databases.
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.32 lines changed: 15, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.7 lines changed: 16, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.26 lines changed: 15, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.74 lines changed: 1, context: html, text, full: html, text
    Made bdtnpChipper full by Mark Biggin's request.
• src/hg/makeDb/trackDb/hiv/vax004PosSelLoc.html
  • 1.3 lines changed: 731, context: html, text, full: html, text
    Got rid of lots of gobbledy-gook.
• src/hg/makeDb/trackDb/hiv/vax004PosSelRace.html
  • 1.3 lines changed: 731, context: html, text, full: html, text
    Get rid of lots of ...
• src/hg/makeDb/trackDb/hiv/vax004PosSelVac.html
  • 1.3 lines changed: 731, context: html, text, full: html, text
    Got rid of lots of gobbledy-gook.
• src/hg/makeDb/trackDb/human/affyHuEx1.html
  • 1.14 lines changed: 110, context: html, text, full: html, text
    Putting back in an old one.
  • 1.13 lines changed: 110, context: html, text, full: html, text
    Top-level affy all-exon supertrack. Removed HTML and entries in human/mouse/rat subdirs.
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to GRIB/IMIM/geneid.
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to wustl.
  • 1.10 lines changed: 4, context: html, text, full: html, text
    Fixed citation format for Ensembl paper.
  • 1.9 lines changed: 1, context: html, text, full: html, text
    edited links in Reference section for *scan*.html files. The links used to go to PDF files -- now they go to the Journal websites.
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fixed link HTML (found by hgTables robot)
  • 1.7 lines changed: 29, context: html, text, full: html, text
    Realphabetized list in Credits section.
  • 1.6 lines changed: 14, context: html, text, full: html, text
    Added information for microRNA and MITOMAP in the Credits section.
  • 1.5 lines changed: 90, context: html, text, full: html, text
    Rearranged some of the links in this file, fixed up a few of the refs, tidied up the HTML to match our format conventions.
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Made the journal references be italicized.
  • 1.3 lines changed: 64, context: html, text, full: html, text
    Fixed the references to be in our standard format. Added links to the papers that were listed. Removed the extra html that tries to take you lower in the page (because the page isn't long enough to warrant it).
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Changes to affy human exon tracks. Put probe track right below microarray track and mention both in each others' details.
  • 1.1 lines changed: 56, context: html, text, full: html, text
    Human Exon Array probe set track from affymetrix splicing sensitive microarray
• src/hg/makeDb/trackDb/human/hg16/description.html
  • 1.19 lines changed: 7, context: html, text, full: html, text
    adding darwin image for his 200th birthday
• src/hg/makeDb/trackDb/human/hg17/description.html
  • 1.24 lines changed: 7, context: html, text, full: html, text
    adding darwin image for his 200th birthday
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • 1.12 lines changed: 3, context: html, text, full: html, text
    Fixed links to tree models
• src/hg/makeDb/trackDb/human/hg18/description.html
  • 1.16 lines changed: 7, context: html, text, full: html, text
    adding darwin image for his 200th birthday
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Added some data for the Asian SNPs.
• src/hg/makeDb/trackDb/human/hg18/snpArray.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    removed stranded </A> found by test robots
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.38 lines changed: 14, context: html, text, full: html, text
    Merged maser sets and added mouse set
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.371 lines changed: 4, context: html, text, full: html, text
    pgSnp: a few more label tweaks for consistency.
  • 1.370 lines changed: 18, context: html, text, full: html, text
    pgSnp: label tweaks at David's request.
  • 1.369 lines changed: 12, context: html, text, full: html, text
    Removed affyHuEx1
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.155 lines changed: 2, context: html, text, full: html, text
    Move RNA seq to Expression track group
  • 1.154 lines changed: 14, context: html, text, full: html, text
    Fix for Pol2(b) tag and for compareGenomeLinks setting
  • 1.153 lines changed: 484, context: html, text, full: html, text
    First version of Wold tracks
  • 1.152 lines changed: 2, context: html, text, full: html, text
    Added compareGenomeLinks links to wgEncodeNhgriBip track
  • 1.151 lines changed: 56, context: html, text, full: html, text
    Added K562/ZNF263 for Yale
  • 1.150 lines changed: 15, context: html, text, full: html, text
    add some itemRgb's
  • 1.149 lines changed: 16, context: html, text, full: html, text
    tweaks to wgEncodeHudsonalphaMethylSeq
  • 1.148 lines changed: 228, context: html, text, full: html, text
    tracks for data from uploaded by rami
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • 1.1 lines changed: 88, context: html, text, full: html, text
    Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/hgdpGeo.html
  • 1.5 lines changed: 14, context: html, text, full: html, text
    Another addition from Graham Coop in Methods, and another reference from John Novembre.
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.1 lines changed: 58, context: html, text, full: html, text
    Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • 1.1 lines changed: 72, context: html, text, full: html, text
    Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.1 lines changed: 66, context: html, text, full: html, text
    Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.437 lines changed: 21, context: html, text, full: html, text
    Added continent colors to hgdpHzy, hgdpIhs and hgdpXpehh to match HGDP Selection Browser coloring.
  • 1.436 lines changed: 178, context: html, text, full: html, text
    Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH.
  • 1.435 lines changed: 11, context: html, text, full: html, text
    Putting back in an old one.
• src/hg/makeDb/trackDb/lowelab/syneElon_PCC_7942/trackDb.ra
  • 1.1 lines changed: 12, context: html, text, full: html, text
    New selfz track
• src/hg/makeDb/trackDb/mouse/komp.html
  • 1.3 lines changed: 56, context: html, text, full: html, text
    Expanded to describe the International Knockout Mouse Consortium of which KOMP is part.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.42 lines changed: 16, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.152 lines changed: 16, context: html, text, full: html, text
    Added alpha and beta release settings for komp, which is having its labels changed from KOMP to IKMC (Int'l Knockout Mouse Consortium).
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.31 lines changed: 15, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    Change in compareGenomeLinks setting
  • 1.37 lines changed: 18, context: html, text, full: html, text
    Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    gap off, and most conserved on pack
  • 1.2 lines changed: 43, context: html, text, full: html, text
    Adding 7-way multiple conservation track
• src/hg/near/hgNear/hgNear.c
  • 1.184 lines changed: 2, context: html, text, full: html, text
    Adding a comment.
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
  • 1.35 lines changed: 18, context: html, text, full: html, text
    Put missing columns back in.
• src/hg/near/hgNear/hgNearData/orderDb.ra
  • 1.29 lines changed: 6, context: html, text, full: html, text
    Put missing ordering back in.
• src/hg/oneShot/freen/freen.c
  • 1.86 lines changed: 27, context: html, text, full: html, text
    Testing simultanious writes.
  • 1.85 lines changed: 10, context: html, text, full: html, text
    Freen makes a 2 column file for testing.
• src/hg/oneShot/freen/test
  • 1.5 lines changed: 100000, context: html, text, full: html, text
    Removing stray (big!) test file that somehow got committed.
  • 1.4 lines changed: 100000, context: html, text, full: html, text
    Freen makes a 2 column file for testing.
• src/hg/utils/makefile
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Adding crTree utilities.
• src/inc/bbiFile.h
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/inc/bigBed.h
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/inc/genoFind.h
  • 1.80 lines changed: 1, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/inc/net.h
  • 1.31 lines changed: 12, context: html, text, full: html, text
    cleaning up, udc stuff already moved by jim to udc.c
• src/inc/sig.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Bumping bigBedSig due to slight change in format.
• src/inc/udc.h
  • 1.7 lines changed: 1, context: html, text, full: html, text
    moving some udc http declarations to .h file so I can call them for testing
  • 1.6 lines changed: 16, context: html, text, full: html, text
    moving some udc http declarations to .h file so I can call them for testing
• src/jkOwnLib/splix.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Wrapping a read in netReadAll instead because it's so big it sometimes seems to come back in parts.
• src/lib/bbiRead.c
  • 1.8 lines changed: 25, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/lib/bigBed.c
  • 1.10 lines changed: 14, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/lib/bwgQuery.c
  • 1.18 lines changed: 106, context: html, text, full: html, text
    Removing unused code.
• src/lib/net.c
  • 1.67 lines changed: 19, context: html, text, full: html, text
    adding FTP support for byterange url
  • 1.66 lines changed: 64, context: html, text, full: html, text
    fixing FTP so it does not waste 1 second waiting to see if there is going to be an error, this should make it faster to retrieve multiple FTP requests
  • 1.65 lines changed: 98, context: html, text, full: html, text
    cleaning up, udc stuff already moved by jim to udc.c
• src/lib/options.c
  • 1.25 lines changed: 3, context: html, text, full: html, text
    fixing options to ignore equals in ftp and https (and not just http)
• src/lib/udc.c
  • 1.12 lines changed: 56, context: html, text, full: html, text
    Removed flocks which seem to be unneeded. Adding qEncoding to make directory names easier to pursue under Unix.
  • 1.11 lines changed: 1, context: html, text, full: html, text
    moving some udc http declarations to .h file so I can call them for testing
  • 1.10 lines changed: 1, context: html, text, full: html, text
    moving some udc http declarations to .h file so I can call them for testing
  • 1.9 lines changed: 7, context: html, text, full: html, text
    moving some udc http declarations to .h file so I can call them for testing
  • 1.8 lines changed: 23, context: html, text, full: html, text
    Cgi-encoding file names in cache dir.
• src/oneShot/test/test.c
  • 1.34 lines changed: 18, context: html, text, full: html, text
    Testing some fool thing.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.47 lines changed: 2, context: html, text, full: html, text
    v201 preview
• src/utils/qa/weeklybld/doNewBranch32.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    dont hang on input
• src/utils/qa/weeklybld/doRobots.csh
  • 1.12 lines changed: 3, context: html, text, full: html, text
    get stdin from dev/null
• src/utils/qa/weeklybld/doZip.csh
  • 1.7 lines changed: 3, context: html, text, full: html, text
    dont hang on input
• src/utils/udcCleanup/udcCleanup.c
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Adding -test flag
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Shortened 'clipDontDie' option to just 'clip'

• lines changed: 212412
• files changed: 117