File Changes for kent

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/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/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.