CVS changes by file

review to branch (2009-09-09 to 2009-09-15) v215

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.78 lines changed: 1, context: html, text, full: html, text
    fix typo in multiz of sulfIslaM_16_4
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.193 lines changed: 1, context: html, text, full: html, text
    fix validator for pairedTagAlign to catch sequence errors
• src/hg/hgTracks/bamTrack.c
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes).
• src/hg/hgTracks/chromGraphTrack.c
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Use imgTrackAddMapItem in case map items need to be split between slices
• src/hg/hgTracks/cytoBandTrack.c
  • 1.10 lines changed: 13, context: html, text, full: html, text
    Make chrom ideo map no longer directly clickable, as per Jim's plan. Instead, by setting class=cytoBand, javascript will control clicking.
• src/hg/hgTracks/expRatioTracks.c
  • 1.44 lines changed: 12, context: html, text, full: html, text
    Use imgTrackAddMapItem in case map items need to be split between slices
• src/hg/hgTracks/hgTracks.c
  • 1.1597 lines changed: 1, context: html, text, full: html, text
    Make curImgTrack global to use imgTrackAddMapItem in case map items need to be split between slices
• src/hg/hgTracks/imageV2.c
  • 1.10 lines changed: 41, context: html, text, full: html, text
    Added imgTrackAddMapItem to let the imgTrack divide map items between slices.
• src/hg/hgTracks/imageV2.h
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Added imgTrackAddMapItem to let the imgTrack divide map items between slices.
• src/hg/hgTracks/makefile
  • 1.87 lines changed: 1, context: html, text, full: html, text
    add LOWELAB_DEFS to link with lowe lab specific code only when LOWELAB environment variable is defined
• src/hg/hgTracks/simpleTracks.c
  • 1.102 lines changed: 22, context: html, text, full: html, text
    Added color methods for the REST track.
  • 1.101 lines changed: 35, context: html, text, full: html, text
    Use imgTrackAddMapItem in case map items need to be split between slices. Experiment with making short map items for full bed.
• src/hg/hgTracks/variation.c
  • 1.144 lines changed: 6, context: html, text, full: html, text
    Use imgTrackAddMapItem in case map items need to be split between slices
• src/hg/hgc/bamClick.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes).
• src/hg/inc/bamFile.h
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes).
• src/hg/inc/jksql.h
  • 1.85 lines changed: 3, context: html, text, full: html, text
    added function to get list of profile names for Fan
• src/hg/inc/jsHelper.h
  • 1.9 lines changed: 6, context: html, text, full: html, text
    make stripRegEx a public function
• src/hg/inc/versionInfo.h
  • 1.155 lines changed: 1, context: html, text, full: html, text
    "New version number v215"
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.71 lines changed: 6, context: html, text, full: html, text
    fixed off-by-one error in heatmap display
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.18 lines changed: 20, context: html, text, full: html, text
    added gbm vs norm affy
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.21 lines changed: 31, context: html, text, full: html, text
    Updated descriptions
• src/hg/instinct/hgPathways/hgCircleMaps.c
  • 1.15 lines changed: 62, context: html, text, full: html, text
    Fixed gene sorting in cgi, need to add to interface
• src/hg/instinct/hgPathways/hgPathways.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed gene sorting in cgi, need to add to interface
• src/hg/instinct/hgPathways/hgPathwaysFrontend/js/hgHeatPath.js
  • 1.13 lines changed: 21, context: html, text, full: html, text
    Fixed gene sorting in cgi, need to add to interface
• src/hg/instinct/webUserAdmin/webUserAdmin.c
  • 1.11 lines changed: 23, context: html, text, full: html, text
    Added "re-enter password" function for both signup and change password tasks.
• src/hg/js/hgTracks.js
  • 1.40 lines changed: 277, context: html, text, full: html, text
    Make the chrom image draggable. Note click gives new position, same window size. Ctrl- gives cytoBand.
  • 1.39 lines changed: 179, context: html, text, full: html, text
    use 'not-allowed' cursor when user drags out of image (suggested by braney); add lots of imageV2 specific code (currently only active in larrym's tree)
• src/hg/js/hui.js
  • 1.34 lines changed: 9, context: html, text, full: html, text
    Handle radio buttons in dependent cfg settings
  • 1.33 lines changed: 17, context: html, text, full: html, text
    Fixed bug which had independent boolshad hidden checkbox support fields erroneously updated by subtrack dependent cfg logic
• src/hg/lib/bamFile.c
  • 1.7 lines changed: 31, context: html, text, full: html, text
    Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes).
• src/hg/lib/jksql.c
  • 1.135 lines changed: 13, context: html, text, full: html, text
    added function to get list of profile names for Fan
• src/hg/lib/jsHelper.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    make stripRegEx a public function
• src/hg/logCrawl/accessLogFilter/accessLogFilter.c
  • 1.1 lines changed: 74, context: html, text, full: html, text
    Seems to work. You need to edit source code to change filter parameters though.
• src/hg/logCrawl/accessLogFilter/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work. You need to edit source code to change filter parameters though.
• src/hg/makeDb/doc/hg18.txt
  • 1.382 lines changed: 13, context: html, text, full: html, text
    updated lsSnpPdb
• src/hg/makeDb/doc/monDom5.txt
  • 1.14 lines changed: 115, context: html, text, full: html, text
    Added chain/net make quasi-instructions.
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.118 lines changed: 4, context: html, text, full: html, text
    added refseq problem
  • 1.117 lines changed: 3, context: html, text, full: html, text
    added to-do item
• src/hg/makeDb/genbank/etc/genbank.tbls
  • 1.13 lines changed: 3, context: html, text, full: html, text
    added ccds tables to genbank table list (thanks B0b)
• src/hg/makeDb/genbank/etc/hgdownload.crontab
  • 1.20 lines changed: 4, context: html, text, full: html, text
    changed frequence of hgdownload rsync to reduce number of email messages
• src/hg/makeDb/genbank/etc/hgwbeta.crontab
  • 1.18 lines changed: 2, context: html, text, full: html, text
    fixed error in cron date specs (there are *not* 8 days in a week)
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • 1.17 lines changed: 2, context: html, text, full: html, text
    fixed error in cron date specs (there are *not* 8 days in a week)
• src/hg/makeDb/genbank/makefile
  • 1.16 lines changed: 6, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/ccds/ccdsImportStep
  • 1.2 lines changed: 1, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/dbload/gbBuildState.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    change maxShrinkage safety net minimum size
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • 1.50 lines changed: 96, context: html, text, full: html, text
    fixed bug where CCDS update failes if UCSC genes doesn't exist. Delete obsolte mgc-related code
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.48 lines changed: 7, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/lsSnpPdb/lsSnpPdbDbLoadStep
  • 1.1 lines changed: 60, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/lsSnpPdb/lsSnpPdbDownloadStep
  • 1.1 lines changed: 63, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/lsSnpPdb/makefile
  • 1.1 lines changed: 10, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/genbank/src/makefile
  • 1.11 lines changed: 2, context: html, text, full: html, text
    added scripts for auto update lsSnpPdb
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.88 lines changed: 4, context: html, text, full: html, text
    added gbm vs norm affy
  • 1.87 lines changed: 11, context: html, text, full: html, text
    updated harvard cgh dataset
• src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
  • 1.4 lines changed: 27, context: html, text, full: html, text
    allow loading from compressed files
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • 1.15 lines changed: 3, context: html, text, full: html, text
    fixup for broken tables that give NULL for every column
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.417 lines changed: 1, context: html, text, full: html, text
    Added chr21 to bamNA12878 -- remote access to 1000Genomes DCC using (for now) samtools' support for FTP.
• src/hg/makeDb/trackDb/human/hg18/trackDb.tcga1.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    added logicalDb line to mskcc1x1m
  • 1.19 lines changed: 1, context: html, text, full: html, text
    
  • 1.18 lines changed: 291, context: html, text, full: html, text
    update genome browser trackDb file for tcga1 control acccess data
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.520 lines changed: 18, context: html, text, full: html, text
    added a hyphen in All-Exon Array longLabels for UW tracks
  • 1.519 lines changed: 527, context: html, text, full: html, text
    Added 10 resubmissions and 1 new submission for Duke,UNC,UTA
  • 1.518 lines changed: 17, context: html, text, full: html, text
    removed some "release alpha" lines
  • 1.517 lines changed: 19, context: html, text, full: html, text
    removed release alphas from HAIB Methyl-seq track
  • 1.516 lines changed: 6, context: html, text, full: html, text
    removed release alphas from the HAIB Methyl27 track
  • 1.515 lines changed: 3, context: html, text, full: html, text
    removed release alphas from ENCODE Common Cell CNV track in preparation for release
• src/hg/makeDb/trackDb/lowelab/allpredictions.html
  • 1.1 lines changed: 27, context: html, text, full: html, text
    reword and reformat original version created by Andrew
• src/hg/makeDb/trackDb/lowelab/cddInfo.html
  • 1.1 lines changed: 17, context: html, text, full: html, text
    make some wordings and format changes from Andrew's original version
• src/hg/makeDb/trackDb/lowelab/sulfIsla_L_S_2_15/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_L_S_2_15/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_14_25/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_14_25/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_27/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_27/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_4/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_4/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    New multiz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_G_57_14/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_G_57_14/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_N_15_51/multizSulfolobes.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_N_15_51/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add multiz
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.86 lines changed: 6, context: html, text, full: html, text
    change color for lowelabTranscripts track
  • 1.85 lines changed: 11, context: html, text, full: html, text
    adjust labels of gene predictions and operons tracks; change ultra-conserved track to dense display mode
  • 1.84 lines changed: 10, context: html, text, full: html, text
    change color of operon tracks
• src/hg/makeDb/trackDb/mouse/mm9/REST.html
  • 1.2 lines changed: 11, context: html, text, full: html, text
    Updated per data provider and added Display Convention section.
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Created REST.html.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.61 lines changed: 8, context: html, text, full: html, text
    changed labels on hg18 chain/nets from orgName db
  • 1.60 lines changed: 24, context: html, text, full: html, text
    moved all searches to bottom, as per usual practice
  • 1.59 lines changed: 20, context: html, text, full: html, text
    Added REST track.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.39 lines changed: 34, context: html, text, full: html, text
    moved all searches to bottom, as per usual practice
• src/hg/oneShot/freen/freen.c
  • 1.89 lines changed: 1, context: html, text, full: html, text
    Seeing if preinitializing things to zero gets rid of an off-by-one problem.
• src/hg/tcga/bamFilter/bamFilter.c
  • 1.4 lines changed: 32, context: html, text, full: html, text
    proper bed reading
  • 1.3 lines changed: 11, context: html, text, full: html, text
    added quality filter
  • 1.2 lines changed: 39, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 201, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamFilter/makefile
  • 1.1 lines changed: 23, context: html, text, full: html, text
    initial commit
• src/hg/tcga/scripts/DataTypes.py
  • 1.7 lines changed: 57, context: html, text, full: html, text
    fixed a few bugs
• src/hg/tcga/scripts/GenericDataType.py
  • 1.7 lines changed: 6, context: html, text, full: html, text
    fixed a few bugs
• src/hg/tcga/scripts/processData.py
  • 1.10 lines changed: 16, context: html, text, full: html, text
    fixed a few bugs
• src/inc/apacheLog.h
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Adding functions involving timestamps to apacheLog.
• src/inc/common.mk
  • 1.70 lines changed: 1, context: html, text, full: html, text
    Backing out a change I didn't mean to commit.
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Adding functions involving timestamps to apacheLog.
  • 1.68 lines changed: 24, context: html, text, full: html, text
    include lowe lab specific definitions and add LOWELAB_DEFS to gcc statement only when LOWELAB environment variable is defined
• src/lib/apacheLog.c
  • 1.5 lines changed: 29, context: html, text, full: html, text
    Checking end coordinate for off-chromosome.
• src/lib/bbiWrite.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Checking end coordinate for off-chromosome.
• src/makefile
  • 1.63 lines changed: 1, context: html, text, full: html, text
    adding bedClip to user utils
• src/utils/bedClip/bedClip.c
  • 1.1 lines changed: 85, context: html, text, full: html, text
    The bedClip utility seems to work.
• src/utils/bedClip/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    The bedClip utility seems to work.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.15 lines changed: 6, context: html, text, full: html, text
    Removing nonfunctional clip option.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Removing nonfunctional clip option.
• src/utils/qa/alertBqueue.csh
  • 1.11 lines changed: 3, context: html, text, full: html, text
    added donna to email list for monthly reminder
• src/utils/qa/checkSync.csh
  • 1.18 lines changed: 2, context: html, text, full: html, text
    put GENBANK variable in central place, to simplify finding the genbank tablelist. changed checkSync.csh to use it
• src/utils/qa/countRows.csh
  • 1.10 lines changed: 8, context: html, text, full: html, text
    added RR results, though not in real time
  • 1.9 lines changed: 3, context: html, text, full: html, text
    removed some debugging statements
  • 1.8 lines changed: 57, context: html, text, full: html, text
    simplified to remove extra processing, including dependence on writing files. fixed so actual rowcount is printed, instead of message that dev and beta agree
• src/utils/qa/getRRdumpfile.csh
  • 1.5 lines changed: 19, context: html, text, full: html, text
    adjusted getRR to look in the dumps for dev and beta values, too. fixed getTableSize.csh to use them properly
• src/utils/qa/getRRtableStatus.csh
  • 1.13 lines changed: 16, context: html, text, full: html, text
    adjusted getRR to look in the dumps for dev and beta values, too. fixed getTableSize.csh to use them properly
• src/utils/qa/getTableSize.csh
  • 1.3 lines changed: 11, context: html, text, full: html, text
    adjusted getRR to look in the dumps for dev and beta values, too. fixed getTableSize.csh to use them properly
• src/utils/qa/qaConfig.bash
  • 1.4 lines changed: 1, context: html, text, full: html, text
    put GENBANK variable in central place, to simplify finding the genbank tablelist. changed checkSync.csh to use it
• src/utils/qa/qaConfig.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    put GENBANK variable in central place, to simplify finding the genbank tablelist. changed checkSync.csh to use it
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.23 lines changed: 30, context: html, text, full: html, text
    fixing cvs-reports with correct by tag sandbox on fast local disk
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.78 lines changed: 3, context: html, text, full: html, text
    v215 final build
  • 1.77 lines changed: 1, context: html, text, full: html, text
    fixing cvs-reports with fast local disk
• src/utils/qa/weeklybld/cvs-reports-delta
  • 1.9 lines changed: 13, context: html, text, full: html, text
    fixing cvs-reports with correct by tag sandbox on fast local disk

• lines changed: 4269
• files changed: 97