All File Changes

v273_preview2 to v273_base (2012-09-11 to 2012-09-18) v273

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 1, context: html, text, full: html, text
    no longer experimental
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 1, context: html, text, full: html, text
    oops, missed including net.h in hgCustom to support setConnFailuresEnabled
  • lines changed 1, context: html, text, full: html, text
    turn setConnFailuresEnabled for v273, do not want to many changes at once
• src/hg/hgGene/hgGene.c
  • lines changed 30, context: html, text, full: html, text
    move things around in the printf in hgGene that prints out the transcript start and stop, and CDS start and stop (#8249)
  • lines changed 3, context: html, text, full: html, text
    more twiddling of the info about a gene (#8249)
  • lines changed 3, context: html, text, full: html, text
    more twiddling (#8249)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 4, context: html, text, full: html, text
    fixing problems related to cut and paste of url which was picking up trailing blanks - now by removing trailing newline before closing-td and adding jquery trim function we prevent those blanks and remove them even if they somehow get added by some other cause.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    Revert "removing arbitrary limit on bigBed -- let users have more control"
    This reverts commit e4aec0c172a44c018885a6b9f33b7d65a8b8047b.
    
    I guess we are back to having a limit, but it will be increased from 500 to 3000
    
  • lines changed 1, context: html, text, full: html, text
    oops should use min instead of max
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Tighting up spacing between button rows.
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    Revert "removing arbitrary limit on bigBed -- let users have more control"
    This reverts commit e4aec0c172a44c018885a6b9f33b7d65a8b8047b.
    
    I guess we are back to having a limit, but it will be increased from 500 to 3000
    
  • lines changed 1, context: html, text, full: html, text
    increasing BIGBEDMAXIMUMITEMS from 500 to 3000
• src/hg/hgTracks/mainMain.c
  • lines changed 2, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 1, context: html, text, full: html, text
    turn setConnFailuresEnabled for v273, do not want to many changes at once
• src/hg/hgTracks/renderMain.c
  • lines changed 2, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 1, context: html, text, full: html, text
    turn setConnFailuresEnabled for v273, do not want to many changes at once
• src/hg/hgc/gencodeClick.c
  • lines changed 5, context: html, text, full: html, text
    add link to GeneCards in GENCODE details page
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    adjust chromosome name from cosmicraw table for output
  • lines changed 27, context: html, text, full: html, text
    added optional (chrom,start,end)-column matching to itemDetailsHtmlTable code
  • lines changed 6, context: html, text, full: html, text
    fix to (chrom,start,end)-check
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 3, context: html, text, full: html, text
    Formating publication reference on ENCODE/analysis.html page, code review RM#9052
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Adding UNC BSU Proteogenomics GENCODE mapping html snippet to ENCODE Downloads for Release 1, RM#8419
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    removing repeated line in archived announcement that Brian found in code review, redmine #9050
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 42, context: html, text, full: html, text
    added PB retirement to home page, and moved others off to archive page
• src/hg/htdocs/indexNews.html
  • lines changed 80, context: html, text, full: html, text
    added PB retirement to home page, and moved others off to archive page
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    Changed css background setting to fix remine #9033...where background image looked funny on pages with little content.
• src/hg/inc/liftOver.h
  • lines changed 8, context: html, text, full: html, text
    Changed liftOver to allow big-sized items by just lifting the ends. Needed library changes as well.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v273
• src/hg/lib/liftOver.c
  • lines changed 110, context: html, text, full: html, text
    Changed liftOver to allow big-sized items by just lifting the ends. Needed library changes as well.
• src/hg/liftOver/liftOver.c
  • lines changed 10, context: html, text, full: html, text
    Changed liftOver to allow big-sized items by just lifting the ends. Needed library changes as well.
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 111, context: html, text, full: html, text
    done with tracks and genbank ready for downloads and pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release3.notes
  • lines changed 4363, context: html, text, full: html, text
    Preparing for release: Adding a notes file, fixing the defualts and the labels, adding release notes
  • lines changed 4174, context: html, text, full: html, text
    Trying to clear the issues with new and revoked
  • lines changed 4174, context: html, text, full: html, text
    Fixing the notes files to still have the two docs that are new and revoked
• src/hg/makeDb/doc/hg19.txt
  • lines changed 75, context: html, text, full: html, text
    Track #8360 (snp137): updated with corrected indel locations andfunction codes (see note-36).
    Track #8886 (Denisova high-cov): added Denisova BAM at David's request.
    
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1316, context: html, text, full: html, text
    Finished ensGene v68 update documentation.
  • lines changed 19, context: html, text, full: html, text
    lift chrM_rCRS data to UCSC chrM for ensGene.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 65, context: html, text, full: html, text
    add assembly fragments and ucscToEnsembl tables
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 14, context: html, text, full: html, text
    done with liftOver to rheMac2
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 14, context: html, text, full: html, text
    done with liftOver to susScr2
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 38, context: html, text, full: html, text
    rebuilt to fix up kg5ToKg6 (#7045)
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    take off verbose flag for initial rsync
• src/hg/makeDb/genbank/src/align/gbAlignFinish
  • lines changed 1, context: html, text, full: html, text
    fix problems with duplicate lines in refGene due to overlapping blat regions (#9008)
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding mouse assemblyFrags table to ignored list
  • lines changed 1, context: html, text, full: html, text
    adding the mm10 ucscToEnsembl table
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing validation doc ref in cv
  • lines changed 1, context: html, text, full: html, text
    Updating NHA tissue assignment in CV
  • lines changed 86, context: html, text, full: html, text
    Standardizing GeneCard: and commenting out trouble antibodies that are not used
  • lines changed 10, context: html, text, full: html, text
    added labels to the open chrom cell lines
  • lines changed 90, context: html, text, full: html, text
    cleaning up the target termId's, commenting out trouble ones that we do not use in the mdb
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    REDfly track.
• src/hg/makeDb/trackDb/gibbon/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Changed display of tracks per discussion in redmine #8887 comment 30.
• src/hg/makeDb/trackDb/human/coriellDelDup.html
  • lines changed 25, context: html, text, full: html, text
    Coriell and genotype track changes.
• src/hg/makeDb/trackDb/human/genotypeArrays.html
  • lines changed 255, context: html, text, full: html, text
    Coriell and genotype track changes.
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
  • lines changed 61, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Adding BAM track at David's request.
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 233, context: html, text, full: html, text
    Coriell and genotype track changes.
  • lines changed 60, context: html, text, full: html, text
    Trying to merge things after a conflict.
    Merge branch 'master' of aamp@hgwdev.cse.ucsc.edu:/data/git/kent
    
    Conflicts:
    src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
    
  • lines changed 47, context: html, text, full: html, text
    Latest description of Affy CytoScan added.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 316, context: html, text, full: html, text
    Removing a duplicate file and adding back in missing md5sums
  • lines changed 65, context: html, text, full: html, text
    changing the names of the spikeins
  • lines changed 452, context: html, text, full: html, text
    Changing the V2 names of the protocols that were never V2, dropping the protocol none
  • lines changed 10, context: html, text, full: html, text
    A few more protocols that should not have been V2
  • lines changed 35, context: html, text, full: html, text
    Adding accessions
  • lines changed 9, context: html, text, full: html, text
    Standardizing GeneCard: and commenting out trouble antibodies that are not used
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 31, context: html, text, full: html, text
    added accessions for fastqs for GisRnaPet
  • lines changed 1, context: html, text, full: html, text
    removing the readType for the composite
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 4, context: html, text, full: html, text
    added 2 GSMs that somehow evaded my script
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
  • lines changed 6, context: html, text, full: html, text
    added accessions for HAIB wgbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 39, context: html, text, full: html, text
    fixed haib dataVersion dates
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 166, context: html, text, full: html, text
    added in new expIds and accessions
  • lines changed 21, context: html, text, full: html, text
    qa fixes for open chrom faire
  • lines changed 88, context: html, text, full: html, text
    updated controlIds
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 19, context: html, text, full: html, text
    added geo accessions for Open Chrom Synth
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.obsolete.ra
  • lines changed 40, context: html, text, full: html, text
    This is cluttering up our metadata dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 883, context: html, text, full: html, text
    Staging on beta CSHL Long RNA-Seq (Release 3) RM#7907
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 569, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisChiaPet.ra
  • lines changed 62, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibGenotype.ra
  • lines changed 90, context: html, text, full: html, text
    Updating GEO numbers for wgEncodeHaibGenotype for RM9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethyl450.ra
  • lines changed 65, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 47, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
  • lines changed 2250, context: html, text, full: html, text
    Staging on beta Open Chrom FAIRE (Release 2) RM#4142
  • lines changed 273, context: html, text, full: html, text
    Restaging some metaData for Open Chrom FAIRE (Release 2) RM# 4142
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 220, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 9, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUmassDekker5C.ra
  • lines changed 46, context: html, text, full: html, text
    Adding GEO numbers for wgEncodeUmassDekker5C RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProt.ra
  • lines changed 31, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProtGenc.ra
  • lines changed 49, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUw5C.ra
  • lines changed 38, context: html, text, full: html, text
    Adding GEO numbers for wgEncodeUw5C RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlShortRnaSeq.ra
  • lines changed 569, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisChiaPet.ra
  • lines changed 62, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibGenotype.ra
  • lines changed 90, context: html, text, full: html, text
    Updating GEO numbers for wgEncodeHaibGenotype for RM9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethyl450.ra
  • lines changed 65, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
  • lines changed 47, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 220, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 9, context: html, text, full: html, text
    Adding GEO numbers for multiple traks RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUmassDekker5C.ra
  • lines changed 46, context: html, text, full: html, text
    Adding GEO numbers for wgEncodeUmassDekker5C RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUncBsuProt.ra
  • lines changed 31, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUncBsuProtGenc.ra
  • lines changed 570, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUw5C.ra
  • lines changed 38, context: html, text, full: html, text
    Adding GEO numbers for wgEncodeUw5C RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 51, context: html, text, full: html, text
    Updating md5sum metaDb/Magic# for Zip file push, RM#8477
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 20, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Adding BAM track at David's request.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 99, context: html, text, full: html, text
    Coriell and genotype track changes.
  • lines changed 9, context: html, text, full: html, text
    add track of Pfam domains in UCSC genes (#8968)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging on public, and updating metaDB for UNC BSU Protegenomics Tracks/Gencode Mapping (Release 1) RM#8419
  • lines changed 2, context: html, text, full: html, text
    Staging on beta Open Chrom FAIRE (Release 2) RM#4142
  • lines changed 3, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
  • lines changed 2, context: html, text, full: html, text
    Staging on beta CSHL Long RNA-Seq (Release 3) RM#7907
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.html
  • lines changed 6, context: html, text, full: html, text
    Preparing for release: Adding a notes file, fixing the defualts and the labels, adding release notes
  • lines changed 1, context: html, text, full: html, text
    Commenting out a V1 that has been replaced
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 1305, context: html, text, full: html, text
    Preparing for release: Adding a notes file, fixing the defualts and the labels, adding release notes
  • lines changed 478, context: html, text, full: html, text
    Standardizing GeneCard: and commenting out trouble antibodies that are not used
  • lines changed 34, context: html, text, full: html, text
    Commenting out a V1 that has been replaced
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adding geo column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
  • lines changed 10, context: html, text, full: html, text
    updated release notes
  • lines changed 116, context: html, text, full: html, text
    qa fixes for open chrom faire
  • lines changed 3, context: html, text, full: html, text
    qa fixes for open chrom faire
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 52, context: html, text, full: html, text
    qa fixes for open chrom faire
  • lines changed 1, context: html, text, full: html, text
    forgot to indicate new html
  • lines changed 55, context: html, text, full: html, text
    qa fixes for open chrom faire
  • lines changed 9, context: html, text, full: html, text
    fixed some shortlabel to be more clear
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing plurality of data
  • lines changed 4, context: html, text, full: html, text
    Making small change to release notes for UNC BSU Prot (Release 2), similar Release 1 language from UncBsuProtGenc snuck in by accident, RM#8419
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
  • lines changed 1, context: html, text, full: html, text
    Fixing plurality of data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch.ra
  • lines changed 12, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch2.html
  • lines changed 139, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch2.ra
  • lines changed 13, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 1, context: html, text, full: html, text
    Adding geo accession column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.html
  • lines changed 137, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.ra
  • lines changed 12, context: html, text, full: html, text
    Trying to clear out the plethora of versions of this file
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Coriell and genotype track changes.
  • lines changed 12, context: html, text, full: html, text
    Trying to merge things after a conflict.
    Merge branch 'master' of aamp@hgwdev.cse.ucsc.edu:/data/git/kent
    
    Conflicts:
    src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
    
• src/hg/makeDb/trackDb/mouse/mm10/assemblyFrags.html
  • lines changed 5, context: html, text, full: html, text
    adding an assemblyFrags track
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 1, context: html, text, full: html, text
    Moved Tree Shrew to end of Euarchontoglire set to match phylo image.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    adding an assemblyFrags track
  • lines changed 10, context: html, text, full: html, text
    add a track that has the lifted over mm9 ucsc genes (#7045)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 311, context: html, text, full: html, text
    added geo accessions for mm9 CSHL long and LICR histone
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 399, context: html, text, full: html, text
    added geo accessions for mm9 CSHL long and LICR histone
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra
  • lines changed 118, context: html, text, full: html, text
    added geo accessions for many mm9 tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 56, context: html, text, full: html, text
    added geo accessions for many mm9 tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 2, context: html, text, full: html, text
    added geo accessions for many mm9 tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 41, context: html, text, full: html, text
    added new md5sums for double-compression fixed files in mm9 UwDnase
  • lines changed 17036, context: html, text, full: html, text
    added geo accessions for many mm9 tracks
  • lines changed 17036, context: html, text, full: html, text
    fixing accidental overwrite of this tracks alpha metadb in previous commit
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 174, context: html, text, full: html, text
    added geo accessions for many mm9 tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechHist.ra
  • lines changed 1, context: html, text, full: html, text
    Updating md5sum metaDb/Magic# for Zip file push, RM#8477
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 311, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrHistone.ra
  • lines changed 399, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuRnaSeq.ra
  • lines changed 118, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 10643, context: html, text, full: html, text
    added new md5sums for double-compression fixed files in mm9 UwDnase
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechHist.ra
  • lines changed 18, context: html, text, full: html, text
    Updating md5sum metaDb/Magic# for Zip file push, RM#8477
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    Updating md5sum metaDb/Magic# for Zip file push, RM#8477
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 311, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrHistone.ra
  • lines changed 399, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuRnaSeq.ra
  • lines changed 118, context: html, text, full: html, text
    Updating GEO numbers per RedMine#9065
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 293, context: html, text, full: html, text
    shortlabels and fixing whitespace
  • lines changed 75, context: html, text, full: html, text
    long labels for uw dnase mm9
• src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
  • lines changed 1, context: html, text, full: html, text
    Fixed typo: Geneome -> Genome.
• src/hg/near/hgNear/getSeq.c
  • lines changed 1, context: html, text, full: html, text
    Code Review #9053: typo fix.
• src/hg/near/hgNear/hgNearData/Mouse/gnfMouseAtlas3.html
  • lines changed 1, context: html, text, full: html, text
    Code Review #9053: simplifying pubmed link format so no encoding is required.
• src/hg/pslCDnaFilter/overlapFilter.c
  • lines changed 44, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/noopTest/filt.out
  • lines changed 2, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/noopTest/keep.psl
  • lines changed 2, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/overlapTest/drop.psl
  • lines changed 1, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/overlapTest/filt.out
  • lines changed 3, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/overlapTest/keep.psl
  • lines changed 1, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/filt.out
  • lines changed 2, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/keep.psl
  • lines changed 2, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/input/README
  • lines changed 4, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/input/overlap.psl
  • lines changed 3, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/pslCDnaFilter/tests/input/overlap.sizes
  • lines changed 1, context: html, text, full: html, text
    fixed bug where identical PSLs were being flags as weird alignments instead of being dropped as duplicate overlaping
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 2, context: html, text, full: html, text
    Track #8360 (snp137): when piping data to hgLoadSqlTab, the load datacommand timed out, I guess because it took too long to get data on
    /dev/stdin. So just create a tmp.tab (it's in TMPDIR not /hive) and
    pass that to hgLoadSqlTab.
    
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    added warning to makeGenomeDb.pl scream if chromosome names are too long
• src/inc/net.h
  • lines changed 17, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 2, context: html, text, full: html, text
    making tcp connect timeout be a define constant
• src/kehayden/alphaChain/DYZ3.pairRdData.txt
  • lines changed 834, context: html, text, full: html, text
    Adding inputs to alphaChain from Y chromosome as a test set.
• src/kehayden/alphaChain/DYZ3_alphaChain_monOrder.txt
  • lines changed 34, context: html, text, full: html, text
    Adding inputs to alphaChain from Y chromosome as a test set.
• src/kehayden/alphaChain/alphaChain.c
  • lines changed 72, context: html, text, full: html, text
    Adding a bunch of debugging code. Preventing higher level counts on output from follang below the children's counts. Thinking about (but not yet implementing) change so ends of input lines are not put in a 2-mers and 1-mers when lines are 3 or more long.
  • lines changed 13, context: html, text, full: html, text
    Converting some debugging code into verbose logging statements.
  • lines changed 95, context: html, text, full: html, text
    Reworking command line and refactoring to add monomer classification info. Not yet implemented, just refactoring.
  • lines changed 58, context: html, text, full: html, text
    Loading in monomer order file.
  • lines changed 46, context: html, text, full: html, text
    Some refactoring. Making it so saves entire generated chain in memory so that can go back further than just last 3.
  • lines changed 37, context: html, text, full: html, text
    Refactoring - working towards making predictNext more general.
  • lines changed 122, context: html, text, full: html, text
    Making program look at the monomer order file to help it's predictions in case where it has nothing it can use in the markov chains.
  • lines changed 7, context: html, text, full: html, text
    Removing pairFile command line parameter since not yet using it. Improving usage message.
• src/kehayden/alphaChain/doIt
  • lines changed 2, context: html, text, full: html, text
    Removing pairFile command line parameter since not yet using it. Improving usage message.
• src/lib/cheapcgi.c
  • lines changed 1, context: html, text, full: html, text
    a full cart on mm9 is much larger than 16K characters on the command line, raise limit to 64K
• src/lib/dnautil.c
  • lines changed 1, context: html, text, full: html, text
    Adding a flag to prevent init from happening twice in dnaUtilOpen.
• src/lib/https.c
  • lines changed 10, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 4, context: html, text, full: html, text
    making tcp connect timeout be a define constant
• src/lib/net.c
  • lines changed 135, context: html, text, full: html, text
    add tracking of connect-failures to hgCustom and hgTracks which may have many bigDataUrls pointing to the same failing site; also fixed a bug in the timeout handling of EINTR
  • lines changed 1, context: html, text, full: html, text
    making tcp connect timeout be a define constant
• src/lib/twoBit.c
  • lines changed 5, context: html, text, full: html, text
    eliminated pointless check for .2bit suffix in file name. There's checks elsewhere for file signature (#9095)
  • lines changed 36, context: html, text, full: html, text
    fix twoBit recognition logic (#9095). Look for signature in file rather than .2bit suffix
• src/utils/faFilter/faFilter.c
  • lines changed 7, context: html, text, full: html, text
    adding ignore case option to faFilter
  • lines changed 2, context: html, text, full: html, text
    fixed bug in faFilter where -namePatList did not do anything
• src/utils/faFilter/tests/expected/testPatList.fa
  • lines changed 6, context: html, text, full: html, text
    fixed bug in faFilter where -namePatList did not do anything
• src/utils/faFilter/tests/expected/testUniqIc.fa
  • lines changed 2, context: html, text, full: html, text
    adding ignore case option to faFilter
• src/utils/faFilter/tests/input/basicIds.lst
  • lines changed 3, context: html, text, full: html, text
    fixed bug in faFilter where -namePatList did not do anything
• src/utils/faFilter/tests/input/uniqIc.fa
  • lines changed 4, context: html, text, full: html, text
    adding ignore case option to faFilter
• src/utils/faFilter/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    adding ignore case option to faFilter
  • lines changed 8, context: html, text, full: html, text
    fixed bug in faFilter where -namePatList did not do anything
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v273 final build
• src/utils/twoBitToFa/makefile
  • lines changed 1, context: html, text, full: html, text
    added -bedPos option and a test for it
• src/utils/twoBitToFa/tests/expected/bed_ml_partial_list.fa
  • lines changed 4, context: html, text, full: html, text
    added -bedPos option and a test for it
• src/utils/twoBitToFa/tests/input/seqlist2.bed
  • lines changed 2, context: html, text, full: html, text
    added -bedPos option and a test for it
• src/utils/twoBitToFa/twoBitToFa.c
  • lines changed 19, context: html, text, full: html, text
    added -bedPos option and a test for it
  • lines changed 1, context: html, text, full: html, text
    help change for twoBitToFa.c
  • lines changed 2, context: html, text, full: html, text
    bugfix: -noMask had no effect when -bed was set
  • lines changed 4, context: html, text, full: html, text
    one more fix for this

• lines changed: 75480
• files changed: 211