All File Changes

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

• src/hg/blastToPsl/makefile
  • lines changed 2, context: html, text, full: html, text
    correctly cleaning tests/output directory refs #12260
• 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.
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    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.
  • lines changed 1, context: html, text, full: html, text
    Fixing compile warning (need TRUE not "TRUE").
• 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/edwQaEvaluate/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding Jim's edwQaEvaluate/makefile to fix broken build.
• 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 1, context: html, text, full: html, text
    Fixing compile-breaking error: undeclared variables.
  • 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.
  • lines changed 10, context: html, text, full: html, text
    Adding #ifdef USE_BAM around encodeDataWarehouse functions that call samtools lib functions.Otherwise compile breaks without USE_BAM and/or USE_SAMTABIX.
    
• 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/edwWebXSendFile/edwWebXSendFile.c
  • lines changed 92, context: html, text, full: html, text
    edwWebXSebdFile CGI created to let user download submitted files through XSendFile
• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.h
  • lines changed 11, context: html, text, full: html, text
    Header for edwWebXSendFile
• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/makefile
  • lines changed 16, context: html, text, full: html, text
    edwWebXSebdFile CGI created to let user download submitted files through XSendFile
• 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.
  • lines changed 4, context: html, text, full: html, text
    Adding #ifdef USE_BAM around encodeDataWarehouse functions that call samtools lib functions.Otherwise compile breaks without USE_BAM and/or USE_SAMTABIX.
    
• 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.
  • lines changed 1, context: html, text, full: html, text
    edwWebXSebdFile CGI created to let user download submitted files through XSendFile
• 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/hg/hgMirror/hgMirror
  • lines changed 902, context: html, text, full: html, text
    hgMirror is a CGI to make partial mirrors and VMs easier to setup. Itpresents the list of tracks, allows the user to select a few, prepares
    a script with udr download commands and runs them. As it requires a lot
    of write permissions and can do harm (mysql directory, gbdb directory),
    it currently does show sizes on hgwdev, but cannot write anything.
    I didn't make it part of the default "make cgi" target.
    
  • lines changed 1, context: html, text, full: html, text
    always copy one small encode table
• src/hg/hgMirror/makefile
  • lines changed 19, context: html, text, full: html, text
    hgMirror is a CGI to make partial mirrors and VMs easier to setup. Itpresents the list of tracks, allows the user to select a few, prepares
    a script with udr download commands and runs them. As it requires a lot
    of write permissions and can do harm (mysql directory, gbdb directory),
    it currently does show sizes on hgwdev, but cannot write anything.
    I didn't make it part of the default "make cgi" target.
    
• src/hg/hgTracks/factorSource.c
  • lines changed 2, context: html, text, full: html, text
    replacing a query with the more apprpriate function call (saves somelittle time in the browser box, as hdb can use the table name cache)
    
• src/hg/hgTracks/pubsTracks.c
  • lines changed 3, context: html, text, full: html, text
    fixing slightly weird code in pubs track color reading
• src/hg/hgc/pubs.c
  • lines changed 5, context: html, text, full: html, text
    removing indiv sequences link, rm #12212
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 54, context: html, text, full: html, text
    adding snakes & HAL help info, refs #10637
• src/hg/htdocs/goldenPath/help/hgRegMotifHelp.html
  • lines changed 133, context: html, text, full: html, text
    Adding new motif Help page with correct file name to match CGI that calls it, hgRegMotifHelp.html, refs #9092
  • lines changed 20, context: html, text, full: html, text
    Staging motifs on beta (removing added beta stanza from bf56993131b5921ae1c4f2c01aef855ed1d35f0d), moving link on help page and making small changes to html refs #9092
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 46, context: html, text, full: html, text
    adding snakes & HAL help info, refs #10637
• src/hg/htdocs/goldenPath/help/motifHelp.html
  • lines changed 133, context: html, text, full: html, text
    Adding new motif Help page for TFBS motif, and matching image, refs #9092
  • lines changed 133, context: html, text, full: html, text
    removing original file motifHelp.html, replaced with hgRegMotifHelp.html, refs #9092
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    Correcting Hub reference to vcfTabIx to vcfTabix, refs # 11271
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 1, context: html, text, full: html, text
    Correcting Hub reference to vcfTabIx to vcfTabix, refs # 11271
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    Adding note about superTracks displaying as default for Hubs Doc refs# 12079
  • lines changed 5, context: html, text, full: html, text
    Correcting Hub reference to vcfTabIx to vcfTabix, refs # 11271
• src/hg/htdocs/images/motifExampleETS1.png
  • lines changed 0, context: html, text, full: html, text
    Adding new motif Help page for TFBS motif, and matching image, refs #9092
• src/hg/lib/customFactory.c
  • lines changed 6, context: html, text, full: html, text
    In MLQ #12367, the user got a blank screen when trying to view a CTusing a Mac-mangled BAM file. Of course we need to show an error message
    instead of SEGV/blank screen; but hgCustom also shouldn't have accepted
    the file as a custom track. It turns out that the samtools lib function
    samopen() may return a non-null file handler with a null header, when the
    header is invalid. So we need to check not only for null result from
    samopen, but also null header inside non-null result. Meanwhile, I noticed
    that hgCustom's error reporting was actually masking more detailed error
    messages from lib code, because of its use of errCatch around bamFileExists.
    errCatch only lets errAbort messages propagate, not warnings; bamFileExists
    has a warn() that is lost in transmission. I added bamFileAndIndexMustExist
    which uses errAbort so that errCatch in callers will get the more informative
    error instead of having to make up one of its own. trackHub checking code
    also needed this stronger form of checking. I also moved some duplicated
    (or triplicated) code in bamFile.c into functions.
    refs #12367
    
• src/hg/lib/hdb.c
  • lines changed 15, context: html, text, full: html, text
    As suggested by Hiram, inversing the strategy for table name checks:First try the full table name, then the split table name. All current
    assemblies use normal, non-split tables so this saves some mysql
    queries (and saves some time in the browser box)
    
• src/hg/lib/tableList.sql
  • lines changed 11, context: html, text, full: html, text
    when I changed the makeTableList command, forgot to check in the sqltable schema for its table
    
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    In MLQ #12367, the user got a blank screen when trying to view a CTusing a Mac-mangled BAM file. Of course we need to show an error message
    instead of SEGV/blank screen; but hgCustom also shouldn't have accepted
    the file as a custom track. It turns out that the samtools lib function
    samopen() may return a non-null file handler with a null header, when the
    header is invalid. So we need to check not only for null result from
    samopen, but also null header inside non-null result. Meanwhile, I noticed
    that hgCustom's error reporting was actually masking more detailed error
    messages from lib code, because of its use of errCatch around bamFileExists.
    errCatch only lets errAbort messages propagate, not warnings; bamFileExists
    has a warn() that is lost in transmission. I added bamFileAndIndexMustExist
    which uses errAbort so that errCatch in callers will get the more informative
    error instead of having to make up one of its own. trackHub checking code
    also needed this stronger form of checking. I also moved some duplicated
    (or triplicated) code in bamFile.c into functions.
    refs #12367
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 21, context: html, text, full: html, text
    Adding next steps in loading of Cooper Developmental Delay track refs #9391
• src/hg/makeDb/doc/hg38.txt
  • lines changed 361, context: html, text, full: html, text
    initial build and masking started refs #11682
  • lines changed 227, context: html, text, full: html, text
    add a cytoBand and the hg19 to hg38 difference track
  • lines changed 159, context: html, text, full: html, text
    working on genscan cpgIslands and PAR regions and added altLocations track refs #11681
  • lines changed 199, context: html, text, full: html, text
    documenting trf procedure refs #11681
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 6, context: html, text, full: html, text
    change the default alignment strategy to ignore repeats and to notreward introns in the alignments #7568
    
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
  • lines changed 2, context: html, text, full: html, text
    can also eliminate repEnd<0 bad records refs #11681
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Adding dasNov3 and oviAri3 to ensGeneDb list and removing them from notEnsemblTranscriptId list, refs #12288
• src/hg/makeDb/trackDb/Nregion.html
  • lines changed 6, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/Nregions.html
  • lines changed 6, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/anopheles/rmsk.html
  • lines changed 3, context: html, text, full: html, text
    Made corrections to references to Repbase Update
• src/hg/makeDb/trackDb/apis/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Made corrections to references to Repbase Update
• src/hg/makeDb/trackDb/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/blastzBestMm2X.html
  • lines changed 3, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/blastzBestMm3X.html
  • lines changed 3, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/blatFr1.html
  • lines changed 3, context: html, text, full: html, text
    Track description page changes related to Code Review, refs #12353
• src/hg/makeDb/trackDb/chainDm1.html
  • lines changed 20, context: html, text, full: html, text
    Fixing links on dp2 track description pages
• src/hg/makeDb/trackDb/chainDm2.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/chainDm3.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 2, context: html, text, full: html, text
    Editing links on rat (rn5) track description pages
• src/hg/makeDb/trackDb/chimp/panTro4/description.html
  • lines changed 2, context: html, text, full: html, text
    Fixing links on chimp (panTro4) track description pages
• src/hg/makeDb/trackDb/chimp/panTro4/gap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links on chimp (panTro4) track description pages
• src/hg/makeDb/trackDb/chimp/panTro4/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links on chimp (panTro4) track description pages
• src/hg/makeDb/trackDb/contrastGene.html
  • lines changed 10, context: html, text, full: html, text
    Fixing links on zebrafish (danRer4) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDm1.html
  • lines changed 21, context: html, text, full: html, text
    Fixing links on dp2 track description pages
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
  • lines changed 4, context: html, text, full: html, text
    Track description page changes related to Code Review, refs #12353
• src/hg/makeDb/trackDb/drosophila/droMoj1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/drosophila/droMoj2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/drosophila/est.html
  • lines changed 14, context: html, text, full: html, text
    Fixing links on dp2 track description pages
• src/hg/makeDb/trackDb/drosophila/intronEst.html
  • lines changed 13, context: html, text, full: html, text
    Fixing links on dp2 track description pages
• src/hg/makeDb/trackDb/drosophila/mrna.html
  • lines changed 12, context: html, text, full: html, text
    Fixing links on dp2 track description pages
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/drosophila/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Made corrections to references to Repbase Update
• src/hg/makeDb/trackDb/drosophila/xenoRefGene.html
  • lines changed 4, context: html, text, full: html, text
    Fixing links on dp2 track description pages
  • lines changed 1, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 2, context: html, text, full: html, text
    Adding PMID/PMCID for track reference, refs #12288
• src/hg/makeDb/trackDb/esRegGeneToMotif.html
  • lines changed 2, context: html, text, full: html, text
    Fixing links on yeast (sacCer1) track description pages
• src/hg/makeDb/trackDb/est.html
  • lines changed 2, context: html, text, full: html, text
    Editing links on rat (rn5) track description pages
• src/hg/makeDb/trackDb/est.new.html
  • lines changed 12, context: html, text, full: html, text
    Editing links on rat (rn5) track description pages
• src/hg/makeDb/trackDb/exoMouse.html
  • lines changed 5, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 3, context: html, text, full: html, text
    Addind PMID/PMCID for track reference, refs #12288
• src/hg/makeDb/trackDb/genMapDb.html
  • lines changed 10, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/genomeScan.html
  • lines changed 8, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/genomicSuperDups.html
  • lines changed 9, context: html, text, full: html, text
    Fixing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/gnfAtlas2.html
  • lines changed 13, context: html, text, full: html, text
    Fixing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/horse/equCab2/ctgPos2.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on horse (equCab2) track description pages
• src/hg/makeDb/trackDb/horse/equCab2/nscanGene.html
  • lines changed 28, context: html, text, full: html, text
    Changing links on horse (equCab2) track description pages
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Trying out new trackDb stanza for Cooper Dev. Delay track #9391
  • lines changed 39, context: html, text, full: html, text
    missed overrides of snp134 when dropping kruft from top-level trackDb.ra. refs 12236
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 18, context: html, text, full: html, text
    Staging motifs on beta (removing added beta stanza from bf56993131b5921ae1c4f2c01aef855ed1d35f0d), moving link on help page and making small changes to html refs #9092
• src/hg/makeDb/trackDb/human/hg38/altLocations.html
  • lines changed 6, context: html, text, full: html, text
    adding altLocations and hg38ContigDiff track descriptions refs #11681
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 63, context: html, text, full: html, text
    hg38 ready to view refs #11681
  • lines changed 1, context: html, text, full: html, text
    changed image to what we use everywhere else
  • lines changed 1, context: html, text, full: html, text
    changed image to what we use everywhere else
• src/hg/makeDb/trackDb/human/hg38/gap.html
  • lines changed 34, context: html, text, full: html, text
    hg38 ready to view refs #11681
• src/hg/makeDb/trackDb/human/hg38/gold.html
  • lines changed 38, context: html, text, full: html, text
    hg38 ready to view refs #11681
• src/hg/makeDb/trackDb/human/hg38/hg38ContigDiff.html
  • lines changed 38, context: html, text, full: html, text
    adding altLocations and hg38ContigDiff track descriptions refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html
  • lines changed 105, context: html, text, full: html, text
    adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html
  • lines changed 125, context: html, text, full: html, text
    adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    hg38 ready to view refs #11681
  • lines changed 54, context: html, text, full: html, text
    adding various repeat masker tracks and ctgPos2 refs #11681
  • lines changed 15, context: html, text, full: html, text
    add correct search rules for gold and ctgPos2 tracks refs #11681
  • lines changed 16, context: html, text, full: html, text
    adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
  • lines changed 9, context: html, text, full: html, text
    adding analysisGap refs #11681
  • lines changed 1, context: html, text, full: html, text
    correct url variable for ctgPos2 refs #11681
  • lines changed 11, context: html, text, full: html, text
    adding the hg19 to hg38 difference track refs #11681
  • lines changed 28, context: html, text, full: html, text
    adding hmmerUnique crossMatchUnique and altLocations tracks refs #11681
• src/hg/makeDb/trackDb/intronEst.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on horse (equCab2) track description pages
• src/hg/makeDb/trackDb/isochores.html
  • lines changed 13, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/loweProbes.html
  • lines changed 114, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    hg38 ready to view refs #11681
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on wallaby and manatee track description pages
• src/hg/makeDb/trackDb/manatee/triMan1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on wallaby and manatee track description pages
• src/hg/makeDb/trackDb/manatee/triMan1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on wallaby and manatee track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 4, context: html, text, full: html, text
    more fixes related to code review feedback, refs #12302
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 4, context: html, text, full: html, text
    more fixes related to code review feedback, refs #12302
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 20, context: html, text, full: html, text
    Fixing links on rat (rn3) track description pages
• src/hg/makeDb/trackDb/mouse/mm4/rmsk.html
  • lines changed 5, context: html, text, full: html, text
    Made corrections to references to Repbase Update
• src/hg/makeDb/trackDb/mouseSynWhd.html
  • lines changed 23, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 2, context: html, text, full: html, text
    Editing links on rat (rn5) track description pages
• src/hg/makeDb/trackDb/ncbiGenes.html
  • lines changed 8, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/nestedRepeatsRM327.html
  • lines changed 3, context: html, text, full: html, text
    Made corrections to references to Repbase Update
• src/hg/makeDb/trackDb/netDm1.html
  • lines changed 15, context: html, text, full: html, text
    Fixing links on dp2 track description pages
• src/hg/makeDb/trackDb/netDm2.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/netDm3.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on drosphila (droMoj1, droMoj2, droAna2) track description pages
• src/hg/makeDb/trackDb/npredGene.html
  • lines changed 9, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/npredGene2.html
  • lines changed 9, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/nscanGene.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on tetraodon (tetNig1, tetNig2) track description pages
• src/hg/makeDb/trackDb/olly2.html
  • lines changed 14, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
• src/hg/makeDb/trackDb/olly25.html
  • lines changed 14, context: html, text, full: html, text
    removing trackDb.ra blocks for 60 tracks for which there are no tables in any assembly. removed all associated search blocks and html files. refs #12236
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    fixup the default clusters and workhorse lists for the ku environment refs #11681
• src/hg/utils/automation/blastz-run-ucsc
  • lines changed 64, context: html, text, full: html, text
    can now use a package of 2bit sequences for the query to modern lastz versions refs #11681
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 75, context: html, text, full: html, text
    can now use a package of 2bit sequences for the query to modern lastz versions refs #11681
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 1, context: html, text, full: html, text
    save the bad records result refs #11681
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 5, context: html, text, full: html, text
    avoid attempting to lift zero length files which is an error refs #11681
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 6, context: html, text, full: html, text
    add type pre draft to recognize in an AGP file and fixup the split threshold to avoid 1,000 directories refs #11681
• src/hg/utils/phyloTrees/120way.commonNames.nh
  • lines changed 120, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/120way.nh
  • lines changed 120, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/120way.scientificNames.nh
  • lines changed 120, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 5, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 6, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 11, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 9, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 17, context: html, text, full: html, text
    adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
• src/inc/bamFile.h
  • lines changed 4, context: html, text, full: html, text
    In MLQ #12367, the user got a blank screen when trying to view a CTusing a Mac-mangled BAM file. Of course we need to show an error message
    instead of SEGV/blank screen; but hgCustom also shouldn't have accepted
    the file as a custom track. It turns out that the samtools lib function
    samopen() may return a non-null file handler with a null header, when the
    header is invalid. So we need to check not only for null result from
    samopen, but also null header inside non-null result. Meanwhile, I noticed
    that hgCustom's error reporting was actually masking more detailed error
    messages from lib code, because of its use of errCatch around bamFileExists.
    errCatch only lets errAbort messages propagate, not warnings; bamFileExists
    has a warn() that is lost in transmission. I added bamFileAndIndexMustExist
    which uses errAbort so that errCatch in callers will get the more informative
    error instead of having to make up one of its own. trackHub checking code
    also needed this stronger form of checking. I also moved some duplicated
    (or triplicated) code in bamFile.c into functions.
    refs #12367
    
• 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/bamFile.c
  • lines changed 71, context: html, text, full: html, text
    In MLQ #12367, the user got a blank screen when trying to view a CTusing a Mac-mangled BAM file. Of course we need to show an error message
    instead of SEGV/blank screen; but hgCustom also shouldn't have accepted
    the file as a custom track. It turns out that the samtools lib function
    samopen() may return a non-null file handler with a null header, when the
    header is invalid. So we need to check not only for null result from
    samopen, but also null header inside non-null result. Meanwhile, I noticed
    that hgCustom's error reporting was actually masking more detailed error
    messages from lib code, because of its use of errCatch around bamFileExists.
    errCatch only lets errAbort messages propagate, not warnings; bamFileExists
    has a warn() that is lost in transmission. I added bamFileAndIndexMustExist
    which uses errAbort so that errCatch in callers will get the more informative
    error instead of having to make up one of its own. trackHub checking code
    also needed this stronger form of checking. I also moved some duplicated
    (or triplicated) code in bamFile.c into functions.
    refs #12367
    
  • lines changed 7, context: html, text, full: html, text
    Oops, forgot to add stub for bamFileAndIndexMustExist to the #else (no USE_BAM) part of bamFile.cfixes #12401
    
• 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/makefile
  • lines changed 1, context: html, text, full: html, text
    correctly clean parasol directory during clean target refs #9104
• 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/bigWigCat/bigWigCat.c
  • lines changed 59, context: html, text, full: html, text
    impose kentian order on the style. Remove -clip options which didnothing.
    
• src/utils/bigWigCat/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    correctly using destbindir for binary access
• 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/qa/copyHgcentral
  • lines changed 396, context: html, text, full: html, text
    Updated version of the script based on code review w/ Kate (redmine #12249)
  • lines changed 19, context: html, text, full: html, text
    Made commenting changes
• src/utils/qa/databaseAday.csh
  • lines changed 1, context: html, text, full: html, text
    Fixed issue where cron invocation failed because it couldn't write to /dev/stderr. Script now calls bash -c to write to stderr
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v294 preview2 refs #12191
• 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.
• src/utils/wigToBigWig/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    correct use of destbindir binary

• lines changed: 22368
• files changed: 491