All File Changes

v297_base to v298_preview (2014-03-17 to 2014-03-24) v298

• src/hg/autoSql/autoSql.c
  • lines changed 3, context: html, text, full: html, text
    Correcting -defaultZero behavior on fixed size char arrays.
• src/hg/autoSql/foo.c
  • lines changed 270, context: html, text, full: html, text
    Correcting -defaultZero behavior on fixed size char arrays.
  • lines changed 270, context: html, text, full: html, text
    Oops did not mean to commit this.
• src/hg/encode3/eap/README
  • lines changed 30, context: html, text, full: html, text
    Improving README
  • lines changed 4, context: html, text, full: html, text
    Adding a little more information about the tempDir. Also describing eapMetaSync.
• src/hg/encode3/eap/eapAddStep/eapAddStep.c
  • lines changed 18, context: html, text, full: html, text
    Adding new eap_phantom_peak_stats step.
  • lines changed 60, context: html, text, full: html, text
    Adding description fields to input and output.
  • lines changed 14, context: html, text, full: html, text
    Adding descriptions.
• src/hg/encode3/eap/eapFinish/eapFinish.c
  • lines changed 218, context: html, text, full: html, text
    Adding new eap_phantom_peak_stats step.
  • lines changed 3, context: html, text, full: html, text
    Removing debugging statements.
  • lines changed 76, context: html, text, full: html, text
    Adding finishing on statistical steps.
• src/hg/encode3/eap/eapFreen/eapFreen.c
  • lines changed 121, context: html, text, full: html, text
    Oh no, eapFreen serves a useful function! Deprecating a bunch of files that pipeline made using wrong inputs.
  • lines changed 91, context: html, text, full: html, text
    eapFreen starts testing posts of JSON. Passwords scribbled in source before commit.
  • lines changed 38, context: html, text, full: html, text
    Freen turns it's attention from Stanford metadata submission to UCSC data submission via script.
• src/hg/encode3/eap/eapMetaSync/eapMetaSync.c
  • lines changed 254, context: html, text, full: html, text
    Code to sync pipeline with Stanford starting up.
  • lines changed 120, context: html, text, full: html, text
    Adding sync of eapStep.
• src/hg/encode3/eap/eapMetaSync/makefile
  • lines changed 4, context: html, text, full: html, text
    Code to sync pipeline with Stanford starting up.
• src/hg/encode3/eap/eapMetaSync/step.json
  • lines changed 30, context: html, text, full: html, text
    Code to sync pipeline with Stanford starting up.
• src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c
  • lines changed 90, context: html, text, full: html, text
    Moving json writing routines from eapRunAddJson to library.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 338, context: html, text, full: html, text
    Adding new eap_phantom_peak_stats step.
  • lines changed 5, context: html, text, full: html, text
    Removing debugging statements.
  • lines changed 93, context: html, text, full: html, text
    Adding scheduleDnaseStats. Getting rid of now obsolete scheduleReplicatedPeaks.
• src/hg/encode3/eap/eapToHub/eapToHub.c
  • lines changed 102, context: html, text, full: html, text
    Fixing minor mismatches, mostly pluralization issues, in symbols in trackDb.ra. It now makes a loadable hub with all the intended data as far as I can tell. It still needs a _lot_ of polishing though!
  • lines changed 391, context: html, text, full: html, text
    Adding table and fastq-file-list output
  • lines changed 26, context: html, text, full: html, text
    Displaying spot score.
  • lines changed 84, context: html, text, full: html, text
    Adding green background color to first replicate to separate replicates.
• src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c
  • lines changed 9, context: html, text, full: html, text
    Adding redoPriority to software updates.
• src/hg/encode3/eap/inc/eapDb.h
  • lines changed 78, context: html, text, full: html, text
    Adding eapPhantomPeakStats table, and eapSwVersion.redoPriority field.
  • lines changed 12, context: html, text, full: html, text
    Adding descriptions to eapStep and metaUuid to all tables we sync with Staford.
• src/hg/encode3/eap/inc/eapGraph.h
  • lines changed 101, context: html, text, full: html, text
    Wrapping a bunch of random access structures and an interface around the graph defined by the eapInput, eapOutput, and eapRun tables.
  • lines changed 24, context: html, text, full: html, text
    Fleshing out eapGraph interface to analysis files and steps.
• src/hg/encode3/eap/inc/eapLib.h
  • lines changed 3, context: html, text, full: html, text
    Defining enum eapRedoPriority
• src/hg/encode3/eap/lib/eapDb.as
  • lines changed 17, context: html, text, full: html, text
    Adding eapPhantomPeakStats table, and eapSwVersion.redoPriority field.
  • lines changed 8, context: html, text, full: html, text
    Adding descriptions to eapStep and metaUuid to all tables we sync with Staford.
• src/hg/encode3/eap/lib/eapDb.c
  • lines changed 206, context: html, text, full: html, text
    Adding eapPhantomPeakStats table, and eapSwVersion.redoPriority field.
  • lines changed 132, context: html, text, full: html, text
    Adding descriptions to eapStep and metaUuid to all tables we sync with Staford.
• src/hg/encode3/eap/lib/eapDb.sql
  • lines changed 18, context: html, text, full: html, text
    Adding eapPhantomPeakStats table, and eapSwVersion.redoPriority field.
  • lines changed 18, context: html, text, full: html, text
    Adding descriptions to eapStep and metaUuid to all tables we sync with Staford.
• src/hg/encode3/eap/lib/eapGraph.c
  • lines changed 352, context: html, text, full: html, text
    Wrapping a bunch of random access structures and an interface around the graph defined by the eapInput, eapOutput, and eapRun tables.
  • lines changed 61, context: html, text, full: html, text
    Fleshing out eapGraph interface to analysis files and steps.
• src/hg/encode3/eap/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Wrapping a bunch of random access structures and an interface around the graph defined by the eapInput, eapOutput, and eapRun tables.
• src/hg/encode3/eap/lib/resetDb
  • lines changed 2, context: html, text, full: html, text
    Adding Rscript and eap_run_phantom_peak_spp
  • lines changed 4, context: html, text, full: html, text
    Adding a few new pieces of software to tracking system.
  • lines changed 3, context: html, text, full: html, text
    Adding a few more pieces of softwrae.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 5, context: html, text, full: html, text
    Version 3 - putting in 1 second delay as default.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 2, context: html, text, full: html, text
    Replacing safef with sqlSafef where appropriate.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 7, context: html, text, full: html, text
    Turning on mail-back
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    Fixing encodedcc URL
  • lines changed 6, context: html, text, full: html, text
    Adding startUploadTime info.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 6, context: html, text, full: html, text
    Improving usage page.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Using submitter's email as opposed to whoever is logged in.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 8, context: html, text, full: html, text
    Added functions for finding or creating wigSpot records.
• src/hg/encode3/encodeDataWarehouse/inc/edwQaWigSpotFromRa.h
  • lines changed 18, context: html, text, full: html, text
    Adding parser for ra files in produced by wig/spot maker.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 212, context: html, text, full: html, text
    Adding edwQaWigSpot table.
  • lines changed 83, context: html, text, full: html, text
    Adding edwQaDnaseSingleStats5m table.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 71, context: html, text, full: html, text
    Added functions for finding or creating wigSpot records.
• src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpot.as
  • lines changed 15, context: html, text, full: html, text
    Removing uniqueness requirement from a fileId index.
  • lines changed 15, context: html, text, full: html, text
    Oops did not mean to commit that.
• src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpotFromRa.c
  • lines changed 136, context: html, text, full: html, text
    Adding parser for ra files in produced by wig/spot maker.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 32, context: html, text, full: html, text
    Adding edwQaWigSpot table.
  • lines changed 23, context: html, text, full: html, text
    Adding edwQaDnaseSingleStats5m table.
  • lines changed 1, context: html, text, full: html, text
    Removing uniqueness requirement from a fileId index.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 490, context: html, text, full: html, text
    Adding edwQaWigSpot table.
  • lines changed 229, context: html, text, full: html, text
    Adding edwQaDnaseSingleStats5m table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 39, context: html, text, full: html, text
    Adding edwQaWigSpot table.
  • lines changed 25, context: html, text, full: html, text
    Adding edwQaDnaseSingleStats5m table.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding wigSpot parser.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Removing edwAddSubscribe, a disused and decaying remenant of a subscription feature.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 1, context: html, text, full: html, text
    Oops, stanford didn't renew their https certificate.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 12, context: html, text, full: html, text
    Being more permissive (warn instead of error) on data type changes within RNA group.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUserTable/rsyncEdwUserTable.c
  • lines changed 14, context: html, text, full: html, text
    User ID created by edwCreateUser in edwUser have uuid defaulted to 0,For this type of user, update the uuid field with the real uuid in the
    Stanford's user json file.
    
  • lines changed 7, context: html, text, full: html, text
    rsyncEdwUserTable.c
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 1, context: html, text, full: html, text
    Adding version to usage.
  • lines changed 99, context: html, text, full: html, text
    Adding sampleBam option
• src/hg/encode3/encodeDataWarehouse/utils/edwBamToWig/edwBamToWig.c
  • lines changed 97, context: html, text, full: html, text
    Might work, but needs a lot of testing.
• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/a.bed
  • lines changed 2, context: html, text, full: html, text
    Little stats program to compute union and intersect seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/b.bed
  • lines changed 3, context: html, text, full: html, text
    Little stats program to compute union and intersect seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/edwComparePeaks.c
  • lines changed 110, context: html, text, full: html, text
    Little stats program to compute union and intersect seems to work.
  • lines changed 4, context: html, text, full: html, text
    Adding iuRatio (intersectSize/unionSize)
• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/expected.ra
  • lines changed 6, context: html, text, full: html, text
    Little stats program to compute union and intersect seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/makefile
  • lines changed 3, context: html, text, full: html, text
    Little stats program to compute union and intersect seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c
  • lines changed 12, context: html, text, full: html, text
    Improving handling of three-peak mergers.
  • lines changed 10, context: html, text, full: html, text
    Fixed bug in midPoint calc. Improved graphic comment.
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c
  • lines changed 1, context: html, text, full: html, text
    Adding version to usage.
• src/hg/hgGene/go.c
  • lines changed 1, context: html, text, full: html, text
    fix a couple of linkout problems with UCSC genes, #12639
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 6, context: html, text, full: html, text
    add links out to neXtProt from human browsers #11888
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 1, context: html, text, full: html, text
    fix a couple of linkout problems with UCSC genes, #12639
• src/hg/hgMirror/hgMirror
  • lines changed 6, context: html, text, full: html, text
    adding a few more tables to hgMirror, refs #11957
  • lines changed 12, context: html, text, full: html, text
    changes after code review refs #12907
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 25, context: html, text, full: html, text
    allow selection of gene name to display on ensGene tracks refs #12870
• src/hg/hgTracks/hgTracks.c
  • lines changed 21, context: html, text, full: html, text
    Since the max arena setting seems to have a bug, we are using a different approach that is probably better anway. -- using RSS instead of DATA for rlimit. This will work with the new glibc malloc for multiple threads.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 73, context: html, text, full: html, text
    allow selection of gene name to display on ensGene tracks refs #12870
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 4, context: html, text, full: html, text
    Update link and add pub citation for Kellis lab TF motifs. By request of Pouya K.
• src/hg/htdocs/ENCODE/encodeTools.html
  • lines changed 64, context: html, text, full: html, text
    Adding ENCODE tools updates per Mike Pazin, refs# 12863
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 10, context: html, text, full: html, text
    Adding a publication per Kate/MikePazin to ENCODE pubs
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 2, context: html, text, full: html, text
    Correcting typos in ENCODE pubsOther.html per code review refs# 12911
• src/hg/htdocs/contacts.html
  • lines changed 5, context: html, text, full: html, text
    Minor edits per code review and Donna's feedback. refs #12921
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 7, context: html, text, full: html, text
    Small edits to help documents about hubs/searaching/stanzas genomes.txt
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 8, context: html, text, full: html, text
    adding one more error message to gbib help doc
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 4, context: html, text, full: html, text
    Code review changes to hgTrackHubHelp page refs# 12911
  • lines changed 2, context: html, text, full: html, text
    Small edits to help documents about hubs/searaching/stanzas genomes.txt
• src/hg/lib/customFactory.c
  • lines changed 23, context: html, text, full: html, text
    Since the max arena setting seems to have a bug, we are using a different approach that is probably better anway. -- using RSS instead of DATA for rlimit. This will work with the new glibc malloc for multiple threads.
• src/hg/lib/spOldNew.as
  • lines changed 6, context: html, text, full: html, text
    adding AS files for tables in the proteome database that didn't havethem.
    
• src/hg/lib/spReactomeEvent.as
  • lines changed 6, context: html, text, full: html, text
    adding AS files for tables in the proteome database that didn't havethem.
    
  • lines changed 2, context: html, text, full: html, text
    oops, fix spelling error in spReactomeEvent field descriptions
• src/hg/lib/spReactomeId.as
  • lines changed 5, context: html, text, full: html, text
    adding AS files for tables in the proteome database that didn't havethem.
    
• src/hg/lib/spVariant.as
  • lines changed 6, context: html, text, full: html, text
    adding AS files for tables in the proteome database that didn't havethem.
    
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 4, context: html, text, full: html, text
    Corrections to factorbook gene alias table. Not essential to push (just a little extra, and all.joiner is appropriately permissive)
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 13, context: html, text, full: html, text
    Added sections for hg19<->felCat5 lift and chain/net refs #12744
• src/hg/makeDb/doc/hg19.txt
  • lines changed 10, context: html, text, full: html, text
    Oops, not all of the snp138Mask files were gzipped. Regenerated allto be safe, then found a better way to background a bunch of gzips.
    refs #12902
    
  • lines changed 46, context: html, text, full: html, text
    Added sections for hg19<->felCat5 lift and chain/net refs #12744
• src/hg/makeDb/doc/hg38.txt
  • lines changed 43, context: html, text, full: html, text
    add full analysis set construction rules refs #12928
• src/hg/makeDb/doc/mm10.txt
  • lines changed 4, context: html, text, full: html, text
    reload fixes multiz60wayFrames table refs #12173
  • lines changed 4, context: html, text, full: html, text
    reload fixes multiz60wayFrames table refs #12173
• src/hg/makeDb/doc/proteins/140122.txt
  • lines changed 4, context: html, text, full: html, text
    update some tables in the uniProt database
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 11, context: html, text, full: html, text
    add instructions to build knownToNextProt
  • lines changed 21, context: html, text, full: html, text
    clean up visigene related stuff #12832
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh
  • lines changed 3, context: html, text, full: html, text
    add mm10 ucsc genes isPCR target to hgcentral
• src/hg/makeDb/trackDb/ensemblGeneScaffold.html
  • lines changed 2, context: html, text, full: html, text
    Adding PMID/PMCID for track reference, refs #12796
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 9, context: html, text, full: html, text
    Removed 'region None' from 8 table objects because they are the only regions defined for table objects in hg19 and this tripped off a bug in track search. Redmine #12946
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUmassDekker5C.ra
  • lines changed 9, context: html, text, full: html, text
    Changing metaData to wgEncodeUmassDekker5C.ra region:none to resolve Track Search bug, refs# 12946
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUmassDekker5C.ra
  • lines changed 9, context: html, text, full: html, text
    Changing metaData to wgEncodeUmassDekker5C.ra region:none to resolve Track Search bug, refs# 12946
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    another track without a regexp, refs #11957
• src/hg/makeDb/trackDb/human/wgRna.html
  • lines changed 1, context: html, text, full: html, text
    Fixing french character on page
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 4, context: html, text, full: html, text
    update gene description characteristics refs #12173
• src/hg/makeDb/trackDb/squirt/ci1/blatCioSav1.html
  • lines changed 7, context: html, text, full: html, text
    fixing links on squirt (ci1) track description pages
• src/hg/makeDb/trackDb/squirt/ci1/jgiGene.html
  • lines changed 14, context: html, text, full: html, text
    fixing links on squirt (ci1) track description pages
• src/hg/makeDb/trackDb/squirt/ci1/snapGene.html
  • lines changed 1, context: html, text, full: html, text
    fixing links on squirt (ci1) track description pages
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    oreganno track needs a regex, trying to make browserbox search faster,refs #11957
    
• src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
  • lines changed 4, context: html, text, full: html, text
    fixing links on zebrafish (danRer6) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer6/gold.html
  • lines changed 2, context: html, text, full: html, text
    fixing links on zebrafish (danRer6) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 16, context: html, text, full: html, text
    fixing links on zebrafish (danRer6) track description pages
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 2, context: html, text, full: html, text
    changes after code review, refs #12907
• src/inc/bigBed.h
  • lines changed 33, context: html, text, full: html, text
    Adding nice usage comment to this C interface to bigBed files.
• src/inc/fq.h
  • lines changed 14, context: html, text, full: html, text
    Adding nice usage comment to this C interface to bigBed files.
• src/inc/jsonWrite.h
  • lines changed 47, context: html, text, full: html, text
    Moving json writing routines from eapRunAddJson to library.
  • lines changed 33, context: html, text, full: html, text
    Renaming dyJson* to jsonWrite* and eliminating isMiddle parameter.
• src/inc/longList.h
  • lines changed 52, context: html, text, full: html, text
    Adding nice usage comment to this C interface to bigBed files.
• src/lib/jsonWrite.c
  • lines changed 101, context: html, text, full: html, text
    Moving json writing routines from eapRunAddJson to library.
  • lines changed 85, context: html, text, full: html, text
    Renaming dyJson* to jsonWrite* and eliminating isMiddle parameter.
• src/lib/longList.c
  • lines changed 100, context: html, text, full: html, text
    longList - this is a way of associating a generic list with a long key.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    longList - this is a way of associating a generic list with a long key.
  • lines changed 1, context: html, text, full: html, text
    Moving json writing routines from eapRunAddJson to library.
• src/parasol/paraHub/paraHub.c
  • lines changed 4, context: html, text, full: html, text
    Added fix to newly broken quit command as elegantly suggested by Galt.
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 1, context: html, text, full: html, text
    Adding version to usage message.
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 52, context: html, text, full: html, text
    Adding stats option.
• src/utils/bigWigMerge/bigWigMerge.c
  • lines changed 36, context: html, text, full: html, text
    Adding inList option.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v298 preview1 refs #12803
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    now using .hg.conf.beta for HGDB_CONF refs #12803
• src/utils/qa/weeklybld/doLiftOverTestRobot.csh
  • lines changed 3, context: html, text, full: html, text
    add email complete message to end of test refs #12803

• lines changed: 6723
• files changed: 150