All File Changes

v330_preview2.1 to v330_base (2016-03-14 to 2016-03-21) v330

• confs/hgwbeta.hg.conf
  • lines changed 4, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/README
  • lines changed 106, context: html, text, full: html, text
    A file that attempts to give an overview of the CIRM Data Warehouse system.
    
  • lines changed 81, context: html, text, full: html, text
    Updating to reflect how things work now.
    
  • lines changed 283, context: html, text, full: html, text
    Adding some program descriptions to README
    
• src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
  • lines changed 1, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/cdwAddQaEnrichTarget/cdwAddQaEnrichTarget.c
  • lines changed 1, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/cdwChangeFormat/cdwChangeFormat.c
  • lines changed 1, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/cdwCorrectFileTags/cdwCorrectFileTags.c
  • lines changed 1, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 15, context: html, text, full: html, text
    Slightly more robust error reporting if tags in database are messed up. Fixing up so that sqlDyStringPrintf is only used at start of command, since it is a bit overaggressive about flagging errors on partially built queries if you use it throughout a query build.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 5, context: html, text, full: html, text
    Adding minimal support for Tabix validation on vcf indices.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Adding verbose status message about copying a file.
    
  • lines changed 14, context: html, text, full: html, text
    Adding -test option so it can look at meta and manifest files without updating database. In test mode it will currently also start checking controlled vocabs.
    
  • lines changed 125, context: html, text, full: html, text
    Removing some unused code. Making a sql command go through sql injection checking that was bypassing it.
    
  • lines changed 8, context: html, text, full: html, text
    Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
    
  • lines changed 2, context: html, text, full: html, text
    Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 5, context: html, text, full: html, text
    Removing a set but not used symbol to get code to compile again with stricter warnings.
    
  • lines changed 35, context: html, text, full: html, text
    Fixing bug where browse tracks errored out when there were no chromosome tags.
    
• src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/cdwFixDoubleHivePath.c
  • lines changed 65, context: html, text, full: html, text
    Another little database fix utility. No longer need to include directory name in path, but forgot that.
    
• src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/makefile
  • lines changed 3, context: html, text, full: html, text
    Another little database fix utility. No longer need to include directory name in path, but forgot that.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 4, context: html, text, full: html, text
    Adding submitId column to job table.
    
  • lines changed 73, context: html, text, full: html, text
    Removing no longer used cdwSubmitJob table.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 2, context: html, text, full: html, text
    Starting to implement checking of tag values for controlled vocabularies.
    
  • lines changed 3, context: html, text, full: html, text
    Adding minimal support for Tabix validation. Making it avoid GEO_SAMPLE and GEO_SERIES tags, which should be lower case since they are ones we get even if the set is not wrangled out of GEO.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 2, context: html, text, full: html, text
    Adding submitId column to job table.
    
  • lines changed 13, context: html, text, full: html, text
    Removing no longer used cdwSubmitJob table.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 20, context: html, text, full: html, text
    Adding submitId column to job table.
    
  • lines changed 179, context: html, text, full: html, text
    Removing no longer used cdwSubmitJob table.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 2, context: html, text, full: html, text
    Adding submitId column to job table.
    
  • lines changed 14, context: html, text, full: html, text
    Removing no longer used cdwSubmitJob table.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 7, context: html, text, full: html, text
    Adding submitId column to job table.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 153, context: html, text, full: html, text
    Starting to implement checking of tag values for controlled vocabularies.
    
  • lines changed 32, context: html, text, full: html, text
    Adding minimal support for Tabix validation. Making it avoid GEO_SAMPLE and GEO_SERIES tags, which should be lower case since they are ones we get even if the set is not wrangled out of GEO.
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 67, context: html, text, full: html, text
    Added the ensemble to human readable gene mapping into this program, refs #16244
    
• src/hg/cirm/cdw/wrangle/addToStepTables/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing paths in makefile so they work on cirm-01 as well as hgwdev.
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix
  • lines changed 2, context: html, text, full: html, text
    Reverting to ensemble gene names for matrices, I will apply the mapping when the meta data is added. refs #16244
    
• src/hg/expMatrixClustersForDendrogram/expMatrixClustersForDendrogram.c
  • lines changed 636, context: html, text, full: html, text
    Seems like something funky happened when I renamed the file, adding in the updated file name refs #16182
    
  • lines changed 12, context: html, text, full: html, text
    Removing a global and adding some comments as suggested by Jim in 17001, refs #16216
    
• src/hg/expMatrixClustersForDendrogram/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    updating the makefile and tests, refs #16216
    
  • lines changed 1, context: html, text, full: html, text
    fixing a spelling mistake, #refs 16216
    
• src/hg/expMatrixClustersForDendrogram/tests/matrix.mx
  • lines changed 2, context: html, text, full: html, text
    updating the makefile and tests, refs #16216
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 37, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    Integrate gene class into GTEx cgi support. refs #15645
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    changed text for Next Exon to Next Exon Edge to clarify situation when you within an exon
    
• src/hg/hgc/gtexClick.c
  • lines changed 4, context: html, text, full: html, text
    Change boxplot to tissue ordering alphabetically, to match hgTracks. Leave in code to sort descending by median score, in case we want to provide that as a user option. refs #15645
    
  • lines changed 11, context: html, text, full: html, text
    Integrate gene class into GTEx cgi support. refs #15645
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    get ws245Genes to deal with its peptide table properly #15209
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 12, context: html, text, full: html, text
    Change boxplot to tissue ordering alphabetically, to match hgTracks. Leave in code to sort descending by median score, in case we want to provide that as a user option. refs #15645
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Adding entry for ce11 assembly, refs #15209
    
• src/hg/htdocs/indexIntro.html
  • lines changed 5, context: html, text, full: html, text
    added disclaimer, not for clinical use
    
  • lines changed 1, context: html, text, full: html, text
    added missing period
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 20, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Libify gene class. refs #15645
    
• src/hg/inc/gtexTranscript.h
  • lines changed 79, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v330
    
• src/hg/lib/gtexGeneBed.as
  • lines changed 2, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 57, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
  • lines changed 30, context: html, text, full: html, text
    Libify gene class. refs #15645
    
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.as
  • lines changed 6, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.c
  • lines changed 162, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.sql
  • lines changed 12, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/jksql.c
  • lines changed 7, context: html, text, full: html, text
    use local error message if database does not exist on mysql failover
    connection. No redmine, bug report received from Jim.
    
  • lines changed 10, context: html, text, full: html, text
    small modification of previous commit to make sure the correct mysql error message
    appears, no redmine
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed schema no longer needed for GTEx build. refs #15645
    
• src/hg/makeDb/doc/gorGor4/initialBuild.txt
  • lines changed 31, context: html, text, full: html, text
    Redo of genscan run to annotate previously missed regions, refs #16220
    
• src/hg/makeDb/doc/gtex/V4.txt
  • lines changed 9, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 10, context: html, text, full: html, text
    Trim sample table
    
  • lines changed 74, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in 1c23add1.
    refs #16910
    
  • lines changed 18, context: html, text, full: html, text
    Re-ran most of snp pipeline on hg19 after fixing bug in doDbSnp.pl; rebuilt snp ortho alleles and masked fasta.
    Ran snp pipeline on hg38 (using rs_fasta from hg19 because dbSNP dumped GRCh38 rs_fasta too soon and it was incomplete).
    refs #16777
    
  • lines changed 4, context: html, text, full: html, text
    refs #14486: fixing missing chrM annotations on mm10 patents
    
  • lines changed 2, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 33, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 86, context: html, text, full: html, text
    Re-ran most of snp pipeline on hg19 after fixing bug in doDbSnp.pl; rebuilt snp ortho alleles and masked fasta.
    Ran snp pipeline on hg38 (using rs_fasta from hg19 because dbSNP dumped GRCh38 rs_fasta too soon and it was incomplete).
    refs #16777
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 44, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
  • lines changed 4, context: html, text, full: html, text
    refs #14486: fixing missing chrM annotations on mm10 patents
    
  • lines changed 41, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    added aptMan1 to genbank updates
    
  • lines changed 2, context: html, text, full: html, text
    Turning on GenBank updates for ce11, refs #15209
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Turning on GenBank updates on the RR for ce11, refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    turning on genbank updates for aptMan1
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 9, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
  • lines changed 7, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 127, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
  • lines changed 11, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 85, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
• src/hg/makeDb/trackDb/birds/aptMan1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing ncbi link, refs #16029
    
• src/hg/makeDb/trackDb/human/gtexGeneExprV4.html
  • lines changed 44, context: html, text, full: html, text
    Preserve V4 track description. refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 32, context: html, text, full: html, text
    A little cleanup to trackDb. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    A little cleanup to trackDb. refs #15645
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
  • lines changed 1, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM8.html
  • lines changed 347, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
  • lines changed 1, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM8.ra
  • lines changed 272, context: html, text, full: html, text
    added GENCODE VM8 (not to push public)
    
  • lines changed 1, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.html
  • lines changed 347, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra
  • lines changed 272, context: html, text, full: html, text
    GENCODE VM9 (#17007)
    
• src/hg/makeDb/trackDb/patSeq.html
  • lines changed 11, context: html, text, full: html, text
    Minor corrections to spelling on patSeq page. Switched long and short labels in trackDb file. refs #14486
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Minor corrections to spelling on patSeq page. Switched long and short labels in trackDb file. refs #14486
    
• src/hg/makeDb/trackDb/worm/ce11/description.html
  • lines changed 12, context: html, text, full: html, text
    Adding note about differences between WBcel235 and WBcel245, refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    get ws245Genes to deal with its peptide table properly #15209
    
• src/hg/utils/automation/doDbSnpMaskSequence.pl
  • lines changed 2, context: html, text, full: html, text
    Avoid non-existent directory error when running in -debug mode.
    
• src/hg/utils/otto/gwas/expectedColumns.txt
  • lines changed 14, context: html, text, full: html, text
    Changes to accomodate new GWAS format
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 9, context: html, text, full: html, text
    Changes to accomodate new GWAS format
    
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Adding isSymbolString function to common string library.
    
• src/lib/common.c
  • lines changed 15, context: html, text, full: html, text
    Adding isSymbolString function to common string library.
    
• src/product/scripts/fetchCramReference.sh
  • lines changed 112, context: html, text, full: html, text
    Script to fetch CRAM reference sequences in conjunction with hgTracks, refs #14717
    
• src/tagStorm/tagStormReformat/tagStormReformat.c
  • lines changed 5, context: html, text, full: html, text
    Changing order of command line interpretation so that -flatten doesn't exclude -tab.
    
• src/utils/patSeqFilterBulkAndAnnotate
  • lines changed 5, context: html, text, full: html, text
    refs #14486: fixing missing chrM annotations on mm10 patents
    
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Some updates to my autopushed track QA script. Added log file info to help message. Script now displays help message if it is run with no arguments. Added some checks to make sure important variables aren't empty. Changed how issue messages are generated. Link to log file is at bottom of list of issues found. Fixed some minor bugs including issue with bc not liking very small numbers and script not correctly reporting large coverage differences. Also added script to makefile. refs #12561
    
• src/utils/qa/qaAutoTrack.sh
  • lines changed 55, context: html, text, full: html, text
    Some updates to my autopushed track QA script. Added log file info to help message. Script now displays help message if it is run with no arguments. Added some checks to make sure important variables aren't empty. Changed how issue messages are generated. Link to log file is at bottom of list of issues found. Fixed some minor bugs including issue with bc not liking very small numbers and script not correctly reporting large coverage differences. Also added script to makefile. refs #12561
    
• src/utils/qa/updateTimesDb.sh
  • lines changed 2, context: html, text, full: html, text
    Minor correction to usage message. Added comment, refs #16553
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v330 final build refs #16963
    
• src/utils/stringify/stringify.c
  • lines changed 20, context: html, text, full: html, text
    Adding array option.
    

• lines changed: 4699
• files changed: 117