All File Changes

v328_preview2 to v328_base (2016-01-25 to 2016-02-08) v328

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 1, context: html, text, full: html, text
    Made field list alphabetization case insensitive.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 20, context: html, text, full: html, text
    Checking that genomics files do have an enriched_in tag.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Bumped version number
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 110, context: html, text, full: html, text
    Adding a bunch of new tags, and handling the ones that are essentially unimplemented reserved words in a separate case that for now just errAborts.
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 38, context: html, text, full: html, text
    Making the program more universal, refs #16341
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 121, context: html, text, full: html, text
    Making the script more universal, handles more input varieties refs #16182
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 2419, context: html, text, full: html, text
    Removing some GEO_ tags, adding in hippocampus bit that was mislabeled in GEO.
    
  • lines changed 1, context: html, text, full: html, text
    Added enriched_in tag, which is necessary for the validator to do it's enrichment checks.
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 108, context: html, text, full: html, text
    Adding in changes recommended by Angie, cleaning things up a bit refs #16341
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    Cosmetics on GTEx Gene trackUI page, with special effort to fit tissue table in popup dialog without scrolling.
    
  • lines changed 1, context: html, text, full: html, text
    Tweak font size of title
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 15, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/bedGraph.c
  • lines changed 17, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 17, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/config.c
  • lines changed 15, context: html, text, full: html, text
    Requested changes to multi-region config see # 16666 note 21
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 4, context: html, text, full: html, text
    Remove rainbow color scheme option. It would require noticeable work to implement fully (e.g. for tissue filter on trackUi and boxplot on hgc) and doesn't have an immediate use case. Leaving in the code as I can see there could be a need for alternate color schemes (e.g. distinct colors for brain). refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixes #16708. ORDER BY is needed for all genePreds except knownGene since the index is defined for chrom+bin key rather than simply chrom or chrom+start. This should only add a small amount of overhead.
    
  • lines changed 11, context: html, text, full: html, text
    Requested changes to multi-region config see # 16666 note 21
    
  • lines changed 46, context: html, text, full: html, text
    A request was made to hide the chromIdeo when we are in custom multi-region mode
    and ther is more than two or more different chroms in the region list.
    This is kind of a compromise. It avoids the seeming asserting that there is just
    one chrom in the view. But we also lose our place-holder that shows
    the multi-region mode that one is in. When a user zooms in far enough
    that the screen only has 1 window from 1 region, then the chromIdeo for that single
    chrom needs to be updated. So I have added a small change where when the
    ideo is hidden we still include an empty hidden map and chromIdeo image html.
    So that hgTracks.js::updateChromImg can update it later at runtime with ajax callbacks.
    This is also a partial step towards supporting multiple chromIdeos someday.
    
    Squashed commit of the following:
    
    commit 764c2932d6be67d6a67b3df47b8cf44f3c5239e4
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Fri Jan 29 19:11:53 2016 -0800
    
    code cleanup
    
    commit 408ee8dadde6d7948740a65e0a298ad006470ab7
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Fri Jan 29 18:37:47 2016 -0800
    
    checkin of fix for more dynamic ideogram
    
    commit ccac0a2f112dabd6e798904bd57b0cb5fe7c0a22
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Thu Jan 28 11:29:33 2016 -0800
    
    initial probing towards a solution for having dynmaic chromIdeos, a step on the way to supporting mulitple chromIdeos
    
  • lines changed 13, context: html, text, full: html, text
    added code to verify that for BED input data the chrom exists in the database and that chromEnd is not > chrom size.
    
  • lines changed 46, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    Requested changes to multi-region config see # 16666 note 21
    
  • lines changed 8, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/multiWig.c
  • lines changed 127, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Requested changes to multi-region config see # 16666 note 21
    
  • lines changed 3, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    close all the files that vcfTabix support opens
    
  • lines changed 2, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
  • lines changed 4, context: html, text, full: html, text
    Currently, disable the haplotype sorting display when multiple windows are found.
    
• src/hg/hgTracks/wigCommon.h
  • lines changed 12, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 1, context: html, text, full: html, text
    False dependency on wiggle.h removed
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 75, context: html, text, full: html, text
    Issue 16666. Makes autoscale work with multi-region for wig, bedGraph, bigWig, and multiWig. doWiggle still TODO.
    
• src/hg/hgc/hgc.c
  • lines changed 74, context: html, text, full: html, text
    first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
    
  • lines changed 146, context: html, text, full: html, text
    improving formatting of ncbiRefSeq click data refs #13673
    
  • lines changed 33, context: html, text, full: html, text
    remove Brian_s prNcbiRefGeneInfo business refs #13673
    
  • lines changed 49, context: html, text, full: html, text
    formatting page for ncbiRefSeq refs #13673
    
  • lines changed 18, context: html, text, full: html, text
    trying to get the psl alignment to display refs #13673
    
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Improving link to ENCODE session and adding Public Hub Guideline link refs #16748
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    Adding a note to VCF file format FAQ that ga4gh now maintains format
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    Improving link to ENCODE session and adding Public Hub Guideline link refs #16748
    
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 9, context: html, text, full: html, text
    Adding section to main hgTracks help page about multi-region, refs #16565
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 57, context: html, text, full: html, text
    Updating Assembly Hub Blat Section about gfServer on GBiB
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 14, context: html, text, full: html, text
    Fixing typo and updating text to go along with new config window, updating picture to remove TEST, refs #16565
    
  • lines changed 25, context: html, text, full: html, text
    Fixed minor text display issue. refs #16720
    
  • lines changed 3, context: html, text, full: html, text
    Adding in padding comment description, refs #16565
    
  • lines changed 23, context: html, text, full: html, text
    Adding sessions to multi-region help doc, refs #16565
    
  • lines changed 5, context: html, text, full: html, text
    Rewording a few sentences, refs #16565
    
• src/hg/htdocs/images/MultiRegionConfigurationWindow.png
  • lines changed 0, context: html, text, full: html, text
    Fixing typo and updating text to go along with new config window, updating picture to remove TEST, refs #16565
    
• src/hg/htdocs/images/MultiRegionMouseHighlighted.png
  • lines changed 0, context: html, text, full: html, text
    Fixing typo and updating text to go along with new config window, updating picture to remove TEST, refs #16565
    
• src/hg/htdocs/images/MultiRegionXGeneOnly.png
  • lines changed 0, context: html, text, full: html, text
    Updating picture that had a typo in it, refs #16565
    
• src/hg/inc/gtexTissue.h
  • lines changed 3, context: html, text, full: html, text
    First cut sortable table to select tissues. refs #15645
    
• src/hg/inc/ncbiRefSeqLink.h
  • lines changed 80, context: html, text, full: html, text
    first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v328
    
• src/hg/js/d3.dendrograms.js
  • lines changed 176, context: html, text, full: html, text
    Adding in new features, fixing bugs and removing code that was written for debug purposes refs #16341
    
• src/hg/js/hgTracks.js
  • lines changed 18, context: html, text, full: html, text
    A request was made to hide the chromIdeo when we are in custom multi-region mode
    and ther is more than two or more different chroms in the region list.
    This is kind of a compromise. It avoids the seeming asserting that there is just
    one chrom in the view. But we also lose our place-holder that shows
    the multi-region mode that one is in. When a user zooms in far enough
    that the screen only has 1 window from 1 region, then the chromIdeo for that single
    chrom needs to be updated. So I have added a small change where when the
    ideo is hidden we still include an empty hidden map and chromIdeo image html.
    So that hgTracks.js::updateChromImg can update it later at runtime with ajax callbacks.
    This is also a partial step towards supporting multiple chromIdeos someday.
    
    Squashed commit of the following:
    
    commit 764c2932d6be67d6a67b3df47b8cf44f3c5239e4
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Fri Jan 29 19:11:53 2016 -0800
    
    code cleanup
    
    commit 408ee8dadde6d7948740a65e0a298ad006470ab7
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Fri Jan 29 18:37:47 2016 -0800
    
    checkin of fix for more dynamic ideogram
    
    commit ccac0a2f112dabd6e798904bd57b0cb5fe7c0a22
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Thu Jan 28 11:29:33 2016 -0800
    
    initial probing towards a solution for having dynmaic chromIdeos, a step on the way to supporting mulitple chromIdeos
    
  • lines changed 3, context: html, text, full: html, text
    Fixes #16756. It needed the position to be disguised in the code-path where the disbleHighlightingDialog is checked in hgTracks.js.
    
  • lines changed 2, context: html, text, full: html, text
    Cosmetics on GTEx Gene trackUI page, with special effort to fit tissue table in popup dialog without scrolling.
    
  • lines changed 8, context: html, text, full: html, text
    Use gene name in GTEx geme right-click menus, even when moused over a tissue. refs #15645
    
  • lines changed 10, context: html, text, full: html, text
    Add apply button to UI popup dialog
    
  • lines changed 5, context: html, text, full: html, text
    Fixes to Apply button on hgTrackUi popup. Cosmetics on GTEx UI.
    
  • lines changed 9, context: html, text, full: html, text
    Fix broken parsing of Safari version, so image update (e.g. for drag-zoom) can be used when version supports it.
    
  • lines changed 11, context: html, text, full: html, text
    Merge branch 'master' into applyButtonBottom
    
  • lines changed 9, context: html, text, full: html, text
    Improvements to GTEx trackUI. Especially right-click menus and popup. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Restore extTools default popup width. Tweak others a little.
    
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    add 'noAltColors' class to sortable table to suppress alternating colored rows
    
  • lines changed 12, context: html, text, full: html, text
    Persist ordering in tissue table (using sortOrder cart var)
    
• src/hg/lib/gtexTissue.c
  • lines changed 22, context: html, text, full: html, text
    First cut sortable table to select tissues. refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 130, context: html, text, full: html, text
    First cut sortable table to select tissues. refs #15645
    
  • lines changed 33, context: html, text, full: html, text
    Cosmetics (stop shouting ;-)
    
  • lines changed 4, context: html, text, full: html, text
    Fix HTML syntax err.
    
  • lines changed 3, context: html, text, full: html, text
    Minor style changes.
    
  • lines changed 22, context: html, text, full: html, text
    Persist ordering in tissue table (using sortOrder cart var)
    
  • lines changed 22, context: html, text, full: html, text
    Cleanup styling.
    
  • lines changed 2, context: html, text, full: html, text
    Remove rainbow color scheme option. It would require noticeable work to implement fully (e.g. for tissue filter on trackUi and boxplot on hgc) and doesn't have an immediate use case. Leaving in the code as I can see there could be a need for alternate color schemes (e.g. distinct colors for brain). refs #15645
    
  • lines changed 106, context: html, text, full: html, text
    Special handling of popup configuration for GTEx track (see RM #15873 for why). refs #155645
    
  • lines changed 28, context: html, text, full: html, text
    Cosmetics on GTEx Gene trackUI page, with special effort to fit tissue table in popup dialog without scrolling.
    
  • lines changed 26, context: html, text, full: html, text
    Fixes to Apply button on hgTrackUi popup. Cosmetics on GTEx UI.
    
• src/hg/lib/hgFind.c
  • lines changed 8, context: html, text, full: html, text
    Fixes #16721. Bug in order of operations employed with user supplied position where start > end, causes both the start and end coordinates to be off by 1. Fixed by just doing the coordinate swap before decrementing the start by 1.
    
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    adding ncbiRefSeqLink.c to the build refs #13673
    
• src/hg/lib/ncbiRefSeqLink.as
  • lines changed 22, context: html, text, full: html, text
    first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
    
• src/hg/lib/ncbiRefSeqLink.c
  • lines changed 254, context: html, text, full: html, text
    first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
    
• src/hg/lib/ncbiRefSeqLink.sql
  • lines changed 28, context: html, text, full: html, text
    first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
    
• src/hg/makeDb/doc/aptMan1/initialBuild.txt
  • lines changed 99, context: html, text, full: html, text
    Adding in the microsattelite track which slipped past me the first time around, refs #16029
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
  • lines changed 11, context: html, text, full: html, text
    adding microsat track refs #15209
    
• src/hg/makeDb/doc/rheMac8/initialBuild.txt
  • lines changed 660, context: html, text, full: html, text
    initial files done, repeat masking done, starting genbank refs #16744
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    Added rheMac8; refs #16744
    
  • lines changed 1, context: html, text, full: html, text
    Added rheMac8; refs #16744
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    turning on genbank updates for OrnAna2, refs #15098
    
  • lines changed 2, context: html, text, full: html, text
    Starting beta genbank updates on micMur2, refs #15292
    
• src/hg/makeDb/hgLoadGenePred/hgLoadGenePred.c
  • lines changed 2, context: html, text, full: html, text
    Fixing typo in description
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Moved gwipsvizRiboseq from hg19 tablesIgnored to tablesIgnored; refs #16765
    
  • lines changed 10, context: html, text, full: html, text
    join the NCBI RefSeq track tables refs #13673
    
• src/hg/makeDb/trackDb/drosophila/droAna2/description.html
  • lines changed 3, context: html, text, full: html, text
    fixing bad url, refs #16714
    
• src/hg/makeDb/trackDb/gwipsvizRiboseq.html
  • lines changed 231, context: html, text, full: html, text
    With new hg38 version of GWIPS-viz track, moved description page from top-level to hg19 and made a copy for hg38 to be edited later; refs #16765
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 2, context: html, text, full: html, text
    Changing release tags for micMur2 release, refs #15292
    
  • lines changed 2, context: html, text, full: html, text
    Fixing mistake of overlapping release tags, refs #15292
    
• src/hg/makeDb/trackDb/human/hg19/gwipsvizRiboseq.html
  • lines changed 231, context: html, text, full: html, text
    With new hg38 version of GWIPS-viz track, moved description page from top-level to hg19 and made a copy for hg38 to be edited later; refs #16765
    
  • lines changed 2, context: html, text, full: html, text
    Updated the URL to Cutadapt; refs #16765
    
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
  • lines changed 231, context: html, text, full: html, text
    With new hg38 version of GWIPS-viz track, moved description page from top-level to hg19 and made a copy for hg38 to be edited later; refs #16765
    
  • lines changed 2, context: html, text, full: html, text
    Updated the URL to Cutadapt; refs #16765
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    Trimming long label a bit
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    making snp144Common lead item in Variation group, refs #15493
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding rheMac8 refs #16744
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #16744
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #16744
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/gold.html
  • lines changed 35, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #16744
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #16744
    
• src/hg/makeDb/trackDb/snail/bioGla0/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added some frames to snail browser maf.
    
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
  • lines changed 10, context: html, text, full: html, text
    subsume existing UCSC refseq track into ncbi refseq composite refs #13673
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    testing NCBI RefSeq track refs #13673
    
  • lines changed 8, context: html, text, full: html, text
    testing NCBI RefSeq track refs #13673
    
  • lines changed 10, context: html, text, full: html, text
    labels on ncbiRefSeqBigPsl track refs #13673
    
  • lines changed 54, context: html, text, full: html, text
    remove Brian_s ncbiRefGene definitions refs #13673
    
  • lines changed 24, context: html, text, full: html, text
    trying to get the psl alignment to display refs #13673
    
  • lines changed 67, context: html, text, full: html, text
    subsume existing UCSC refseq track into ncbi refseq composite refs #13673
    
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
  • lines changed 2, context: html, text, full: html, text
    Fixing codon translation table for 26-way conservation page, refs #15209
    
• src/hg/mouseStuff/simpleChain/simpleChain.c
  • lines changed 1, context: html, text, full: html, text
    fix simpleChain to output the correct values for the psl insert columns
    
• src/hg/oneShot/freen/freen.c
  • lines changed 63, context: html, text, full: html, text
    Freen tests timing of floating point ops when numbers are all zero vs nonzero, and testing long, single and double precision timing.
    
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 280, context: html, text, full: html, text
    working up script for NCBI RefSeq gene track processing refs #13673
    
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 359, context: html, text, full: html, text
    working up script for NCBI RefSeq gene track processing refs #13673
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 38, context: html, text, full: html, text
    added option to create genePreds records from GFF3 when exons are contained in genes, as NCBI does for psuedogenes
    
  • lines changed 97, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToGenePred/tests/expected/genesWithExonsTest.gp
  • lines changed 1, context: html, text, full: html, text
    added option to create genePreds records from GFF3 when exons are contained in genes, as NCBI does for psuedogenes
    
  • lines changed 1, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToGenePred/tests/expected/minimalGenesTest.gp
  • lines changed 1, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
  • lines changed 8, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToGenePred/tests/expected/minimalGenesTest.unprocessed
  • lines changed 2, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
  • lines changed 5, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToGenePred/tests/input/ncbiRefSeq.pseudoGenes.gff3
  • lines changed 15, context: html, text, full: html, text
    added option to create genePreds records from GFF3 when exons are contained in genes, as NCBI does for psuedogenes
    
  • lines changed 12, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    added option to create genePreds records from GFF3 when exons are contained in genes, as NCBI does for psuedogenes
    
  • lines changed 5, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 1, context: html, text, full: html, text
    Gap= lines are on the cDNA_match lines not just match lines refs #13673
    
  • lines changed 1, context: html, text, full: html, text
    use strand, rather than targetStrand, in gff3ToPsl
    
  • lines changed 13, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl
  • lines changed 20, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 266, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 1, context: html, text, full: html, text
    get otto GWAS to understand cedilla
    
• src/inc/gff3.h
  • lines changed 4, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/inc/tagStorm.h
  • lines changed 2, context: html, text, full: html, text
    Adding -leaves flag to tagStormReformat.
    
• src/lib/gff3.c
  • lines changed 4, context: html, text, full: html, text
    added options to process minimally structured genes and to output root records that are not processed
    
• src/lib/linefile.c
  • lines changed 5, context: html, text, full: html, text
    close all the files that vcfTabix support opens
    
  • lines changed 2, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
  • lines changed 1, context: html, text, full: html, text
    tweak the linefile tabix code to assume .tbi indices.
    
• src/lib/memgfx.c
  • lines changed 19, context: html, text, full: html, text
    Adding a plausible but as yet untested basic graphic function to copy part of an image to another part. It is surrounded with ifdefs, this mgBlit function, so not actually compiled.
    
• src/lib/tagStorm.c
  • lines changed 14, context: html, text, full: html, text
    Adding -leaves flag to tagStormReformat.
    
• src/lib/vcf.c
  • lines changed 7, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
  • lines changed 2, context: html, text, full: html, text
    one more time! Close vcf file if read in at open time
    
• src/tagStorm/tagStormReformat/tagStormReformat.c
  • lines changed 6, context: html, text, full: html, text
    Adding -leaves flag to tagStormReformat.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v328 final build refs #16669
    
• src/utils/userApps/fetchChromSizes
  • lines changed 50, context: html, text, full: html, text
    fixup broken zcat for Mac, fix broken FTP options refs #14987 #16763
    

• lines changed: 7939
• files changed: 151