All File Changes

v327_preview to v327_preview2 (2015-12-14 to 2016-01-04) v327

• src/browserbox/root/updateBrowser.sh
  • lines changed 7, context: html, text, full: html, text
    adding gbib link to help menu, refs #16499
    
• src/hg/hgGene/malacards.c
  • lines changed 16, context: html, text, full: html, text
    fixing malacards outlink after code review, HT to kate, refs #14417
    
  • lines changed 1, context: html, text, full: html, text
    changing descriptive text to suggestion by Cath, refs #14417
    
  • lines changed 1, context: html, text, full: html, text
    fixing malacards linkout again, refs #14417
    
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 6, context: html, text, full: html, text
    adding a comment to describe hgMenubar, no redmine
    
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    some tweaks to CRAM support #14717
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 2, context: html, text, full: html, text
    some tweaks to CRAM support #14717
    
• src/hg/hgTracks/config.c
  • lines changed 6, context: html, text, full: html, text
    Added a link to multiRegion help in multi-region config popup
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 37, context: html, text, full: html, text
    Make gene model more vivid (and useful) when it's not too busy (<500K window and single graph), by using pack instead of squish. refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 14, context: html, text, full: html, text
    Earlier, the only way to turn on EM mode was via config dialog box. But with the new "e v" hotkeys, it can come in with no default emGeneTrack defined yet.
    
  • lines changed 8, context: html, text, full: html, text
    Handle when the emGeneTable has poor coverage for a chromosome, leaving regionList empty. Gives the user a warning and returns to default view.
    
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    Removing unused argument - caused a warning in Mac clang but not on hgwdev.
    
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    some tweaks to CRAM support #14717
    
• src/hg/hgc/gencodeClick.c
  • lines changed 72, context: html, text, full: html, text
    include APPRIS classification in GENCODE details display (RM #16528)
    
  • lines changed 1, context: html, text, full: html, text
    fixed bug with APPRIS changes generating invalid select in certain cases
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Adding felCat8 to release table
    
  • lines changed 3, context: html, text, full: html, text
    Adding section for xenTro7, refs #9868
    
  • lines changed 1, context: html, text, full: html, text
    Correcting date of felCat8 assembly
    
  • lines changed 1, context: html, text, full: html, text
    Updating acknowledgements for felCat8 and fixing underscore
    
• src/hg/htdocs/FAQ/index.html
  • lines changed 14, context: html, text, full: html, text
    Fixing character limit, refs # 16519
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    Adding info for xenTro7 release, refs #9868
    
  • lines changed 32, context: html, text, full: html, text
    Updating acknowledgements for felCat8 and fixing underscore
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 23, context: html, text, full: html, text
    Adding info for new related tables output feature to hgIntegrator help docs, refs #16539
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 19, context: html, text, full: html, text
    Updating cv.ra to fix some broken vendor links, minor work on multi-region document
    
  • lines changed 102, context: html, text, full: html, text
    More work on multi-region help page
    
  • lines changed 48, context: html, text, full: html, text
    Adding notes about gene and exon views, mostly finished. Started section about BED regions, refs #16526
    
  • lines changed 62, context: html, text, full: html, text
    More work on multi region help doc
    
  • lines changed 51, context: html, text, full: html, text
    More additions to bed file help section in multiregion doc
    
  • lines changed 8, context: html, text, full: html, text
    Minor changes to multi-region help doc, refs #16526
    
  • lines changed 30, context: html, text, full: html, text
    More help doc work, refs 16526
    
  • lines changed 81, context: html, text, full: html, text
    added some haplotype and general viewing info to multi-region help doc, refs #16565
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    Adding announcement for hgIntegrator related tables feature, refs #15544
    
  • lines changed 1, context: html, text, full: html, text
    Correcting name tag for hgIntegrator related tables announcement, refs #15544
    
  • lines changed 1, context: html, text, full: html, text
    Adding missing word to announcement, refs #15544
    
  • lines changed 48, context: html, text, full: html, text
    Adding news announcements for felCat8 and xenTro7 release
    
  • lines changed 3, context: html, text, full: html, text
    Fixes to xenTro7 and felCat8 announcements, refs #9868 #14412
    
• src/hg/htdocs/images/gtex/gtexSampleAge.V4.png
  • lines changed 0, context: html, text, full: html, text
    Include proper sample plots. refs #15645
    
• src/hg/htdocs/images/gtex/gtexSampleRin.V4.png
  • lines changed 0, context: html, text, full: html, text
    Include proper sample plots. refs #15645
    
• src/hg/htdocs/images/hgIntegratorRelatedTablesAnnouncement.png
  • lines changed 0, context: html, text, full: html, text
    Adding announcement for hgIntegrator related tables feature, refs #15544
    
• src/hg/htdocs/indexNews.html
  • lines changed 38, context: html, text, full: html, text
    Adding announcement for hgIntegrator related tables feature, refs #15544
    
  • lines changed 1, context: html, text, full: html, text
    Adding missing word to announcement, refs #15544
    
  • lines changed 134, context: html, text, full: html, text
    Adding news announcements for felCat8 and xenTro7 release
    
  • lines changed 23, context: html, text, full: html, text
    Fixes to xenTro7 and felCat8 announcements, refs #9868 #14412
    
  • lines changed 1, context: html, text, full: html, text
    Adding in missing line, no redmine
    
• src/hg/htdocs/staff.html
  • lines changed 0, context: html, text, full: html, text
    testing
    
• src/hg/inc/hgBam.h
  • lines changed 5, context: html, text, full: html, text
    some tweaks to CRAM support #14717
    
• src/hg/lib/hgBam.c
  • lines changed 14, context: html, text, full: html, text
    some tweaks to CRAM support #14717
    
• src/hg/makeDb/doc/hg38/hg38Patch5.txt
  • lines changed 168, context: html, text, full: html, text
    Docs and ra files for hg38Patch5, refs #16261
    
• src/hg/makeDb/doc/oxyTri2/initialBuild.txt
  • lines changed 604, context: html, text, full: html, text
    catching build procedure up to date refs #16535
    
• src/hg/makeDb/genbank/common.mk
  • lines changed 1, context: html, text, full: html, text
    Adding unused-but-set warning to genbank make, refs #16121
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added aptMan1 - Brown Kiwi refs #16029
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Turning on GenBank updates for xenTro7, refs #9868
    
  • lines changed 2, context: html, text, full: html, text
    Adding felCat8 to autoupdates, refs #14412
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added aptMan1 - Brown Kiwi refs #16029
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding xenTro7 to rr updates, refs #9868
    
  • lines changed 2, context: html, text, full: html, text
    Adding felCat8 to genbank updates rr
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/coverage.ra
  • lines changed 100, context: html, text, full: html, text
    adding coverage bigWig tracks refs #16535
    
  • lines changed 16, context: html, text, full: html, text
    setting default viz refs #16535
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/rnaSeq.ra
  • lines changed 86, context: html, text, full: html, text
    adding BAM file tracks refs #16535
    
  • lines changed 1, context: html, text, full: html, text
    turning off default name display refs #16535
    
  • lines changed 7, context: html, text, full: html, text
    setting default viz refs #16535
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/selfChainPileUps.html
  • lines changed 16, context: html, text, full: html, text
    adding selfChainPileUps and NCBI Gene tracks
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/sequences.html
  • lines changed 12, context: html, text, full: html, text
    adding sequences track refs #16535
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    adding selfChainPileUps and NCBI Gene tracks
    
  • lines changed 1, context: html, text, full: html, text
    for some odd reason the gene names are not showing on ncbiGene refs no redmine
    
  • lines changed 25, context: html, text, full: html, text
    adding sequences track refs #16535
    
  • lines changed 27, context: html, text, full: html, text
    adding tracks from Zahler browser ncRNAs microGenes and mergeJunctions refs #16535
    
  • lines changed 8, context: html, text, full: html, text
    add pileUps200 location track and mergeJunctions should be in regulation group refs #16535
    
  • lines changed 2, context: html, text, full: html, text
    adding BAM file tracks refs #16535
    
  • lines changed 1, context: html, text, full: html, text
    adding coverage bigWig tracks refs #16535
    
  • lines changed 19, context: html, text, full: html, text
    convert ncbiGenes genePred to xNcbiGenes bed track refs #16535
    
  • lines changed 4, context: html, text, full: html, text
    setting default viz refs #16535
    
  • lines changed 5, context: html, text, full: html, text
    *ncbiGene has become genbankGenes with correct indexes refs #16535
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7, context: html, text, full: html, text
    Updating cv.ra to fix some broken vendor links, minor work on multi-region document
    
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 7, context: html, text, full: html, text
    Updating cv.ra to fix some broken vendor links, minor work on multi-region document
    
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 7, context: html, text, full: html, text
    Updating cv.ra to fix some broken vendor links, minor work on multi-region document
    
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra
  • lines changed 58, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
  • lines changed 2, context: html, text, full: html, text
    Chainging matrix for cat on dog and html escaps on hg38, refs #14412
    
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    moved RefSeq track to first place on horse assemblies
    
• src/hg/makeDb/trackDb/human/chainNetFelCat8.ra
  • lines changed 15, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 1, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 5, context: html, text, full: html, text
    Add sample characterization plots. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Include proper sample plots. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Fix path to images.
    
  • lines changed 6, context: html, text, full: html, text
    Spell fix and point to portal.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
  • lines changed 1, context: html, text, full: html, text
    adding a comment to describe why the tRNAs track is being overwritten
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch5.ra
  • lines changed 118, context: html, text, full: html, text
    Docs and ra files for hg38Patch5, refs #16261
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Docs and ra files for hg38Patch5, refs #16261
    
  • lines changed 1, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
  • lines changed 1, context: html, text, full: html, text
    Removing release tag for xenTro7 chain/nets, refs #9868
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
  • lines changed 32, context: html, text, full: html, text
    added documentation on APPRIS (RM 16528)
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.html
  • lines changed 32, context: html, text, full: html, text
    added documentation on APPRIS (RM 16528)
    
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Chainging matrix for cat on dog and html escaps on hg38, refs #14412
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.html
  • lines changed 32, context: html, text, full: html, text
    added documentation on APPRIS (RM 16528)
    
• src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
  • lines changed 2, context: html, text, full: html, text
    Removed bad url (no RM#)
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
    
• src/hg/makeDb/trackDb/xenTro/xenTro7/description.html
  • lines changed 2, context: html, text, full: html, text
    Updating links on xenTro7 gateway page, refs #9868
    
• src/hg/mouseStuff/chainToPsl/chainToPsl.c
  • lines changed 478, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
  • lines changed 4, context: html, text, full: html, text
    Enabling verbosity and suppressing extra text during make test for chainToPsl
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example1.psl
  • lines changed 1, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example2.psl
  • lines changed 1, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
• src/hg/mouseStuff/chainToPsl/tests/input/example1.chain
  • lines changed 98, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
• src/hg/mouseStuff/chainToPsl/tests/input/example2.chain
  • lines changed 98, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
• src/hg/mouseStuff/chainToPsl/tests/makefile
  • lines changed 37, context: html, text, full: html, text
    Fixed PSL output from chainToPsl and added tests, refs #16546
    
  • lines changed 2, context: html, text, full: html, text
    Enabling verbosity and suppressing extra text during make test for chainToPsl
    
• src/hg/utils/automation/genbank/README.txt
  • lines changed 19, context: html, text, full: html, text
    expanding the README file and adding the hub file layout construction scripts
    
• src/hg/utils/automation/genbank/assemblyDescription.pl
  • lines changed 3, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/buildStats.pl
  • lines changed 6, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/cpg.sh
  • lines changed 17, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/cronUpdate.sh
  • lines changed 45, context: html, text, full: html, text
    expanding the README file and adding the hub file layout construction scripts
    
• src/hg/utils/automation/genbank/gapDescription.pl
  • lines changed 3, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/gatewayPage.pl
  • lines changed 144, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/gc5Description.pl
  • lines changed 4, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/hubHtml.pl
  • lines changed 16, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/hubIndexInclude.sh
  • lines changed 138, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/mkGenomesTxt.sh
  • lines changed 156, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/mkHubIndex.sh
  • lines changed 135, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/mkPartitionedGenomes.txt.sh
  • lines changed 223, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/mkPartitionedHubIndexInclude.sh
  • lines changed 111, context: html, text, full: html, text
    adding hub construction scripts refs #16078
    
• src/hg/utils/automation/genbank/ncbiGeneDescription.pl
  • lines changed 5, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/ncbiToUcsc.sh
  • lines changed 33, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/ucscAltNames.sh
  • lines changed 1, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/automation/genbank/ucscPatchNames.sh
  • lines changed 1, context: html, text, full: html, text
    up to date with current versions now working on both refseq and genbank hierarchies refs #16078
    
• src/hg/utils/otto/lovd/checkAndLoad.sh
  • lines changed 1, context: html, text, full: html, text
    bad typo found in code review, refs #16518
    
• src/inc/common.mk
  • lines changed 3, context: html, text, full: html, text
    move htslib to a more standard place
    
  • lines changed 12, context: html, text, full: html, text
    tweak the HTSLIB rules a little
    
• src/lib/https.c
  • lines changed 14, context: html, text, full: html, text
    Fixes #16554
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v327 preview2 refs #16513
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 19, context: html, text, full: html, text
    improved email sending scheme refs #16516
    
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 59, context: html, text, full: html, text
    improved email sending scheme refs #16516
    

• lines changed: 4376
• files changed: 132