Commits for kent

v294_preview to v294_preview2 (2013-12-16 to 2014-01-06) v294

• Adding edwExperiment table.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 70, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 10, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 172, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 11, context: html, text, full: html, text
• Tool to do summary evaluation of qa is about 2/3rds baked.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 415, context: html, text, full: html, text
• Now 3/4 baked.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 71, context: html, text, full: html, text
• First version of overall edwQaEvaluate seems to work.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 59, context: html, text, full: html, text
• Starting to work on 'glue script' based analysis pipeline.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 159, context: html, text, full: html, text
• For ENCODE3 experiments try and figure out subtype of RNA-seq
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 79, context: html, text, full: html, text
• Bumping to version 2 including splitting out RNA-seq into subtypes.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 62, context: html, text, full: html, text
• Making it so unicode escapes just get passed through instead of aborting. There are some of these in the json we're parsing from Stanford in ENCODE.
  • src/lib/jsonParse.c - lines changed 3, context: html, text, full: html, text
• Making edwMakeValidFile used it's own query for fetching intact files since during revalidation it does pay attention to files with error messages.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 16, context: html, text, full: html, text
• Moving in routines to find other file in a pair of paired-ended fastqs to library. Exposing edwBwaIndexPath. Making some eap (encode analysis pipeline) directories.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 19, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 79, context: html, text, full: html, text
• Adding edwQaFail, edwAnalysisJob and edwAnalysisRun tables.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 218, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 43, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 566, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 46, context: html, text, full: html, text
• Moving routines to find other file in a paired-end pair of fastqs to library.
  • src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 41, context: html, text, full: html, text
• Relaxing RNA enrichment threshold.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 1, context: html, text, full: html, text
• Adding edwQaEvaluate to make chain.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
• Making new daemon for analysis jobs.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 12, context: html, text, full: html, text
• Adding script to restart daemons. Needed when daemons hand or hgwdev reboots.
  • src/hg/encode3/encodeDataWarehouse/lib/restartDaemons - lines changed 14, context: html, text, full: html, text
• Analysis scheduler is starting to work.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 89, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/makefile - lines changed 4, context: html, text, full: html, text
• Routine to store analysis results in database is about half baked.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 242, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/makefile - lines changed 4, context: html, text, full: html, text
• Starting to work on json output.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 167, context: html, text, full: html, text
• Seems to mostly work. It is creating valid edwFile records for the output, scheduling validation, and making json output in the draft format we've agreed to with Stanford.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 63, context: html, text, full: html, text
• Adding cgiDictionaryFreeList function.
  • src/inc/cheapcgi.h - lines changed 3, context: html, text, full: html, text
  • src/lib/cheapcgi.c - lines changed 14, context: html, text, full: html, text
• Adding edwFinishAnalysis and edwScheduleAnalysis to make chain.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 2, context: html, text, full: html, text
• Adding edwAnalysisSoftware and edwAnalysisStep tables. Rearranging some things in edwAnalysisRun. Part of getting analysis pipeline going.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 143, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 26, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 422, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 30, context: html, text, full: html, text
• Adding -again option and some debugging
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 40, context: html, text, full: html, text
• Improving error handling when software not in table. Taking out an unnecessary level in json inputs.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 9, context: html, text, full: html, text
• Separated json addition into a separate utility so it can be run after validation so can get license plates.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 223, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 161, context: html, text, full: html, text
• Adding fields to edwAnalysisRun to store fileIds of created files.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 43, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 3, context: html, text, full: html, text
• Adding edwAnalysisJobAdd to library.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 12, context: html, text, full: html, text
• Fixing spelling of aligment, moving addAnalysisJob to libray, and putting bash wrapper around commandLine passed to edwRunDaemon.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 22, context: html, text, full: html, text
• Adding edwAnalysisAddJson to make chain.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
• Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 105, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h - lines changed 1914, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 5, context: html, text, full: html, text
• Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 16, context: html, text, full: html, text
• Fixing spelling of inFilesId field.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 10, context: html, text, full: html, text
• Making it associate a submit record with files created.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 88, context: html, text, full: html, text
• Adding edw@encodedcc.sdsc.edu user (the user for the automatic daemons)
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 2, context: html, text, full: html, text
• Fixing two issues in file name indexes in edwFile. One is making the edwFileName index non-unique, since there may be more than one record that is in progress where the field is still blank. Also making the index on submitFileName bigger so as to reach the unique parts of the file names generated by the analysis pipeline.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 1, context: html, text, full: html, text
• Relaxing DNase enrichment threshold and bumping version.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 3, context: html, text, full: html, text
• Removing edwFinishAnalysis command from generated bash command line - it works better elsewhere.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 2, context: html, text, full: html, text
• Initial software list.
  • src/hg/encode3/encodeDataWarehouse/lib/software.tab - lines changed 14, context: html, text, full: html, text
• Adding initial analysis steps.
  • src/hg/encode3/encodeDataWarehouse/lib/step.tab - lines changed 2, context: html, text, full: html, text
• Oops, plural single mixup.
  • src/hg/encode3/encodeDataWarehouse/lib/step.tab - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/steps.tab - lines changed 2, context: html, text, full: html, text
• Working on sql-generating helper to replace unsorted bams.
  • src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/eapFixSortedBams.c - lines changed 176, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/makefile - lines changed 4, context: html, text, full: html, text
• Adding macs2 steps for dnase
  • src/hg/encode3/encodeDataWarehouse/lib/steps.tab - lines changed 2, context: html, text, full: html, text
• Adding version to usage statement
  • src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 1, context: html, text, full: html, text
• Initializing steps and software tables and grabbing local copy of experiment.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 11, context: html, text, full: html, text
• Forcing unique ness among step and software name fields.
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 2, context: html, text, full: html, text
• Improving comments
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 2, context: html, text, full: html, text
• Adding support for version checker.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 19, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 101, context: html, text, full: html, text
• Adding support for macs2 peak calling on dnase.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 247, context: html, text, full: html, text
• Moving faster md5-checking to library. Calling version checker before adding new record to edwAnalysisRun. Hooking up analysis generated files with analysis submission record.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 49, context: html, text, full: html, text
• Removing stray.
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h - lines changed 1914, context: html, text, full: html, text
• Detecting a strange result that causes crash later.
  • src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/eapFixSortedBams.c - lines changed 4, context: html, text, full: html, text
• Program to make a manifest for submitting to test site that echos a manifest submitted to real site is in place.
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/edwFakeSubmit.c - lines changed 127, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/makefile - lines changed 4, context: html, text, full: html, text
• CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/edwFakeSubmit.c - lines changed 6, context: html, text, full: html, text
• CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/edwFakeManifestFromSubmit.c - lines changed 127, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/edwFakeSubmit.c - lines changed 127, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/makefile - lines changed 1, context: html, text, full: html, text
• CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/edwFakeManifestFromSubmit.c - lines changed 127, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/ENCFF000ABK.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/ENCFF000ABL.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/manifest.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/validated.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/ENCFF000ABM.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/ENCFF000ABN.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/manifest.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/validated.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/ENCFF000ABO.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/manifest.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/validated.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABQ.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABR.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABS.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/manifest.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/validated.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/edwFakeManifestFromSubmit.c - lines changed 127, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/makefile - lines changed 4, context: html, text, full: html, text
• CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/ENCFF000ABK.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/ENCFF000ABL.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/manifest.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test2/validated.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/ENCFF000ABM.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/ENCFF000ABN.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/manifest.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test3/validated.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/ENCFF000ABO.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/manifest.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/validated.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABQ.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABR.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABS.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/manifest.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/validated.txt - lines changed 5, context: html, text, full: html, text
• Refactoring to use an cache and to set up for getting antibody info too.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 183, context: html, text, full: html, text
• Getting immunoprecipitation target from stanford.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 45, context: html, text, full: html, text
• Fixing value return types for jsonBooleanVal and jsonDoubleVal.
  • src/inc/jsonParse.h - lines changed 2, context: html, text, full: html, text
  • src/lib/jsonParse.c - lines changed 2, context: html, text, full: html, text
• Adding edw library.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/makefile - lines changed 1, context: html, text, full: html, text
• Setting up a bunch of users as admins. Adding Seth to the pool.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 8, context: html, text, full: html, text
• Adding uuid and isAdmin fields to edwUser, and assayType and ipTarget to edwExperiment.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 13, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 9, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 38, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 19, context: html, text, full: html, text
• Adding edwPokeFifo to make scheduling to happen sooner.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 24, context: html, text, full: html, text
• Removing an unused subroutine and adding md5 field to output.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 10, context: html, text, full: html, text
• Improving error handling. a trifle.
  • src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/edwFakeManifestFromSubmit.c - lines changed 3, context: html, text, full: html, text
• Moving validation to validation queue instead of analysis queue.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 1, context: html, text, full: html, text
• Making it so that the long term temp files are readable by other users.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 11, context: html, text, full: html, text
• Massaging macs2 output, starting to add hotspot.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 39, context: html, text, full: html, text
• Utility to merge adjacent same-valued bedGraph records seems to work.
  • src/utils/bedGraphPack/bedGraphPack.c - lines changed 112, context: html, text, full: html, text
  • src/utils/bedGraphPack/expected.bedGraph - lines changed 13, context: html, text, full: html, text
  • src/utils/bedGraphPack/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/bedGraphPack/test.bedGraph - lines changed 19, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• Creating new xf view that joine edwFile, edwValidFile, and edwExperiment
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 3, context: html, text, full: html, text
• Adding version number to usage statement.
  • src/utils/bedGraphPack/bedGraphPack.c - lines changed 1, context: html, text, full: html, text
• Utility to compute bam stats seems to work.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 195, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/makefile - lines changed 3, context: html, text, full: html, text
• Adding uniqMapRatio.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 12, context: html, text, full: html, text
• Making option to output a sample bed.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 117, context: html, text, full: html, text
• Adding slListRandomReduce and slListRandomSample for making samples of larger lists.
  • src/inc/obscure.h - lines changed 6, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 42, context: html, text, full: html, text
• Adding edwBamStats parser.
  • src/hg/encode3/encodeDataWarehouse/lib/edwBamFileFromRa.c - lines changed 191, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/makefile - lines changed 1, context: html, text, full: html, text
• Adding uniqueMapRatio to vf and xf view.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 2, context: html, text, full: html, text
• Adding edwBamFile table, and new field, uniqueMapRatio, to edwValidFile.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 82, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 21, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 218, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 23, context: html, text, full: html, text
• Adding stuff to capture uniquely mapping ratio. Adding support for edwBamFile table. Fixing old and bad bug on minus strand when making beds out of bams.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 15, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 98, context: html, text, full: html, text
• Adding up option to easily update change software, and noJob option to avoid launching a job right away, so can look at it in analysis table first. Updating to match changes in edw_run_hotspot. Jumping through some hoops to figure out if a bam file is paired.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 109, context: html, text, full: html, text
• Reworking bam file validation to create edwBamFile table.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 94, context: html, text, full: html, text
• Adding byte and ubyte to the list of numerical types handled.
  • src/utils/raToStructGen/raToStructGen.c - lines changed 4, context: html, text, full: html, text
• Making it consider things sorted by chrom even if strand flips back and forth.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 13, context: html, text, full: html, text
• Oops forgot header file.
  • src/hg/encode3/encodeDataWarehouse/inc/edwBamFileFromRa.h - lines changed 15, context: html, text, full: html, text
• Updating for new parameter to library function.
  • src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c - lines changed 3, context: html, text, full: html, text
• Fixing order of delete.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixUniqueMapRatio/edwFixUniqueMapRatio.c - lines changed 210, context: html, text, full: html, text
• Reducing memory footprint on large BAM files by periodically halving the list we save. Making the u4mSize be a command line option instead of always 4 million.
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 54, context: html, text, full: html, text
• Automatic retrier works in a basic sense.
  • src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c - lines changed 90, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwRetryJob/makefile - lines changed 4, context: html, text, full: html, text
• Automatic retrier works in a basic sense.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
• Making it not add jobs that failed multiple time more than onece. Making it not add a failed job when replacement is in progress.
  • src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c - lines changed 6, context: html, text, full: html, text
• Moving jobResult to lib directory so it can be shared.
  • src/parasol/inc/jobResult.h - lines changed 59, context: html, text, full: html, text
  • src/parasol/lib/jobResult.as - lines changed 18, context: html, text, full: html, text
  • src/parasol/lib/jobResult.c - lines changed 207, context: html, text, full: html, text
  • src/parasol/lib/jobResult.sql - lines changed 21, context: html, text, full: html, text
  • src/parasol/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/para/jobResult.as - lines changed 18, context: html, text, full: html, text
  • src/parasol/para/jobResult.c - lines changed 207, context: html, text, full: html, text
  • src/parasol/para/jobResult.h - lines changed 59, context: html, text, full: html, text
  • src/parasol/para/jobResult.sql - lines changed 21, context: html, text, full: html, text
  • src/parasol/para/makefile - lines changed 1, context: html, text, full: html, text
• Removing some debugging and adding commented out pseudocode.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 13, context: html, text, full: html, text
• Fixing bug that occurred in small minority of files.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 1, context: html, text, full: html, text
• Moving a couple of routines to library so they can be shared.
  • src/parasol/inc/jobResult.h - lines changed 2, context: html, text, full: html, text
  • src/parasol/inc/paraMessage.h - lines changed 6, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 31, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 32, context: html, text, full: html, text
• Adding -wait option to parasol add job to wait for job to finish.
  • src/parasol/parasol/parasol.c - lines changed 42, context: html, text, full: html, text
• Reducing verbosity of waiting message.
  • src/parasol/parasol/parasol.c - lines changed 1, context: html, text, full: html, text
• Changing ownership of batch file to job owner.
  • src/parasol/paraHub/paraHub.c - lines changed 13, context: html, text, full: html, text
• Fixing a divide by zero in mapRatio. Making it warn rather than about on rcc and idat files.
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 7, context: html, text, full: html, text
• Changing daemon in two big ways - making it so it just takes one job at a time from the database, and so that it will do a bursty retry attempt to keep alive through missed database connections without flooding logs.
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c - lines changed 71, context: html, text, full: html, text
• Adding pid field to job tables.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 6, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 30, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 3, context: html, text, full: html, text
• Forking off a new daemon, edwAnalysisJob, intended to run longer lasting things via parasol.
  • src/hg/encode3/encodeDataWarehouse/lib/restartDaemons - lines changed 2, context: html, text, full: html, text
• Upgrading to version 4, see comments top of file for details.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 14, context: html, text, full: html, text