Commits for kent

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

• 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/inc/eapGraph.h - lines changed 101, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapGraph.c - lines changed 352, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/makefile - lines changed 1, 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!
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 102, context: html, text, full: html, text
• Improving handling of three-peak mergers.
  • src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c - lines changed 12, context: html, text, full: html, text
• Fixed bug in midPoint calc. Improved graphic comment.
  • src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c - lines changed 10, context: html, text, full: html, text
• Oh no, eapFreen serves a useful function! Deprecating a bunch of files that pipeline made using wrong inputs.
  • src/hg/encode3/eap/eapFreen/eapFreen.c - lines changed 121, context: html, text, full: html, text
• Adding table and fastq-file-list output
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 391, context: html, text, full: html, text
• Added fix to newly broken quit command as elegantly suggested by Galt.
  • src/parasol/paraHub/paraHub.c - lines changed 4, context: html, text, full: html, text
• Little stats program to compute union and intersect seems to work.
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/a.bed - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/b.bed - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/edwComparePeaks.c - lines changed 110, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/expected.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/makefile - lines changed 3, context: html, text, full: html, text
• Adding iuRatio (intersectSize/unionSize)
  • src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/edwComparePeaks.c - lines changed 4, context: html, text, full: html, text
• Adding new eap_phantom_peak_stats step.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 18, context: html, text, full: html, text
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 218, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 338, context: html, text, full: html, text
• Displaying spot score.
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 26, context: html, text, full: html, text
• Adding redoPriority to software updates.
  • src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c - lines changed 9, context: html, text, full: html, text
• Adding eapPhantomPeakStats table, and eapSwVersion.redoPriority field.
  • src/hg/encode3/eap/inc/eapDb.h - lines changed 78, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.as - lines changed 17, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.c - lines changed 206, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.sql - lines changed 18, context: html, text, full: html, text
• Fleshing out eapGraph interface to analysis files and steps.
  • src/hg/encode3/eap/inc/eapGraph.h - lines changed 24, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapGraph.c - lines changed 61, context: html, text, full: html, text
• Adding Rscript and eap_run_phantom_peak_spp
  • src/hg/encode3/eap/lib/resetDb - lines changed 2, context: html, text, full: html, text
• Defining enum eapRedoPriority
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 3, context: html, text, full: html, text
• Adding nice usage comment to this C interface to bigBed files.
  • src/inc/bigBed.h - lines changed 33, context: html, text, full: html, text
  • src/inc/fq.h - lines changed 14, context: html, text, full: html, text
  • src/inc/longList.h - lines changed 52, context: html, text, full: html, text
• longList - this is a way of associating a generic list with a long key.
  • src/lib/longList.c - lines changed 100, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
• Adding stats option.
  • src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c - lines changed 52, context: html, text, full: html, text
• Adding inList option.
  • src/utils/bigWigMerge/bigWigMerge.c - lines changed 36, context: html, text, full: html, text
• Adding edwQaWigSpot table.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 212, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 32, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 490, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 39, context: html, text, full: html, text
• Adding wigSpot parser.
  • src/hg/encode3/encodeDataWarehouse/lib/makefile - lines changed 1, context: html, text, full: html, text
• Added functions for finding or creating wigSpot records.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 8, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 71, context: html, text, full: html, text
• Fixing encodedcc URL
  • src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c - lines changed 1, context: html, text, full: html, text
• Turning on mail-back
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 7, context: html, text, full: html, text
• Version 3 - putting in 1 second delay as default.
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c - lines changed 5, context: html, text, full: html, text
• Oops, stanford didn't renew their https certificate.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 1, 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/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 12, context: html, text, full: html, text
• Adding version to usage.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 1, context: html, text, full: html, text
• Adding version to usage.
  • src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c - lines changed 1, context: html, text, full: html, text
• Removing debugging statements.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 3, context: html, text, full: html, text
• Removing debugging statements.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 5, context: html, text, full: html, text
• Improving README
  • src/hg/encode3/eap/README - lines changed 30, context: html, text, full: html, text
• Might work, but needs a lot of testing.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamToWig/edwBamToWig.c - lines changed 97, context: html, text, full: html, text
• Moving json writing routines from eapRunAddJson to library.
  • src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c - lines changed 90, context: html, text, full: html, text
  • src/inc/jsonWrite.h - lines changed 47, context: html, text, full: html, text
  • src/lib/jsonWrite.c - lines changed 101, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
• Code to sync pipeline with Stanford starting up.
  • src/hg/encode3/eap/eapMetaSync/eapMetaSync.c - lines changed 254, context: html, text, full: html, text
  • src/hg/encode3/eap/eapMetaSync/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/eapMetaSync/step.json - lines changed 30, context: html, text, full: html, text
• Adding description fields to input and output.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 60, context: html, text, full: html, text
• Correcting -defaultZero behavior on fixed size char arrays.
  • src/hg/autoSql/autoSql.c - lines changed 3, context: html, text, full: html, text
  • src/hg/autoSql/foo.c - lines changed 270, context: html, text, full: html, text
• Oops did not mean to commit this.
  • src/hg/autoSql/foo.c - lines changed 270, context: html, text, full: html, text
• Adding a little more information about the tempDir. Also describing eapMetaSync.
  • src/hg/encode3/eap/README - lines changed 4, context: html, text, full: html, text
• Renaming dyJson* to jsonWrite* and eliminating isMiddle parameter.
  • src/inc/jsonWrite.h - lines changed 33, context: html, text, full: html, text
  • src/lib/jsonWrite.c - lines changed 85, context: html, text, full: html, text
• Adding descriptions.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 14, context: html, text, full: html, text
• Adding finishing on statistical steps.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 76, context: html, text, full: html, text
• eapFreen starts testing posts of JSON. Passwords scribbled in source before commit.
  • src/hg/encode3/eap/eapFreen/eapFreen.c - lines changed 91, context: html, text, full: html, text
• Adding sync of eapStep.
  • src/hg/encode3/eap/eapMetaSync/eapMetaSync.c - lines changed 120, context: html, text, full: html, text
• Adding scheduleDnaseStats. Getting rid of now obsolete scheduleReplicatedPeaks.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 93, context: html, text, full: html, text
• Adding green background color to first replicate to separate replicates.
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 84, context: html, text, full: html, text
• Adding descriptions to eapStep and metaUuid to all tables we sync with Staford.
  • src/hg/encode3/eap/inc/eapDb.h - lines changed 12, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.as - lines changed 8, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.c - lines changed 132, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.sql - lines changed 18, context: html, text, full: html, text
• Adding a few new pieces of software to tracking system.
  • src/hg/encode3/eap/lib/resetDb - lines changed 4, context: html, text, full: html, text
• Adding startUploadTime info.
  • src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c - lines changed 6, context: html, text, full: html, text
• Using submitter's email as opposed to whoever is logged in.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 2, context: html, text, full: html, text
• Adding edwQaDnaseSingleStats5m table.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 83, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 23, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 229, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 25, context: html, text, full: html, text
• Adding sampleBam option
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 99, context: html, text, full: html, text
• Adding version to usage message.
  • src/utils/bigBedToBed/bigBedToBed.c - lines changed 1, context: html, text, full: html, text
• Adding parser for ra files in produced by wig/spot maker.
  • src/hg/encode3/encodeDataWarehouse/inc/edwQaWigSpotFromRa.h - lines changed 18, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpotFromRa.c - lines changed 136, context: html, text, full: html, text
• Replacing safef with sqlSafef where appropriate.
  • src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c - lines changed 2, 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/eapFreen/eapFreen.c - lines changed 38, context: html, text, full: html, text
• Adding a few more pieces of softwrae.
  • src/hg/encode3/eap/lib/resetDb - lines changed 3, context: html, text, full: html, text
• Removing edwAddSubscribe, a disused and decaying remenant of a subscription feature.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 1, context: html, text, full: html, text
• Removing uniqueness requirement from a fileId index.
  • src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpot.as - lines changed 15, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 1, context: html, text, full: html, text
• Oops did not mean to commit that.
  • src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpot.as - lines changed 15, context: html, text, full: html, text
• Improving usage page.
  • src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c - lines changed 6, context: html, text, full: html, text