All File Changes

v304_base to v305_preview (2014-08-11 to 2014-08-18) v305

• src/hg/hgTables/genomeSpace.c
  • lines changed 1, context: html, text, full: html, text
    fixing wording in genomeSpace upload progress page
  • lines changed 1, context: html, text, full: html, text
    tiny improvement in error message
  • lines changed 16, context: html, text, full: html, text
    trying to improve error-handling a little by including the stderr output of the background task if it looks like it stopped running.
  • lines changed 4, context: html, text, full: html, text
    do not copy in stderr background output if the file was already successfully uploaded
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 47, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHg18.html
  • lines changed 11, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHg18.html
  • lines changed 11, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 2, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 2, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 139, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 9, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/fileFormats.html
  • lines changed 2, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/index.html
  • lines changed 269, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 3, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 12, context: html, text, full: html, text
    Added marmoset paper.
• src/hg/htdocs/images/encode/browser.png
  • lines changed 0, context: html, text, full: html, text
    Add screenshots of tools for new UCSC ENCODE home page. refs #13616
• src/hg/htdocs/images/encode/dataMatrix.png
  • lines changed 0, context: html, text, full: html, text
    Add screenshots of tools for new UCSC ENCODE home page. refs #13616
• src/hg/htdocs/images/encode/search.png
  • lines changed 0, context: html, text, full: html, text
    Add screenshots of tools for new UCSC ENCODE home page. refs #13616
• src/hg/htdocs/images/encode/stanfordSearch.png
  • lines changed 0, context: html, text, full: html, text
    Add screenshots of tools for new UCSC ENCODE home page. refs #13616
• src/hg/htdocs/images/gbLogoOnly.png
  • lines changed 0, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/images/humanNew.jpg
  • lines changed 0, context: html, text, full: html, text
    adding new version of human gateway page image that Branwyn asked us to use
• src/hg/htdocs/inc/encodeProjectSoftware.topbar.html
  • lines changed 8, context: html, text, full: html, text
    Second round of UCSC-ifying ENCODE pages. Change color scheme and logo, and revamp home page. Intended as final pass for QA before cutover of encodeproject.org to Stanford. refs #13616
• src/hg/htdocs/indexIntro.html
  • lines changed 2, context: html, text, full: html, text
    adding back in 'alt=' to links to FB, Twitter & donation site and adding @ to twitter handle. refs #13797
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    adding back in 'alt=' to links to FB, Twitter & donation site and adding @ to twitter handle. refs #13797
• src/hg/inc/gtexData.h
  • lines changed 64, context: html, text, full: html, text
    Cleanup
• src/hg/inc/gtexDonor.h
  • lines changed 69, context: html, text, full: html, text
    Add lib files for gtexDonor table. refs #13504
• src/hg/inc/gtexSample.h
  • lines changed 5, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/inc/gtexSampleData.h
  • lines changed 69, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/inc/gtexTissue.h
  • lines changed 69, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/inc/gtexTissueData.h
  • lines changed 64, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/chromInfo.sql
  • lines changed 1, context: html, text, full: html, text
    allow maximum length for mirror site builds refs #13792
• src/hg/lib/gtexData.as
  • lines changed 7, context: html, text, full: html, text
    Cleanup
• src/hg/lib/gtexData.c
  • lines changed 156, context: html, text, full: html, text
    Cleanup
• src/hg/lib/gtexDonor.as
  • lines changed 8, context: html, text, full: html, text
    Add lib files for gtexDonor table. refs #13504
• src/hg/lib/gtexDonor.c
  • lines changed 152, context: html, text, full: html, text
    Add lib files for gtexDonor table. refs #13504
• src/hg/lib/gtexDonor.sql
  • lines changed 14, context: html, text, full: html, text
    Add lib files for gtexDonor table. refs #13504
• src/hg/lib/gtexSample.as
  • lines changed 4, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexSample.c
  • lines changed 21, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexSample.sql
  • lines changed 13, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexSampleData.as
  • lines changed 8, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexSampleData.c
  • lines changed 155, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
  • lines changed 2, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/lib/gtexSampleData.sql
  • lines changed 14, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
  • lines changed 2, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/lib/gtexTissue.as
  • lines changed 8, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexTissue.c
  • lines changed 155, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexTissue.sql
  • lines changed 14, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexTissueData.as
  • lines changed 7, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexTissueData.c
  • lines changed 158, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/gtexTissueData.sql
  • lines changed 13, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
  • lines changed 1, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/lib/sqlProg.c
  • lines changed 25, context: html, text, full: html, text
    for hgsql and related utils, try to remove old temp .hgsql.cnf-* files that have not been accessed for 30 days.
  • lines changed 2, context: html, text, full: html, text
    oops that would not work anyways
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    use the udcCache for trackDb ra files. Fixes problem with track hubsthat had include statements in their trackDb.txt files.
    
• src/hg/makeDb/doc/gtex/2014-jan.txt
  • lines changed 59, context: html, text, full: html, text
    Add table of levels for all GTEX samples. refs #13504
  • lines changed 7, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/doc/hg38.txt
  • lines changed 43, context: html, text, full: html, text
    building genomicSuperDups track refs #13580
  • lines changed 54, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/outside/hgGtex/expected/gtexTest.tab
  • lines changed 3, context: html, text, full: html, text
    Cleanup
• src/hg/makeDb/outside/hgGtex/expected/gtexTestDonor.tab
  • lines changed 214, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/outside/hgGtex/expected/gtexTestSample.tab
  • lines changed 2921, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
• src/hg/makeDb/outside/hgGtex/expected/gtexTestSampleData.tab
  • lines changed 8763, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/outside/hgGtex/expected/gtexTestSamples.tab
  • lines changed 2921, context: html, text, full: html, text
    Cleanup
• src/hg/makeDb/outside/hgGtex/expected/gtexTestTissue.tab
  • lines changed 53, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/outside/hgGtex/expected/gtexTestTissueData.tab
  • lines changed 3, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 2, context: html, text, full: html, text
    Swap param order for consistency
  • lines changed 96, context: html, text, full: html, text
    Add table of levels for all GTEX samples. refs #13504
  • lines changed 380, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
  • lines changed 21, context: html, text, full: html, text
    Make it more readable, as per braney code review. refs #13801
  • lines changed 112, context: html, text, full: html, text
    Add gtexDonor table. Fix some table loading problems. refs #13504
• src/hg/makeDb/outside/hgGtex/makefile
  • lines changed 2, context: html, text, full: html, text
    Add table of levels for all GTEX samples. refs #13504
  • lines changed 12, context: html, text, full: html, text
    Expand schema for GTex. Create tissue short names and use these in sample and data tables. refs #13504
  • lines changed 3, context: html, text, full: html, text
    Clean up test targets
• src/hg/makeDb/outside/makefile
  • lines changed 1, context: html, text, full: html, text
    Make it more readable, as per braney code review. refs #13801
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    tables ignored centromeres for hg38 refs #12689
  • lines changed 84, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/trackDb/cgapSage.html
  • lines changed 109, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/affyGnf1h.html
  • lines changed 15, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/affyU133.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/affyU133Plus2.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/affyU95.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 80, context: html, text, full: html, text
    trying visibility settings refs #13713
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/decodeRmap.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/eioJcviNAS.html
  • lines changed 48, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/est.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 37, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg16/description.html
  • lines changed 1, context: html, text, full: html, text
    switching from the old image (with 'UCSC' to the new image for the human gateway description pages
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 1, context: html, text, full: html, text
    switching from the old image (with 'UCSC' to the new image for the human gateway description pages
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 1, context: html, text, full: html, text
    switching from the old image (with 'UCSC' to the new image for the human gateway description pages
• src/hg/makeDb/trackDb/human/hg19/acembly.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/affyExonArray.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 52, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 53, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/consIndelsHgMmCanFam.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 23, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 1, context: html, text, full: html, text
    switching from the old image (with 'UCSC' to the new image for the human gateway description pages
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 19, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/evoCpg.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 57, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 6, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
  • lines changed 31, context: html, text, full: html, text
    adding methods and credits sections refs #12689
  • lines changed 1, context: html, text, full: html, text
    Moving parentheses outside of link, refs #12689
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 1, context: html, text, full: html, text
    switching from the old image (with 'UCSC' to the new image for the human gateway description pages
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    override for genomicSuperDups to get them into the rep group refs #13580
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.html
  • lines changed 334, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.ra
  • lines changed 263, context: html, text, full: html, text
    Loaded GENCODE V20
• src/hg/makeDb/trackDb/human/ntOoaHaplo.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/ntSssTop5p.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
  • lines changed 78, context: html, text, full: html, text
    Added regular expressions for mm10 NCBI Ends track; refs #10083
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Adding missing origAssembly line for lifted FaceBase track
• src/hg/oneShot/ga4ghToBed/ga4ghToBed.c
  • lines changed 169, context: html, text, full: html, text
    First cut of a utility to grab reads out of google using GA4GH API.
  • lines changed 2, context: html, text, full: html, text
    Adding timing information.
  • lines changed 7, context: html, text, full: html, text
    Improving usage message.
  • lines changed 26, context: html, text, full: html, text
    Improving commenting
• src/hg/oneShot/ga4ghToBed/makefile
  • lines changed 3, context: html, text, full: html, text
    First cut of a utility to grab reads out of google using GA4GH API.
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 31, context: html, text, full: html, text
    allow loading of a different named table refs #9741
• src/hg/utils/automation/fetchOneNcbi.sh
  • lines changed 34, context: html, text, full: html, text
    operating the rsync to fetch a new assembly refs #252
• src/hg/utils/automation/quickDbBuild.sh
  • lines changed 71, context: html, text, full: html, text
    simple database and dbDb builds for a database refs #252
• src/hg/utils/automation/quickDbdbBuild.sh
  • lines changed 115, context: html, text, full: html, text
    simple database and dbDb builds for a database refs #252
• src/hg/utils/automation/unplacedScaffolds.pl
  • lines changed 78, context: html, text, full: html, text
    now with -mito argument to add chrM sequence from genbank id refs #272
• src/hg/utils/phyloTrees/120way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/122way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/123way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/126way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/129way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/130way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/131way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/166way.commonNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/166way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/171way.commonNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/171way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/172way.commonNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/172way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/174way.commonNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/181way.commonNames.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/181way.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/181way.scientificNames.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 15, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/db.ncbiTaxId.tab
  • lines changed 9, context: html, text, full: html, text
    adding new assemblies bosTau bucRhi chaVoc cypVar esoLuc halLeu manVit notCor tinGut refs #11636
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    adding new orgs corCor manPen refs #11636
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 15, context: html, text, full: html, text
    adding new orgs hg38 bosTau8 manPen1 chaVoc2 bucRhi1 tinGut2 halLeu1 corCor1 manVit2 phaCar1 croPor0 gavGan0 notCor cypVar1 esoLuc1 refs #11636
  • lines changed 1, context: html, text, full: html, text
    fixup notCor name refs #11636
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    add order key for manPen1 refs #11636
• src/hg/utils/phyloTrees/makefile
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    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/placentals.txt
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    adding galVar Malayan flying lemur and phyCat sperm whale - Physeter catodon refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/speciesList.sh
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    fixup tricky name mangling refs #10272
• src/inc/jsonWrite.h
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    Making 'var' parameter, which describes tag, optional so can be used for unnamed fields, such as in an array.
• src/lib/htmlPage.c
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    Fixing case on Content-Length
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    oops, htmlWarnBoxSetUpAlready has been declared above so I could reset it in genomeSpace when outputting multiple pages during progress updates. Looks like this line should have been removed, but somehow survived the merge.
  • lines changed 1, context: html, text, full: html, text
    newline makes the html more readable and easier to parse
• src/lib/jsonWrite.c
  • lines changed 19, context: html, text, full: html, text
    Making 'var' parameter, which describes tag, optional so can be used for unnamed fields, such as in an array.
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 61, context: html, text, full: html, text
    Adding -minMax option.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v305 preview1 refs #13703

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• files changed: 173