All File Changes

v355_preview to v355_preview2 (2017-09-04 to 2017-09-11) v355

• src/browserbox/home/browser/.bashrc
  • lines changed 12, context: html, text, full: html, text
    e744f49e62f6f92b61e4deaf6cc39ad18afb0cf2 Mon Sep 11 09:41:13 2017 -0700
    Fixing gbibAddTools command and bringing .bashrc in line with the gbib .bashrc, refs #19276
• src/browserbox/home/browser/README.txt
  • lines changed 1, context: html, text, full: html, text
    5165c11759ccb35928ef9c7566cfdc02f9331958 Mon Sep 11 09:45:25 2017 -0700
    Mentioning that gbibAddTools requires sudo access in gbib README, refs #19276
• src/hg/hgCollection/hgCollection.c
  • lines changed 33, context: html, text, full: html, text
    b159fa56513cfc78d000a66cc65ff1a85a2e0c27 Tue Sep 5 17:23:40 2017 -0700
    ongoing work on hgCollection
  • lines changed 9, context: html, text, full: html, text
    9602d19ee87ad78e36ba6970cf4372937406d170 Thu Sep 7 15:57:32 2017 -0700
    copy hgCollection hubs when saved or restored from sessions
• src/hg/hgTracks/simpleTracks.c
  • lines changed 48, context: html, text, full: html, text
    b159fa56513cfc78d000a66cc65ff1a85a2e0c27 Tue Sep 5 17:23:40 2017 -0700
    ongoing work on hgCollection
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    c84bb93c44e2b071ff91f655a89ed866a36cb31c Thu Aug 31 05:17:05 2017 -0700
    Clarify messages displayed when we can't find an alignment in ncbiRefSeqPsl and/or seqNcbiRefSeq.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 26, context: html, text, full: html, text
    dc1378ce8132661f5f2b3b49693c5b3eec6afeb5 Thu Sep 7 13:42:42 2017 -0700
    Announcing Ensembl v89, refs #19526
  • lines changed 8, context: html, text, full: html, text
    9dc0727358448b711d7de660e6bb59a167a809cc Thu Sep 7 14:04:09 2017 -0700
    Fix minor typo on index, make urls relative on newsarch, refs #19526
  • lines changed 1, context: html, text, full: html, text
    7bd702dba56e4e33001d495fe1a96ed3940f9d3e Mon Sep 11 08:11:33 2017 -0700
    Fixing a minor typo: Playpus --> Platypus, no Redmine.
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 62, context: html, text, full: html, text
    b159fa56513cfc78d000a66cc65ff1a85a2e0c27 Tue Sep 5 17:23:40 2017 -0700
    ongoing work on hgCollection
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    dc1378ce8132661f5f2b3b49693c5b3eec6afeb5 Thu Sep 7 13:42:42 2017 -0700
    Announcing Ensembl v89, refs #19526
  • lines changed 1, context: html, text, full: html, text
    9dc0727358448b711d7de660e6bb59a167a809cc Thu Sep 7 14:04:09 2017 -0700
    Fix minor typo on index, make urls relative on newsarch, refs #19526
• src/hg/inc/ncbiRefSeqOther.as
  • lines changed 33, context: html, text, full: html, text
    ac99b14fc67a6843f6751148bd97358b1f93fddd Sat Sep 9 12:06:12 2017 -0700
    New script to build ncbiRefSeqOther BED with extra columns sourced from an attributes file generated by gff3ToGenePred -attrsOut. Refining attributes for ncbiRefSeqOther: * Split Dbxref into separate columns GeneID, MIM, HGNC, miRBase for linking out * Remove Name2 column which is now redundant with gene column * Remove ncrna_class column which doesn't appear in p11 GFF * Reorder columns to flow a bit better * Reword some column descriptions that appear in hgc table display
• src/hg/js/hgCollection.js
  • lines changed 90, context: html, text, full: html, text
    b159fa56513cfc78d000a66cc65ff1a85a2e0c27 Tue Sep 5 17:23:40 2017 -0700
    ongoing work on hgCollection
• src/hg/lib/cart.c
  • lines changed 54, context: html, text, full: html, text
    9602d19ee87ad78e36ba6970cf4372937406d170 Thu Sep 7 15:57:32 2017 -0700
    copy hgCollection hubs when saved or restored from sessions
• src/hg/lib/trackHub.c
  • lines changed 23, context: html, text, full: html, text
    9602d19ee87ad78e36ba6970cf4372937406d170 Thu Sep 7 15:57:32 2017 -0700
    copy hgCollection hubs when saved or restored from sessions
• src/hg/makeDb/doc/danRer10/drBlastTab.txt
  • lines changed 148, context: html, text, full: html, text
    3c142f822ddc21bc317b554c3113b8675cfbce66 Thu Sep 7 14:32:45 2017 -0700
    document the drBlastTab production refs #19526
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 19, context: html, text, full: html, text
    fb8c3a6bc30ab45bd090d04b93e8d12e434b90f7 Sat Sep 9 13:31:59 2017 -0700
    Ran updated ncbiRefSeq pipeline on hg38 (NCBI annotation release GCF_000001405.37_GRCh38.p11)
• src/hg/makeDb/doc/hg38/snpedia.txt
  • lines changed 34, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    c4af60b20c961b6595e44bfe1f148a718a04d025 Wed Sep 6 14:20:53 2017 -0700
    adding hg38Patch11 rules refs #19665
  • lines changed 5, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/scripts/snpedia/download.py
  • lines changed 23, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/scripts/snpedia/downloadHtml.py
  • lines changed 18, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/scripts/snpedia/filterPages.py
  • lines changed 14, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/scripts/snpedia/getPos.py
  • lines changed 26, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/scripts/snpedia/makeBed.py
  • lines changed 103, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
  • lines changed 12, context: html, text, full: html, text
    2320531bfc19dfbef5dca9f55919cb40838626f8 Wed Sep 6 17:04:51 2017 -0700
    fixing up snpedia maker, refs #19811
• src/hg/makeDb/scripts/snpedia/snpediaHtml.sql
  • lines changed 1, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/trackDb/animalQtl.html
  • lines changed 17, context: html, text, full: html, text
    93d63316e7470958555ffe964a97af421bb0f74b Tue Sep 5 10:57:28 2017 -0700
    Fixing broken links found by the broken link report for bosTau7, no Redmine
• src/hg/makeDb/trackDb/crispr10K.ra
  • lines changed 32, context: html, text, full: html, text
    ed794299b55fdb8f8f105821838e5ca3d8faec0e Fri Sep 8 09:48:16 2017 -0700
    crispr10K turned off for a while refs #19874
• src/hg/makeDb/trackDb/fugu/fr2/gap.html
  • lines changed 2, context: html, text, full: html, text
    3a57580a5eab3f77ef7727a90cb2c86540eecc7e Fri Sep 8 08:43:52 2017 -0700
    Fixing broken links found by the broken link report for fr2, no Redmine
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 17, context: html, text, full: html, text
    3a57580a5eab3f77ef7727a90cb2c86540eecc7e Fri Sep 8 08:43:52 2017 -0700
    Fixing broken links found by the broken link report for fr2, no Redmine
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    3a57580a5eab3f77ef7727a90cb2c86540eecc7e Fri Sep 8 08:43:52 2017 -0700
    Fixing broken links found by the broken link report for fr2, no Redmine
• src/hg/makeDb/trackDb/fugu/xenoMrna.html
  • lines changed 6, context: html, text, full: html, text
    3a57580a5eab3f77ef7727a90cb2c86540eecc7e Fri Sep 8 08:43:52 2017 -0700
    Fixing broken links found by the broken link report for fr2, no Redmine
• src/hg/makeDb/trackDb/human/gtexTranscExpr.html
  • lines changed 33, context: html, text, full: html, text
    e44246334b84dc0fef175617b6838581cb292f5c Thu Sep 7 13:11:36 2017 -0700
    Trim HTML to a single file. refs #19350
• src/hg/makeDb/trackDb/human/hg19/gtexTranscExpr.html
  • lines changed 6, context: html, text, full: html, text
    e44246334b84dc0fef175617b6838581cb292f5c Thu Sep 7 13:11:36 2017 -0700
    Trim HTML to a single file. refs #19350
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6a6c0c167b824839fabb92a7609c6ab8f3f16a55 Tue Sep 5 15:06:25 2017 -0700
    Adding html attribute for cosmic v82 track so description page shows up, refs #19932
  • lines changed 7, context: html, text, full: html, text
    6fa18d43d2d63144de98493b2e08bd813d379149 Wed Sep 6 12:25:03 2017 -0700
    fix up cosmicRegions NOT to use a different table name
  • lines changed 1, context: html, text, full: html, text
    cd28db02317ee06a07e75ce32395b45009fc44ec Thu Sep 7 13:12:10 2017 -0700
    Add setting for lifted tracks. refs #19350
• src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html
  • lines changed 126, context: html, text, full: html, text
    e44246334b84dc0fef175617b6838581cb292f5c Thu Sep 7 13:11:36 2017 -0700
    Trim HTML to a single file. refs #19350
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.html
  • lines changed 98, context: html, text, full: html, text
    92173b2ff147fc87e53c7bb51b32371a75e364fa Wed Sep 6 14:22:01 2017 -0700
    Adding additional text as seen in hg38Patch9.html, fixing bad FTP url, and adding GRCp.11 details, refs #19665
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6a6c0c167b824839fabb92a7609c6ab8f3f16a55 Tue Sep 5 15:06:25 2017 -0700
    Adding html attribute for cosmic v82 track so description page shows up, refs #19932
  • lines changed 7, context: html, text, full: html, text
    6fa18d43d2d63144de98493b2e08bd813d379149 Wed Sep 6 12:25:03 2017 -0700
    fix up cosmicRegions NOT to use a different table name
  • lines changed 1, context: html, text, full: html, text
    11c0d11d3b8bfb3a2359126634de71872f6a2dde Wed Sep 6 15:09:02 2017 -0700
    Adding beta release tag to stage hg38Patch11 on beta, refs #19665
  • lines changed 1, context: html, text, full: html, text
    b1876e8efce42a1efd7bfc9967f8b0a712cea7d9 Wed Sep 6 16:45:11 2017 -0700
    Removing hg38.Patch9 from beta, adding hg38.Patch11 to beta, refs #19665
  • lines changed 2, context: html, text, full: html, text
    bbee1d99f9f523add70b017d9a9db5867eebd79b Thu Sep 7 11:47:15 2017 -0700
    Releasing hg38Patch11 and removing p.9, refs #19665
  • lines changed 2, context: html, text, full: html, text
    aabbfa81736bf20b463e64fd3427c4c306cec3d8 Thu Sep 7 12:17:48 2017 -0700
    Correcting .ra file to remove p.9 alltogether and remove tags on p.11 include, refs #19665
• src/hg/makeDb/trackDb/human/hg38Patch11/description.html
  • lines changed 63, context: html, text, full: html, text
    55115536e37f2dd62483fe3fdd7684cc3fb0e68b Wed Sep 6 14:47:28 2017 -0700
    trackDb files for hg38Patch11 updated from Patch9 files refs #19665
• src/hg/makeDb/trackDb/human/hg38Patch11/gap.html
  • lines changed 30, context: html, text, full: html, text
    55115536e37f2dd62483fe3fdd7684cc3fb0e68b Wed Sep 6 14:47:28 2017 -0700
    trackDb files for hg38Patch11 updated from Patch9 files refs #19665
• src/hg/makeDb/trackDb/human/hg38Patch11/gold.html
  • lines changed 37, context: html, text, full: html, text
    55115536e37f2dd62483fe3fdd7684cc3fb0e68b Wed Sep 6 14:47:28 2017 -0700
    trackDb files for hg38Patch11 updated from Patch9 files refs #19665
• src/hg/makeDb/trackDb/human/hg38Patch11/trackDb.ra
  • lines changed 38, context: html, text, full: html, text
    55115536e37f2dd62483fe3fdd7684cc3fb0e68b Wed Sep 6 14:47:28 2017 -0700
    trackDb files for hg38Patch11 updated from Patch9 files refs #19665
• src/hg/makeDb/trackDb/human/snpedia.html
  • lines changed 1, context: html, text, full: html, text
    b6f8e5e6ba097e3ded6f28a36c506131023888b8 Thu Sep 7 07:23:50 2017 -0700
    Fixing minor typo on snpedia desc page, refs #19811
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    7d7906dc8876134f5084b7a96117b01b21d739be Wed Sep 6 16:32:03 2017 -0700
    adding snpedia makedoc, all.joiner and all make scripts, refs #19811
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    43ee5127573bde96cefb7e38a2837c492dec02ce Wed Sep 6 14:48:27 2017 -0700
    adding hg38Patch11 to the build refs #19665
• src/hg/makeDb/trackDb/mgcFullMrna.html
  • lines changed 5, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 17, context: html, text, full: html, text
    3d72d4abfb9d3cb2391c9dc24d8ea6008172d0fc Wed Sep 6 09:51:10 2017 -0700
    Fixing broken links found by the broken link report for monDom4, no Redmine
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
  • lines changed 9, context: html, text, full: html, text
    3d72d4abfb9d3cb2391c9dc24d8ea6008172d0fc Wed Sep 6 09:51:10 2017 -0700
    Fixing broken links found by the broken link report for monDom4, no Redmine
• src/hg/makeDb/trackDb/rat/rn6/cloneEndSuper.html
  • lines changed 7, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 19, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/rat/rn6/gap.html
  • lines changed 1, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/rat/rn6/gold.html
  • lines changed 1, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
  • lines changed 5, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 3, context: html, text, full: html, text
    a3b4dc2a065b0d8cb6b86142e3d9aaf05524c2cc Wed Aug 30 10:02:50 2017 -0700
    Use gene as the label field for ncbiRefSeqOther.
  • lines changed 1, context: html, text, full: html, text
    0a601e8e0818ed1b7dcfb3186b21c6d1b112b910 Sat Sep 9 12:07:21 2017 -0700
    Add 'urls' setting to ncbiRefSeqOther to link out to Entrez Gene, OMIM, HGNC and miRBase.
• src/hg/makeDb/trackDb/snp138.html
  • lines changed 1, context: html, text, full: html, text
    93d63316e7470958555ffe964a97af421bb0f74b Tue Sep 5 10:57:28 2017 -0700
    Fixing broken links found by the broken link report for bosTau7, no Redmine
• src/hg/makeDb/trackDb/snp138.shared.html
  • lines changed 16, context: html, text, full: html, text
    93d63316e7470958555ffe964a97af421bb0f74b Tue Sep 5 10:57:28 2017 -0700
    Fixing broken links found by the broken link report for bosTau7, no Redmine
• src/hg/makeDb/trackDb/snp138Common.html
  • lines changed 1, context: html, text, full: html, text
    93d63316e7470958555ffe964a97af421bb0f74b Tue Sep 5 10:57:28 2017 -0700
    Fixing broken links found by the broken link report for bosTau7, no Redmine
• src/hg/makeDb/trackDb/snp138Mult.html
  • lines changed 1, context: html, text, full: html, text
    93d63316e7470958555ffe964a97af421bb0f74b Tue Sep 5 10:57:28 2017 -0700
    Fixing broken links found by the broken link report for bosTau7, no Redmine
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 78, context: html, text, full: html, text
    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351
  • lines changed 35, context: html, text, full: html, text
    119930f9bf7b08a75efc8424cc06553444cda345 Wed Sep 6 11:41:12 2017 -0700
    short term fix for spAnnot duplicate track entry
  • lines changed 177, context: html, text, full: html, text
    65a1b82250c63386c904daa3d6de40afb2e102cb Wed Sep 6 12:34:44 2017 -0700
    fixing trackDb again, last commit was entirely wrong
  • lines changed 32, context: html, text, full: html, text
    ed794299b55fdb8f8f105821838e5ca3d8faec0e Fri Sep 8 09:48:16 2017 -0700
    crispr10K turned off for a while refs #19874
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
  • lines changed 2, context: html, text, full: html, text
    908359c3087326c619910653dcb9b7908cbcf500 Wed Sep 6 14:19:15 2017 -0700
    Fixing broken links found by the broken link for monDom4. Forgot to include the transMapAlnSplicedEst.html page in the last commit, no Redmine
• src/hg/makeDb/trackDb/treeShrew/tupBel1/gap.html
  • lines changed 1, context: html, text, full: html, text
    80b34607311cc19f1b116149856d00095518377f Thu Sep 7 08:01:36 2017 -0700
    Fixing broken links found by the broken link report for tupBel1, no Redmine
• src/hg/makeDb/trackDb/treeShrew/tupBel1/gold.html
  • lines changed 1, context: html, text, full: html, text
    80b34607311cc19f1b116149856d00095518377f Thu Sep 7 08:01:36 2017 -0700
    Fixing broken links found by the broken link report for tupBel1, no Redmine
• src/hg/makeDb/trackDb/ucscToRefSeq.html
  • lines changed 2, context: html, text, full: html, text
    afa967087ce1052f4b74096aa8d117531566a150 Tue Sep 5 09:51:57 2017 -0700
    Fixing broken links found by the broken link report for rn6, no Redmine
• src/hg/makeDb/trackDb/wallaby/macEug2/gap.html
  • lines changed 1, context: html, text, full: html, text
    4de8c9b8e6952b8cc187a7f3ab3a3215d962007d Mon Sep 11 09:15:58 2017 -0700
    Fixing broken links found by the broken link report for macEug2, no Redmine.
• src/hg/makeDb/trackDb/wallaby/macEug2/gold.html
  • lines changed 1, context: html, text, full: html, text
    4de8c9b8e6952b8cc187a7f3ab3a3215d962007d Mon Sep 11 09:15:58 2017 -0700
    Fixing broken links found by the broken link report for macEug2, no Redmine.
• src/hg/pslRecalcMatch/pslRecalcMatch.c
  • lines changed 9, context: html, text, full: html, text
    9ab015136bbc854a5dc03b71d5d465771539f6c3 Thu Sep 7 11:31:20 2017 -0700
    pslRecalcMatch: new option -ignoreQMissing for when we have fasta for only a subset of query sequences.
• src/hg/pslSomeRecords/pslSomeRecords.c
  • lines changed 14, context: html, text, full: html, text
    9ddd5d9026bdcec1b2ff1652c2abc5ddf9f56900 Tue Aug 22 14:35:28 2017 -0700
    pslSomeRecords: fixed interaction of -tToo and -not; support multiple qName+tName combos for -tToo.
• src/hg/utils/automation/asmHubEnsGene.pl
  • lines changed 18, context: html, text, full: html, text
    8f84aa73ab9ee8e74a9bbf244265207eb6eb1989 Thu Sep 7 11:21:36 2017 -0700
    updated description pages to catch up with source tree trackDb/ensGene.html refs #19526
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 171, context: html, text, full: html, text
    eb3e0997a32a9d1ac61dd848d8bad9217f689e71 Sat Sep 9 12:07:38 2017 -0700
    doNcbiRefSeq.pl: Improvements to ncbiRefSeqPsl and ncbiRefSeqOther generation as well as streamlining some steps. * Check /hive/data/inside $local2Bit independently of /hive/data/outside files so we can still link to outside files if inside files don't exist. * Use gff3ToGenePred -processAllGeneChildren to avoid losing some NR/XR accessions for items with uncommon feature types * Add RefSeq Summary descriptions to ncbiRefSeqLink using gff3ToRefLink.pl (previously the join failed) * Load ncbiRefSeq mysql without ncbiRefSeqOther items * Load ncbiRefSeqOther as bigBed with extra columns not genePred, to be consistent with existing trackDb & released data * Generate trix index for ncbiRefSeqOther * Use both qName and tName in pslSomeRecords so that we don't drop a clean mapping on a regular chrom when the transcript happens to also have an odd mapping on some alt chrom. * Use pslRecalcMatch to get correct misMatches counts in ncbiRefSeqPsl (formerly all 0). * Removed unused bigPsl * Update hgFixed.trackVersion.
• src/hg/utils/automation/gff3ToRefLink.pl
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    b609f36d5cf53941c1444f394814746d1bb93383 Sat Sep 9 12:05:10 2017 -0700
    gff3ToRefLink.pl: get both status and descriptions (RefSeq summaries) from raFile; clean up flattened text within ##*-START / ##*-END semi-structured text sections.
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
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    ac99b14fc67a6843f6751148bd97358b1f93fddd Sat Sep 9 12:06:12 2017 -0700
    New script to build ncbiRefSeqOther BED with extra columns sourced from an attributes file generated by gff3ToGenePred -attrsOut. Refining attributes for ncbiRefSeqOther: * Split Dbxref into separate columns GeneID, MIM, HGNC, miRBase for linking out * Remove Name2 column which is now redundant with gene column * Remove ncrna_class column which doesn't appear in p11 GFF * Reorder columns to flow a bit better * Reword some column descriptions that appear in hgc table display
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    93b0fc1eac4eb20023b87b4933cb94d3c6b5ad8c Thu Aug 24 09:25:38 2017 -0700
    gff3ToGenePred: add option -processAllGeneChildren so we don't have to compare feature type to an ever-expanding list of types used in NCBI GFF3.
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    fd2f56503ce9f077fffdeea36c8602dac0504484 Fri Sep 8 12:08:02 2017 -0700
    gff3ToGenePred: changing some names to be more clear (to me anyway)
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    7505d424eab3a98bef75efab99e4b1312040d337 Fri Sep 8 15:49:27 2017 -0700
    gff3ToGenePred -attrsOut: print attributes for genes in addition to transcripts (for inheritance)
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    9863cd2542194ede314729e866efed9ed7967d0a Fri Sep 8 15:40:18 2017 -0700
    gff3ToGenePred -attrsOut: when attribute value has been split by comma into a list, join the pieces back together instead of printing only the first item.
• src/hg/utils/otto/uniprot/README.txt
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    723a3ed5b1fe1254bbbab0f762a9e9c416b33678 Tue Sep 5 17:34:47 2017 -0700
    another step towards an automated uniprot pipeline
• src/hg/utils/otto/uniprot/bed12UniProtAnnot.as
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    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351
• src/hg/utils/otto/uniprot/bed12UniProtMut.as
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    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351
• src/hg/utils/otto/uniprot/makefile
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    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351
• src/hg/utils/otto/uniprot/uniprotLift
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    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351
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    723a3ed5b1fe1254bbbab0f762a9e9c416b33678 Tue Sep 5 17:34:47 2017 -0700
    another step towards an automated uniprot pipeline
• src/hg/utils/uniprotMutations/bed12UniProtAnnot.as
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    92c36154e4ab662b0b9b228c7aeb695d21526975 Thu Sep 7 11:22:26 2017 -0700
    removing duplicated .as files, refs #19351
• src/hg/utils/uniprotMutations/bed12UniProtMut.as
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    92c36154e4ab662b0b9b228c7aeb695d21526975 Thu Sep 7 11:22:26 2017 -0700
    removing duplicated .as files, refs #19351
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    8ee925a2c358c9c7b028bf0a211fb637e3bc099e Sat Sep 9 13:40:30 2017 -0700
    Sort results to prevent test failure caused by different order of transcripts in table.
• src/hg/utils/vcfToHgvs/tests/makefile
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    8ee925a2c358c9c7b028bf0a211fb637e3bc099e Sat Sep 9 13:40:30 2017 -0700
    Sort results to prevent test failure caused by different order of transcripts in table.
• src/inc/common.mk
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    25d3c5346f2049356174f7487b4be5606c87cd60 Thu Sep 7 15:40:15 2017 -0700
    now using static libm.a on hgwdev refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
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    8c9124c2fdce3d1650c6c46b765993d69ef42288 Mon Sep 11 09:53:58 2017 -0700
    v355 preview2 refs #20085
• src/utils/uniprotLift
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    0e029fa9d8deb0b20ba6cd85a43844698aa631e0 Mon Jul 24 01:08:01 2017 -0400
    major changes to the uniprot track: splitting by annotation into more subtracks, reorg of the code so it can handle that many files, getting ready for ottomization and multi-org running. refs #19351

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