CVS changes by file

review to branch (2009-02-17 to 2009-02-24) v201

• src/hg/encode/DAFs/GisRnaSeq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    transfrags not avaialble for feb freeze
  • 1.2 lines changed: 6, context: html, text, full: html, text
    SOLiD colorspace fasta format, not fastq
  • 1.1 lines changed: 43, context: html, text, full: html, text
    New datatype for Gingeras GIS project
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.74 lines changed: 1, context: html, text, full: html, text
    fix description for HAL
  • 1.73 lines changed: 25, context: html, text, full: html, text
    add descriptions for terms recently added by HA
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.157 lines changed: 6, context: html, text, full: html, text
    added comment about quality scores
  • 1.156 lines changed: 1, context: html, text, full: html, text
    fix typo
  • 1.155 lines changed: 23, context: html, text, full: html, text
    deal with +/- in cell type
• src/hg/hgBlat/hgBlat.c
  • 1.125 lines changed: 3, context: html, text, full: html, text
    prevent apache cgi timeout by outputting something, also fixed reversed closing tags
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Set of organisms for sacCer2 orthologs
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.473 lines changed: 46, context: html, text, full: html, text
    Added dgvUi: filter items by publication reference.
• src/hg/hgTracks/encode.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Added filters to encodePeak tracks that work in the composite multi-view.
• src/hg/hgTracks/simpleTracks.c
  • 1.63 lines changed: 43, context: html, text, full: html, text
    Added dgvMethods: filter items by publication reference.
  • 1.62 lines changed: 1, context: html, text, full: html, text
    inadvertently commited timing on
  • 1.61 lines changed: 2, context: html, text, full: html, text
    Hopefully this is a better error message - I ran into this a few times with new encode track types
• src/hg/hgc/hgc.c
  • 1.1509 lines changed: 2, context: html, text, full: html, text
    Added processing for Illumina 1M array.
• src/hg/inc/jksql.h
  • 1.80 lines changed: 1, context: html, text, full: html, text
    sc->conn->db can be NULL -- when printing out monitor messages, use 'db=?' instead of NULL.
  • 1.79 lines changed: 1, context: html, text, full: html, text
    public functions should conform to naming conventions
  • 1.78 lines changed: 3, context: html, text, full: html, text
    allow addDatabaseFields() function to be seen external for use in joinerCheck
• src/hg/inc/versionInfo.h
  • 1.141 lines changed: 1, context: html, text, full: html, text
    "New version number v201"
• src/hg/instinct/bioIntegrator/bioIntDb.c
  • 1.5 lines changed: 27, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDb.sql
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDriver.c
  • 1.11 lines changed: 91, context: html, text, full: html, text
    updated
  • 1.10 lines changed: 139, context: html, text, full: html, text
    updated
  • 1.9 lines changed: 20, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntDriver.h
  • 1.10 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.9 lines changed: 2, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioIntegrator.c
  • 1.14 lines changed: 26, context: html, text, full: html, text
    updated
  • 1.13 lines changed: 30, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/populateDb.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 325, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 12, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 512, context: html, text, full: html, text
    updated
• src/hg/instinct/xRefLookup/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    adding simple script for steve to access kgXref table
• src/hg/instinct/xRefLookup/xRefLookup.c
  • 1.1 lines changed: 49, context: html, text, full: html, text
    adding simple script for steve to access kgXref table
• src/hg/lib/dgv.as
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Corrected description of thickStart and thickEnd.
• src/hg/lib/hdb.c
  • 1.395 lines changed: 6, context: html, text, full: html, text
    added dbProfile as the prefered name for a trackDb database profile setting
• src/hg/lib/hgFind.c
  • 1.217 lines changed: 4, context: html, text, full: html, text
    When testing xrefTable existence, use sqlTableExists instead of hTableOrSplitExists in order to support an xrefTable in some other db. hTableOrSplitExists actually uses a cached 'show tables' from the current db.
  • 1.216 lines changed: 2, context: html, text, full: html, text
    Bugfix: addPslResultToHgp: strip initial all_ from tableName (we used to use the lowercased GenBank type!).
  • 1.215 lines changed: 193, context: html, text, full: html, text
    Refactored findMrnaPos and its callees, and added support for intronEst.
• src/hg/lib/hui.c
  • 1.158 lines changed: 97, context: html, text, full: html, text
    Added filters to encodePeak tracks that work in the composite multi-view.
• src/hg/lib/jksql.c
  • 1.127 lines changed: 12, context: html, text, full: html, text
    sc->conn->db can be NULL -- when printing out monitor messages, use 'db=?' instead of NULL.
  • 1.126 lines changed: 2, context: html, text, full: html, text
    public functions should conform to naming conventions
  • 1.125 lines changed: 1, context: html, text, full: html, text
    allow addDatabaseFields() function to be seen external for use in joinerCheck
• src/hg/makeDb/doc/dm2.txt
  • 1.23 lines changed: 5, context: html, text, full: html, text
    bdtnpChipper (old change): corrected regex, found another subtrack.
• src/hg/makeDb/doc/dm3.txt
  • 1.24 lines changed: 116, context: html, text, full: html, text
    Added bdtnpChipper (liftOver from dm2).
• src/hg/makeDb/doc/hg17.txt
  • 1.119 lines changed: 14, context: html, text, full: html, text
    Remove thin tails from DGV (SAB feedback).
• src/hg/makeDb/doc/hg18.txt
  • 1.351 lines changed: 1, context: html, text, full: html, text
    Fixed the 2nd part of a typo in omimGene build.
  • 1.350 lines changed: 160, context: html, text, full: html, text
    Remove thin tails from DGV (SAB feedback). Added 5 tracks from Human Genome Diversity Project.
  • 1.349 lines changed: 1, context: html, text, full: html, text
    Corrected a typo.
  • 1.348 lines changed: 13, context: html, text, full: html, text
    Updated omimGene build process to include "NR_..." related omim entries to omimToKnownCanonical.
  • 1.347 lines changed: 4, context: html, text, full: html, text
    Updated omimGene build process to correct a typo.
  • 1.346 lines changed: 7, context: html, text, full: html, text
    Revised and added more omimGene entries that are related to "NR_..." RefSeqs.
• src/hg/makeDb/doc/mm9.txt
  • 1.90 lines changed: 54, context: html, text, full: html, text
    Updated komp (now called IKMC) w/new data from Carol Bult.
• src/hg/makeDb/genbank/etc/hgofbeta-dbload
  • 1.1 lines changed: 24, context: html, text, full: html, text
    added genbank updates for hgofbeta
• src/hg/makeDb/genbank/etc/hgofbeta.crontab
  • 1.1 lines changed: 16, context: html, text, full: html, text
    added genbank updates for hgofbeta
• src/hg/makeDb/genbank/etc/hgofbeta.dbs
  • 1.1 lines changed: 76, context: html, text, full: html, text
    added genbank updates for hgofbeta
• src/hg/makeDb/genbank/etc/hgwbeta-dbload
  • 1.41 lines changed: 1, context: html, text, full: html, text
    use /data/tmp for tmp files during loads
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.95 lines changed: 5, context: html, text, full: html, text
    remove comments out databases
• src/hg/makeDb/genbank/etc/hgwdev-dbload
  • 1.31 lines changed: 1, context: html, text, full: html, text
    use /data/tmp for tmp files during loads
• src/hg/makeDb/genbank/etc/rr-dbload
  • 1.33 lines changed: 1, context: html, text, full: html, text
    use /data/tmp for tmp files during loads
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.80 lines changed: 5, context: html, text, full: html, text
    remove comments out databases
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • 1.23 lines changed: 21, context: html, text, full: html, text
    fixed bug were previous build partial matches were being excluded from current build
• src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
  • 1.1 lines changed: 81, context: html, text, full: html, text
    Created hgGetNrOmimGene.c. This program is needed during omimGene build. The old version MySQL on hgwdev does not support the "NOT IN (....)" syntax, hence a C program is needed to provide the needed function.
• src/hg/makeDb/hgGetNrOmimGene/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Created makefile.
• src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    remove duplicated rows caused by using a subset of the data in the LSSNP database
• src/hg/makeDb/schema/all.joiner
  • 1.695 lines changed: 1, context: html, text, full: html, text
    tightened up the minCheck for this rule
  • 1.694 lines changed: 2, context: html, text, full: html, text
    Added restriction enzyme track tables to tables ignored.
  • 1.693 lines changed: 14, context: html, text, full: html, text
    Adding sacCer2 rules
  • 1.692 lines changed: 12, context: html, text, full: html, text
    Changing up the lsSnpPdb rules with the consulting input from Markd
  • 1.691 lines changed: 2, context: html, text, full: html, text
    Added oryLat2 to human proteins checks.
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • 1.40 lines changed: 1, context: html, text, full: html, text
    public functions should conform to naming conventions
  • 1.39 lines changed: 18, context: html, text, full: html, text
    Do not use sqlAllFields() in jksql.c since it doesn't know about databasesIgnored
• src/hg/makeDb/trackDb/ccdsGene.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changed again per Rachel's request
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changed to the correct name (we had been using the wrong name!)
• src/hg/makeDb/trackDb/human/affyHumanExon.html
  • 1.6 lines changed: 23, context: html, text, full: html, text
    Need to add this back too
  • 1.5 lines changed: 23, context: html, text, full: html, text
    Top-level affy all-exon supertrack. Removed HTML and entries in human/mouse/rat subdirs.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed a typo
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Forgot the <LI>.
  • 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: 20, context: html, text, full: html, text
    Added details for affy all human exon track.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.6 lines changed: 75, context: html, text, full: html, text
    New ref for NA18507, new links, reformatting and a couple wording tweaks.
  • 1.5 lines changed: 11, context: html, text, full: html, text
    Fixed refs to conform to standard format.
• src/hg/makeDb/trackDb/human/hg18/snpArray.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    point Illumina 1M Duo to actual product sheet
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.377 lines changed: 1, context: html, text, full: html, text
    a tweak to the subgroup to which the multiz44way belongs -- untying it from the vert clade
  • 1.376 lines changed: 1, context: html, text, full: html, text
    adding another ID type to snpArray search
  • 1.375 lines changed: 9, context: html, text, full: html, text
    Added search term for Illumina 1M array.
  • 1.374 lines changed: 9, context: html, text, full: html, text
    Oops, PSU didn't do the sequencing of NA18507; dropping the SOLiD NA18507 subtrack, at least until I can get more info about it. Thanks Belinda!
  • 1.373 lines changed: 4, context: html, text, full: html, text
    pgSnp: if I were not making slides for the SAB meeting I would not be spending so much time on capitalization and punctuation, but here we are.
  • 1.372 lines changed: 9, context: html, text, full: html, text
    pgSnp: New info from Belinda (thanks!) and a couple more label tweaks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.164 lines changed: 6, context: html, text, full: html, text
    Turned on p-value filtering (peaks) on each of the big wgEncode supertracks.
  • 1.163 lines changed: 122, context: html, text, full: html, text
    re-doing Riken Cage
  • 1.162 lines changed: 16, context: html, text, full: html, text
    fix H9ES-AFP+/H9ES-AFP- tracks
  • 1.161 lines changed: 6, context: html, text, full: html, text
    color some HA MethylSeq sub-tracks
  • 1.160 lines changed: 6, context: html, text, full: html, text
    added wiggle ranges after load
  • 1.159 lines changed: 275, context: html, text, full: html, text
    new tracks from RIKEN
  • 1.158 lines changed: 8, context: html, text, full: html, text
    pairedTagAlign not implemented yet
  • 1.157 lines changed: 60, context: html, text, full: html, text
    new data for GIS PET GM12878
  • 1.156 lines changed: 61, context: html, text, full: html, text
    new data for GIS PET GM12878
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.1 lines changed: 93, context: html, text, full: html, text
    first version of caltech doco
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    minor tweaks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.3 lines changed: 13, context: html, text, full: html, text
    minor tweaks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.438 lines changed: 13, context: html, text, full: html, text
    Put this back in for missing RR track.
• src/hg/makeDb/trackDb/mouse/komp.html
  • 1.4 lines changed: 45, context: html, text, full: html, text
    komp (IKMC): updates from Carol Bult.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.499 lines changed: 12, context: html, text, full: html, text
    fixed search for mgc and orfeome
• src/hg/utils/automation/HgAutomate.pm
  • 1.21 lines changed: 13, context: html, text, full: html, text
    Restore memk to the list of clusters to use
• src/inc/common.h
  • 1.146 lines changed: 20, context: html, text, full: html, text
    Adding byte-swapping routines for floating point items. Using them in the bigWig read routines.
• src/inc/net.h
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Adding FTP support for udc cache lib
• src/inc/udc.h
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Adding FTP support for udc cache lib
• src/lib/bbiRead.c
  • 1.9 lines changed: 24, context: html, text, full: html, text
    Adding byte-swapping routines for floating point items. Using them in the bigWig read routines.
• src/lib/bwgQuery.c
  • 1.19 lines changed: 6, context: html, text, full: html, text
    Adding byte-swapping routines for floating point items. Using them in the bigWig read routines.
• src/lib/common.c
  • 1.127 lines changed: 75, context: html, text, full: html, text
    Adding byte-swapping routines for floating point items. Using them in the bigWig read routines.
• src/lib/net.c
  • 1.68 lines changed: 173, context: html, text, full: html, text
    Adding FTP support for udc cache lib
• src/lib/twoBit.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Fixing bug where isSwapped flag got overwritten false.
• src/lib/udc.c
  • 1.13 lines changed: 55, context: html, text, full: html, text
    Adding FTP support for udc cache lib
• src/oneShot/test/test.c
  • 1.35 lines changed: 3, context: html, text, full: html, text
    Testing floating point binary representation.
• src/utils/qa/copyExtSeqRows.csh
  • 1.2 lines changed: 4, context: html, text, full: html, text
    cleaned up an ouput comment to make it specific to a certain type of run (thanks Brooke!)
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.16 lines changed: 3, context: html, text, full: html, text
    need to create sub-dirs as well
  • 1.15 lines changed: 25, context: html, text, full: html, text
    new system to remember the history of review reports
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.48 lines changed: 3, context: html, text, full: html, text
    v201 final build
• src/utils/qa/weeklybld/cvs-reports-delta
  • 1.8 lines changed: 1, context: html, text, full: html, text
    new system to remember the history of review reports
• src/utils/wigSort/makefile
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Seems to work.
  • 1.1 lines changed: 14, context: html, text, full: html, text
    expected.wig
• src/utils/wigSort/test.wig
  • 1.1 lines changed: 494, context: html, text, full: html, text
    expected.wig
• src/utils/wigSort/wigSort.c
  • 1.1 lines changed: 222, context: html, text, full: html, text
    expected.wig

• lines changed: 4556
• files changed: 73