File Changes for kent

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

• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c
  • lines changed 223, 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.
  • lines changed 5, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling of inFilesId field.
  • lines changed 10, context: html, text, full: html, text
    Removing an unused subroutine and adding md5 field to output.
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/makefile
  • lines changed 4, 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/edwFakeManifestFromSubmit/edwFakeManifestFromSubmit.c
  • lines changed 127, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 3, context: html, text, full: html, text
    Improving error handling. a trifle.
• src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/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
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test2/ENCFF000ABL.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test2/manifest.txt
  • lines changed 4, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/validated.txt
  • lines changed 4, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test3/ENCFF000ABM.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test3/ENCFF000ABN.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test3/manifest.txt
  • lines changed 4, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test3/validated.txt
  • lines changed 4, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test4/ENCFF000ABO.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test4/manifest.txt
  • lines changed 3, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 3, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
• src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test4/validated.txt
  • lines changed 3, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 3, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
• src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/ENCFF000ABQ.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test6/ENCFF000ABR.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test6/ENCFF000ABS.fastq.gz
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • 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/test6/manifest.txt
  • lines changed 5, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 5, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
• src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/test6/validated.txt
  • lines changed 5, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 5, 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
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 127, 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 127, 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.
  • lines changed 6, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 127, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
• src/hg/encode3/encodeDataWarehouse/edwFakeSubmit/makefile
  • 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.
  • lines changed 1, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
  • lines changed 4, context: html, text, full: html, text
    CHanging name to edwFakeManifestFromSubmit to make it a bit more specific.
• src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c
  • lines changed 242, context: html, text, full: html, text
    Routine to store analysis results in database is about half baked.
  • lines changed 167, context: html, text, full: html, text
    Starting to work on json output.
  • lines changed 63, 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.
  • lines changed 9, context: html, text, full: html, text
    Improving error handling when software not in table. Taking out an unnecessary level in json inputs.
  • lines changed 161, 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.
  • lines changed 5, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling of inFilesId field.
  • lines changed 88, context: html, text, full: html, text
    Making it associate a submit record with files created.
  • lines changed 49, 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.
  • lines changed 1, context: html, text, full: html, text
    Moving validation to validation queue instead of analysis queue.
• src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/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/edwMakeContaminationQa/edwMakeContaminationQa.c
  • lines changed 3, context: html, text, full: html, text
    Updating for new parameter to library function.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c
  • lines changed 41, 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/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 7, 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/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 16, 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.
  • lines changed 11, context: html, text, full: html, text
    Making it so that the long term temp files are readable by other users.
  • lines changed 12, context: html, text, full: html, text
    Adding uniqMapRatio.
  • lines changed 94, context: html, text, full: html, text
    Reworking bam file validation to create edwBamFile table.
• src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c
  • lines changed 415, context: html, text, full: html, text
    Tool to do summary evaluation of qa is about 2/3rds baked.
  • lines changed 71, context: html, text, full: html, text
    Now 3/4 baked.
  • lines changed 59, context: html, text, full: html, text
    First version of overall edwQaEvaluate seems to work.
  • lines changed 62, context: html, text, full: html, text
    Bumping to version 2 including splitting out RNA-seq into subtypes.
  • lines changed 1, context: html, text, full: html, text
    Relaxing RNA enrichment threshold.
  • lines changed 3, context: html, text, full: html, text
    Relaxing DNase enrichment threshold and bumping version.
  • lines changed 14, context: html, text, full: html, text
    Upgrading to version 4, see comments top of file for details.
• src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c
  • lines changed 90, context: html, text, full: html, text
    Automatic retrier works in a basic sense.
  • lines changed 6, 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/makefile
  • lines changed 4, context: html, text, full: html, text
    Automatic retrier works in a basic sense.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 2, 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.
  • lines changed 71, 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/edwScheduleAnalysis/edwScheduleAnalysis.c
  • lines changed 159, context: html, text, full: html, text
    Starting to work on 'glue script' based analysis pipeline.
  • lines changed 89, context: html, text, full: html, text
    Analysis scheduler is starting to work.
  • lines changed 40, context: html, text, full: html, text
    Adding -again option and some debugging
  • lines changed 22, context: html, text, full: html, text
    Fixing spelling of aligment, moving addAnalysisJob to libray, and putting bash wrapper around commandLine passed to edwRunDaemon.
  • lines changed 16, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 4, context: html, text, full: html, text
    Fixing spelling of inFilesId field.
  • lines changed 2, context: html, text, full: html, text
    Removing edwFinishAnalysis command from generated bash command line - it works better elsewhere.
  • lines changed 247, context: html, text, full: html, text
    Adding support for macs2 peak calling on dnase.
  • lines changed 39, context: html, text, full: html, text
    Massaging macs2 output, starting to add hotspot.
  • lines changed 109, 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.
  • lines changed 13, context: html, text, full: html, text
    Removing some debugging and adding commented out pseudocode.
• src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/makefile
  • lines changed 4, context: html, text, full: html, text
    Analysis scheduler is starting to work.
• src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/eapFixSortedBams.c
  • lines changed 176, context: html, text, full: html, text
    Working on sql-generating helper to replace unsorted bams.
  • lines changed 4, context: html, text, full: html, text
    Detecting a strange result that causes crash later.
• src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/makefile
  • lines changed 4, context: html, text, full: html, text
    Working on sql-generating helper to replace unsorted bams.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixUniqueMapRatio/edwFixUniqueMapRatio.c
  • lines changed 210, context: html, text, full: html, text
    Fixing order of delete.
• src/hg/encode3/encodeDataWarehouse/inc/edwBamFileFromRa.h
  • lines changed 15, context: html, text, full: html, text
    Oops forgot header file.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 19, 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.
  • lines changed 3, context: html, text, full: html, text
    Adding edwAnalysisJobAdd to library.
  • lines changed 19, context: html, text, full: html, text
    Adding support for version checker.
  • lines changed 3, context: html, text, full: html, text
    Adding edwPokeFifo to make scheduling to happen sooner.
  • lines changed 15, 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/encodeDataWarehouse.h
  • lines changed 70, context: html, text, full: html, text
    Adding edwExperiment table.
  • lines changed 218, context: html, text, full: html, text
    Adding edwQaFail, edwAnalysisJob and edwAnalysisRun tables.
  • lines changed 143, context: html, text, full: html, text
    Adding edwAnalysisSoftware and edwAnalysisStep tables. Rearranging some things in edwAnalysisRun. Part of getting analysis pipeline going.
  • lines changed 4, context: html, text, full: html, text
    Adding fields to edwAnalysisRun to store fileIds of created files.
  • lines changed 5, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 1, 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.
  • lines changed 2, context: html, text, full: html, text
    Improving comments
  • lines changed 13, context: html, text, full: html, text
    Adding uuid and isAdmin fields to edwUser, and assayType and ipTarget to edwExperiment.
  • lines changed 82, context: html, text, full: html, text
    Adding edwBamFile table, and new field, uniqueMapRatio, to edwValidFile.
  • lines changed 6, context: html, text, full: html, text
    Adding pid field to job tables.
• src/hg/encode3/encodeDataWarehouse/lib/edwBamFileFromRa.c
  • lines changed 191, context: html, text, full: html, text
    Adding edwBamStats parser.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 79, 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.
  • lines changed 12, context: html, text, full: html, text
    Adding edwAnalysisJobAdd to library.
  • lines changed 101, context: html, text, full: html, text
    Adding support for version checker.
  • lines changed 24, context: html, text, full: html, text
    Adding edwPokeFifo to make scheduling to happen sooner.
  • lines changed 98, 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/lib/encodeDataWarehouse.as
  • lines changed 10, context: html, text, full: html, text
    Adding edwExperiment table.
  • lines changed 43, context: html, text, full: html, text
    Adding edwQaFail, edwAnalysisJob and edwAnalysisRun tables.
  • lines changed 26, context: html, text, full: html, text
    Adding edwAnalysisSoftware and edwAnalysisStep tables. Rearranging some things in edwAnalysisRun. Part of getting analysis pipeline going.
  • lines changed 3, context: html, text, full: html, text
    Adding fields to edwAnalysisRun to store fileIds of created files.
  • lines changed 5, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 3, 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.
  • lines changed 2, context: html, text, full: html, text
    Forcing unique ness among step and software name fields.
  • lines changed 9, context: html, text, full: html, text
    Adding uuid and isAdmin fields to edwUser, and assayType and ipTarget to edwExperiment.
  • lines changed 21, context: html, text, full: html, text
    Adding edwBamFile table, and new field, uniqueMapRatio, to edwValidFile.
  • lines changed 3, context: html, text, full: html, text
    Adding pid field to job tables.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 172, context: html, text, full: html, text
    Adding edwExperiment table.
  • lines changed 566, context: html, text, full: html, text
    Adding edwQaFail, edwAnalysisJob and edwAnalysisRun tables.
  • lines changed 422, context: html, text, full: html, text
    Adding edwAnalysisSoftware and edwAnalysisStep tables. Rearranging some things in edwAnalysisRun. Part of getting analysis pipeline going.
  • lines changed 43, context: html, text, full: html, text
    Adding fields to edwAnalysisRun to store fileIds of created files.
  • lines changed 105, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 10, context: html, text, full: html, text
    Fixing spelling of inFilesId field.
  • lines changed 38, context: html, text, full: html, text
    Adding uuid and isAdmin fields to edwUser, and assayType and ipTarget to edwExperiment.
  • lines changed 218, context: html, text, full: html, text
    Adding edwBamFile table, and new field, uniqueMapRatio, to edwValidFile.
  • lines changed 30, context: html, text, full: html, text
    Adding pid field to job tables.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h
  • lines changed 1914, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 1914, context: html, text, full: html, text
    Removing stray.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 11, context: html, text, full: html, text
    Adding edwExperiment table.
  • lines changed 46, context: html, text, full: html, text
    Adding edwQaFail, edwAnalysisJob and edwAnalysisRun tables.
  • lines changed 30, context: html, text, full: html, text
    Adding edwAnalysisSoftware and edwAnalysisStep tables. Rearranging some things in edwAnalysisRun. Part of getting analysis pipeline going.
  • lines changed 3, context: html, text, full: html, text
    Adding fields to edwAnalysisRun to store fileIds of created files.
  • lines changed 5, context: html, text, full: html, text
    Renaming numerous fields in edwAnalysisRun and adding new inputTypes field.
  • lines changed 1, 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.
  • lines changed 19, context: html, text, full: html, text
    Adding uuid and isAdmin fields to edwUser, and assayType and ipTarget to edwExperiment.
  • lines changed 23, context: html, text, full: html, text
    Adding edwBamFile table, and new field, uniqueMapRatio, to edwValidFile.
  • lines changed 3, context: html, text, full: html, text
    Adding pid field to job tables.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding edwBamStats parser.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 12, context: html, text, full: html, text
    Making new daemon for analysis jobs.
  • lines changed 2, context: html, text, full: html, text
    Adding edw@encodedcc.sdsc.edu user (the user for the automatic daemons)
  • lines changed 11, context: html, text, full: html, text
    Initializing steps and software tables and grabbing local copy of experiment.
  • lines changed 8, context: html, text, full: html, text
    Setting up a bunch of users as admins. Adding Seth to the pool.
  • lines changed 3, context: html, text, full: html, text
    Creating new xf view that joine edwFile, edwValidFile, and edwExperiment
  • lines changed 2, context: html, text, full: html, text
    Adding uniqueMapRatio to vf and xf view.
• src/hg/encode3/encodeDataWarehouse/lib/restartDaemons
  • lines changed 14, context: html, text, full: html, text
    Adding script to restart daemons. Needed when daemons hand or hgwdev reboots.
  • lines changed 2, 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/software.tab
  • lines changed 14, context: html, text, full: html, text
    Initial software list.
• src/hg/encode3/encodeDataWarehouse/lib/step.tab
  • lines changed 2, context: html, text, full: html, text
    Adding initial analysis steps.
  • lines changed 2, context: html, text, full: html, text
    Oops, plural single mixup.
• src/hg/encode3/encodeDataWarehouse/lib/steps.tab
  • lines changed 2, context: html, text, full: html, text
    Oops, plural single mixup.
  • lines changed 2, context: html, text, full: html, text
    Adding macs2 steps for dnase
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding edwQaEvaluate to make chain.
  • lines changed 2, context: html, text, full: html, text
    Adding edwFinishAnalysis and edwScheduleAnalysis to make chain.
  • lines changed 1, context: html, text, full: html, text
    Adding edwAnalysisAddJson to make chain.
  • lines changed 1, context: html, text, full: html, text
    Automatic retrier works in a basic sense.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding edw library.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 79, context: html, text, full: html, text
    For ENCODE3 experiments try and figure out subtype of RNA-seq
  • lines changed 183, context: html, text, full: html, text
    Refactoring to use an cache and to set up for getting antibody info too.
  • lines changed 45, context: html, text, full: html, text
    Getting immunoprecipitation target from stanford.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 195, context: html, text, full: html, text
    Utility to compute bam stats seems to work.
  • lines changed 117, context: html, text, full: html, text
    Making option to output a sample bed.
  • lines changed 13, context: html, text, full: html, text
    Making it consider things sorted by chrom even if strand flips back and forth.
  • lines changed 54, 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.
  • lines changed 1, context: html, text, full: html, text
    Fixing bug that occurred in small minority of files.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to compute bam stats seems to work.
• src/inc/cheapcgi.h
  • lines changed 3, context: html, text, full: html, text
    Adding cgiDictionaryFreeList function.
• src/inc/jsonParse.h
  • lines changed 2, context: html, text, full: html, text
    Fixing value return types for jsonBooleanVal and jsonDoubleVal.
• src/inc/obscure.h
  • lines changed 6, context: html, text, full: html, text
    Adding slListRandomReduce and slListRandomSample for making samples of larger lists.
• src/lib/cheapcgi.c
  • lines changed 14, context: html, text, full: html, text
    Adding cgiDictionaryFreeList function.
• src/lib/jsonParse.c
  • lines changed 3, 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.
  • lines changed 2, context: html, text, full: html, text
    Fixing value return types for jsonBooleanVal and jsonDoubleVal.
• src/lib/obscure.c
  • lines changed 42, context: html, text, full: html, text
    Adding slListRandomReduce and slListRandomSample for making samples of larger lists.
• src/parasol/inc/jobResult.h
  • lines changed 59, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
  • lines changed 2, context: html, text, full: html, text
    Moving a couple of routines to library so they can be shared.
• src/parasol/inc/paraMessage.h
  • lines changed 6, context: html, text, full: html, text
    Moving a couple of routines to library so they can be shared.
• src/parasol/lib/jobResult.as
  • lines changed 18, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/lib/jobResult.c
  • lines changed 207, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/lib/jobResult.sql
  • lines changed 21, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/lib/paraMessage.c
  • lines changed 31, context: html, text, full: html, text
    Moving a couple of routines to library so they can be shared.
• src/parasol/para/jobResult.as
  • lines changed 18, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/para/jobResult.c
  • lines changed 207, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/para/jobResult.h
  • lines changed 59, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/para/jobResult.sql
  • lines changed 21, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/para/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving jobResult to lib directory so it can be shared.
• src/parasol/para/para.c
  • lines changed 32, context: html, text, full: html, text
    Moving a couple of routines to library so they can be shared.
• src/parasol/paraHub/paraHub.c
  • lines changed 13, context: html, text, full: html, text
    Changing ownership of batch file to job owner.
• src/parasol/parasol/parasol.c
  • lines changed 42, context: html, text, full: html, text
    Adding -wait option to parasol add job to wait for job to finish.
  • lines changed 1, context: html, text, full: html, text
    Reducing verbosity of waiting message.
• src/utils/bedGraphPack/bedGraphPack.c
  • lines changed 112, context: html, text, full: html, text
    Utility to merge adjacent same-valued bedGraph records seems to work.
  • lines changed 1, context: html, text, full: html, text
    Adding version number to usage statement.
• src/utils/bedGraphPack/expected.bedGraph
  • lines changed 13, context: html, text, full: html, text
    Utility to merge adjacent same-valued bedGraph records seems to work.
• src/utils/bedGraphPack/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to merge adjacent same-valued bedGraph records seems to work.
• src/utils/bedGraphPack/test.bedGraph
  • lines changed 19, context: html, text, full: html, text
    Utility to merge adjacent same-valued bedGraph records seems to work.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
  • lines changed 1, context: html, text, full: html, text
    Adding version to usage statement
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Utility to merge adjacent same-valued bedGraph records seems to work.
• src/utils/raToStructGen/raToStructGen.c
  • lines changed 4, context: html, text, full: html, text
    Adding byte and ubyte to the list of numerical types handled.