All File Changes

v361_preview to v361_preview2 (2018-01-29 to 2018-02-05) v361

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 7, context: html, text, full: html, text
    d484e0663d0fb0e8ada6a0bf84dde4ddeb5c4d9e Mon Jan 29 19:44:34 2018 -0800
    Added some reminders that sqlSafef functions are not available in tabToSql.c because of its location.
  • lines changed 1, context: html, text, full: html, text
    e74b66326b84b2492bc8afb15b3bb56d58b819ed Tue Jan 30 18:19:34 2018 -0800
    Fixing sql for allowing a list of fields.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    206b0af134d75c2397b56a7ee65800a1eb5456a0 Mon Jan 29 21:15:07 2018 -0800
    Use sqlSafef family of functions for safety and consistency.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 13, context: html, text, full: html, text
    206b0af134d75c2397b56a7ee65800a1eb5456a0 Mon Jan 29 21:15:07 2018 -0800
    Use sqlSafef family of functions for safety and consistency.
  • lines changed 9, context: html, text, full: html, text
    c118b41f4a28f79fa50b48c47ddd753016d5e1fc Tue Jan 30 00:28:53 2018 -0800
    fixing field lists. rqlQuery is not real db query. added a couple of new sqlSafef family helper functions in jksql
  • lines changed 3, context: html, text, full: html, text
    36b71a06f6f24eb5aaf27f135f6cc0a921f6a059 Wed Jan 31 13:55:45 2018 -0800
    oops, need the rest of the changes for facet field selections
  • lines changed 3, context: html, text, full: html, text
    60f1001d3a232c29adb505f3c38c0469e0151b09 Wed Jan 31 16:43:20 2018 -0800
    adding selectedRowCount
• src/hg/cirm/cdw/oneShot/facetFieldTest/facetFieldTest.c
  • lines changed 75, context: html, text, full: html, text
    b6f3cb2168d55aea6c6b7bc5f971d4c0fa2f0cec Wed Jan 31 13:47:22 2018 -0800
    initial test code for selected facet values
  • lines changed 16, context: html, text, full: html, text
    60f1001d3a232c29adb505f3c38c0469e0151b09 Wed Jan 31 16:43:20 2018 -0800
    adding selectedRowCount
• src/hg/cirm/cdw/oneShot/facetFieldTest/makefile
  • lines changed 3, context: html, text, full: html, text
    b6f3cb2168d55aea6c6b7bc5f971d4c0fa2f0cec Wed Jan 31 13:47:22 2018 -0800
    initial test code for selected facet values
• src/hg/hgCollection/hgCollection.c
  • lines changed 1, context: html, text, full: html, text
    c0dd6baeb704807fc0ba385e5a5cb53b553cb40d Mon Jan 29 10:12:36 2018 -0800
    fixed some weirdnesses with empty collections
  • lines changed 3, context: html, text, full: html, text
    e9c2ef7b4be9c688fb3692944457971519c152b5 Wed Jan 31 12:21:07 2018 -0800
    put priority back into trackDb stanzas in custom composites
  • lines changed 2, context: html, text, full: html, text
    beee82d43659b3f682f57301c4a64feec96314ff Thu Feb 1 14:25:25 2018 -0800
    add support for math on bedGraph (including custom tracks)
• src/hg/hgTables/vcf.c
  • lines changed 15, context: html, text, full: html, text
    a29e98e451251954d3c79928eda4ea4111f11151 Tue Jan 30 14:34:52 2018 -0800
    hgTables vcfFileName wasn't handling plain VCF custom tracks correctly.
• src/hg/hgTracks/extTools.ra
  • lines changed 4, context: html, text, full: html, text
    be73c0cbd92abcd738ff27592ec01e64a10e5a81 Tue Jan 30 15:44:50 2018 -0800
    silently fixing ext. tools menu for hg19, no redmine
• src/hg/hgTracks/imageV2.c
  • lines changed 3, context: html, text, full: html, text
    fbcf25a42d55e73ac10d4f9ba265faf92f697e92 Mon Jan 29 14:56:58 2018 -0800
    fix weird behavior of custom tracks going to the bottom after a track reorder #20903
• src/hg/hgTracks/simpleTracks.c
  • lines changed 20, context: html, text, full: html, text
    beee82d43659b3f682f57301c4a64feec96314ff Thu Feb 1 14:25:25 2018 -0800
    add support for math on bedGraph (including custom tracks)
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    a6cdf21626f0dc03d6d1d0f2015e39a636822675 Wed Jan 31 11:09:03 2018 -0800
    more general use of ensemblIdUrl from trackDb for ensGene refs #20696
• src/hg/htdocs/goldenPath/help/hgCollectionHelp.html
  • lines changed 2, context: html, text, full: html, text
    beee82d43659b3f682f57301c4a64feec96314ff Thu Feb 1 14:25:25 2018 -0800
    add support for math on bedGraph (including custom tracks)
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    6bc3bf267fe4c18543e9c1217752a6a58d3b5720 Thu Feb 1 08:45:32 2018 -0800
    In trackDbLibrary removing color in an example about about spectrum as it is misleading, and also adding the word show in a superTrack Ex. to give a hint about visibility. ref #20915
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 141, context: html, text, full: html, text
    d73972cda29db9adb897c2fd1cb01ad0075927ea Thu Feb 1 16:03:46 2018 -0800
    Announcing Ensembl v90 and v91 release, refs #20304 and #20696
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 7, context: html, text, full: html, text
    715772ef8ddcd9b9473fbc1201c15fb1cad691e7 Tue Jan 30 07:27:27 2018 -0800
    some styles on the hgCollection dialog box
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    d73972cda29db9adb897c2fd1cb01ad0075927ea Thu Feb 1 16:03:46 2018 -0800
    Announcing Ensembl v90 and v91 release, refs #20304 and #20696
• src/hg/htdocs/training/index.html
  • lines changed 29, context: html, text, full: html, text
    8b15f04f311caf358c154288d56f8baa3b764220 Thu Feb 1 11:46:16 2018 -0800
    adding florida workshop
• src/hg/inc/facetField.h
  • lines changed 6, context: html, text, full: html, text
    36b71a06f6f24eb5aaf27f135f6cc0a921f6a059 Wed Jan 31 13:55:45 2018 -0800
    oops, need the rest of the changes for facet field selections
  • lines changed 1, context: html, text, full: html, text
    60f1001d3a232c29adb505f3c38c0469e0151b09 Wed Jan 31 16:43:20 2018 -0800
    adding selectedRowCount
• src/hg/inc/jksql.h
  • lines changed 6, context: html, text, full: html, text
    c118b41f4a28f79fa50b48c47ddd753016d5e1fc Tue Jan 30 00:28:53 2018 -0800
    fixing field lists. rqlQuery is not real db query. added a couple of new sqlSafef family helper functions in jksql
• src/hg/js/hgCollection.js
  • lines changed 25, context: html, text, full: html, text
    c0dd6baeb704807fc0ba385e5a5cb53b553cb40d Mon Jan 29 10:12:36 2018 -0800
    fixed some weirdnesses with empty collections
  • lines changed 15, context: html, text, full: html, text
    e5179bc8d5f2500ff7c51e74f6b5529dcea17612 Mon Jan 29 20:45:15 2018 -0800
    tweaks to hgCollection to renable drag and drop in collections
  • lines changed 1, context: html, text, full: html, text
    715772ef8ddcd9b9473fbc1201c15fb1cad691e7 Tue Jan 30 07:27:27 2018 -0800
    some styles on the hgCollection dialog box
  • lines changed 2, context: html, text, full: html, text
    5bbf49f70aefeb86408e66aefd4fc3da439263dd Tue Jan 30 14:19:34 2018 -0800
    fix bug with collections being deleted when their folder was clicked
• src/hg/lib/annoStreamDb.c
  • lines changed 6, context: html, text, full: html, text
    7e88d971aeed23ac14b271ba65bbc2d0514d0378 Tue Jan 30 01:19:50 2018 -0800
    little cleanup.
• src/hg/lib/facetField.c
  • lines changed 75, context: html, text, full: html, text
    36b71a06f6f24eb5aaf27f135f6cc0a921f6a059 Wed Jan 31 13:55:45 2018 -0800
    oops, need the rest of the changes for facet field selections
  • lines changed 5, context: html, text, full: html, text
    60f1001d3a232c29adb505f3c38c0469e0151b09 Wed Jan 31 16:43:20 2018 -0800
    adding selectedRowCount
• src/hg/lib/genePix.c
  • lines changed 4, context: html, text, full: html, text
    7e88d971aeed23ac14b271ba65bbc2d0514d0378 Tue Jan 30 01:19:50 2018 -0800
    little cleanup.
• src/hg/lib/hgFind.c
  • lines changed 4, context: html, text, full: html, text
    7e88d971aeed23ac14b271ba65bbc2d0514d0378 Tue Jan 30 01:19:50 2018 -0800
    little cleanup.
• src/hg/lib/jksql.c
  • lines changed 20, context: html, text, full: html, text
    c118b41f4a28f79fa50b48c47ddd753016d5e1fc Tue Jan 30 00:28:53 2018 -0800
    fixing field lists. rqlQuery is not real db query. added a couple of new sqlSafef family helper functions in jksql
  • lines changed 1, context: html, text, full: html, text
    8b7bdf678599ede2f46b3e697845e94927806cb3 Tue Jan 30 01:25:20 2018 -0800
    oops comment typo fix.
• src/hg/lib/mathWig.c
  • lines changed 59, context: html, text, full: html, text
    beee82d43659b3f682f57301c4a64feec96314ff Thu Feb 1 14:25:25 2018 -0800
    add support for math on bedGraph (including custom tracks)
• src/hg/lib/tablesTables.c
  • lines changed 31, context: html, text, full: html, text
    206b0af134d75c2397b56a7ee65800a1eb5456a0 Mon Jan 29 21:15:07 2018 -0800
    Use sqlSafef family of functions for safety and consistency.
  • lines changed 3, context: html, text, full: html, text
    c118b41f4a28f79fa50b48c47ddd753016d5e1fc Tue Jan 30 00:28:53 2018 -0800
    fixing field lists. rqlQuery is not real db query. added a couple of new sqlSafef family helper functions in jksql
• src/hg/lib/variantProjector.c
  • lines changed 4, context: html, text, full: html, text
    47f7e3e01a4acd51d8114c79880b6496f7b290a5 Mon Jan 29 15:57:30 2018 -0800
    spliceInBlk was demanding positive overlap between region/variant and block, but region and variant can be 0-length insertion points.
  • lines changed 424, context: html, text, full: html, text
    5cf6d3bf319a850cac1bd51c0b71ba016add589c Thu Feb 1 14:17:34 2018 -0800
    Added more accurate exon/intron/CDS predictions for complex variants (those that span multiple regions). Still need to catch transcript_ablation and splice_region_variant in vpTxToFxExon. HGVSP should reflect when the whole transcript has been deleted (IMO anyway).
  • lines changed 9, context: html, text, full: html, text
    c537ea714a6d43e286175be9e713bb7aff9bef72 Sun Feb 4 22:42:35 2018 -0800
    The previous change caused vpTranscriptToProtein to make predictions when it really shouldn't, e.g. for a purely intronic variant (or even for a variant that probably wipes out a splice site and extends into the exon). What I really want to add support for is complete transcript deletions -- so bring back the previous restrictive check and add an exception for complete deletions (start upstream, end downstream).
  • lines changed 67, context: html, text, full: html, text
    d8164d0a9702a2b3d4e20cd2afc0cee6f5ee0275 Fri Feb 2 15:26:47 2018 -0800
    Detect transcript_ablation and splice_region_variant in vpTxToFxExon.
• src/hg/lib/visiGene.c
  • lines changed 2, context: html, text, full: html, text
    7e88d971aeed23ac14b271ba65bbc2d0514d0378 Tue Jan 30 01:19:50 2018 -0800
    little cleanup.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 40, context: html, text, full: html, text
    33bfe82b5253bd58caedbc3c90357b11041daf32 Mon Jan 29 16:54:29 2018 -0800
    hgmd hg19 makedoc, refs #15536
  • lines changed 2, context: html, text, full: html, text
    7b67f88f96596ad6d011511375cd63d920f0cfc6 Thu Feb 1 15:37:10 2018 -0800
    fixing colors following Chris's advice after HGMD email, also inserts and deletes in grey, refs #15536
• src/hg/makeDb/doc/hg38/hgmd.txt
  • lines changed 2, context: html, text, full: html, text
    7b67f88f96596ad6d011511375cd63d920f0cfc6 Thu Feb 1 15:37:10 2018 -0800
    fixing colors following Chris's advice after HGMD email, also inserts and deletes in grey, refs #15536
• src/hg/makeDb/doc/melGal5/initialBuild.txt
  • lines changed 33, context: html, text, full: html, text
    d7ba35700e4cf209dd14aac4b38d6ebfe290f06c Wed Jan 31 13:10:08 2018 -0800
    adding chromAlias table refs #20911
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    2b7dacf4d5f13c28b12263ff0d658c21587c6c74 Fri Feb 2 20:52:31 2018 -0800
    clean up check on oreNil2 refs #20911
• src/hg/makeDb/trackDb/blastHg16KG.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d0d0dd4b1b430349c117e6fffd3c9127e6f2605a Wed Jan 31 11:09:44 2018 -0800
    fixup ensemblIdUrl with specific species name refs #20696
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 2, context: html, text, full: html, text
    15b2a45b8e40250bd7d300c2b61ad213dfc51968 Fri Feb 2 09:58:19 2018 -0800
    Use track variable to specify right path to crispr10k hgdownload link, refs #19874
• src/hg/makeDb/trackDb/esRegGeneToMotif.html
  • lines changed 2, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    7b62fe211d818a5471b217f378c6658597bef32b Wed Jan 31 11:12:41 2018 -0800
    fixup ensemblIdUrl with specific species name refs #20696
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 4, context: html, text, full: html, text
    4e97d71db246be3adb81086c81731ff8f878e890 Fri Feb 2 08:43:55 2018 -0800
    Fixing broken links for gorGor3, no Redmine.
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 7, context: html, text, full: html, text
    002130f9fbb3ce726eff88cca19d1b3321e2619f Tue Jan 30 16:31:40 2018 -0800
    fixing clinvar track description page, no redmine, but talked to ChrisV
• src/hg/makeDb/trackDb/human/hgmd.html
  • lines changed 4, context: html, text, full: html, text
    9d15b51428cb06640992785fefd64d4d69c7e0a1 Tue Jan 30 12:58:51 2018 -0800
    Adding Jonathan's code review comments to hgmd track description, refs #20858
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    107c95a61d8d414c9439bf023bfe37ce90228933 Thu Feb 1 15:39:27 2018 -0800
    allowing colors for hgmd, refs #15536
• src/hg/makeDb/trackDb/moleRat/hetGla1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    f337553f95ea222f6502ff8748c2e2dbaca406ae Wed Jan 31 11:16:57 2018 -0800
    fixup ensemblIdUrl with specific species name refs #20696
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    f337553f95ea222f6502ff8748c2e2dbaca406ae Wed Jan 31 11:16:57 2018 -0800
    fixup ensemblIdUrl with specific species name refs #20696
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/mrna.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • lines changed 7, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sgdClone.html
  • lines changed 3, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sgdGene.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sgdOther.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/transRegCode.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
  • lines changed 1, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/sacCer/uwFootprints.html
  • lines changed 2, context: html, text, full: html, text
    fb65aa10656c93e20aa323e86eff9b158085ac14 Mon Feb 5 09:41:09 2018 -0800
    Fixing broken links for sacCer1, no Redmine.
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    a0d229ef73611ba40e93e17d85c0d371afadce86 Wed Jan 31 11:19:35 2018 -0800
    fixup ensemblIdUrl with specific species name refs #20696
• src/hg/makeDb/trackDb/worm/25mersRepeats.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 3, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
  • lines changed 3, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCb3.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/chainSelf.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/netCaePb1.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/netCaeRem2.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/netCb3.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/netPriPac1.html
  • lines changed 1, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/nucleosome.html
  • lines changed 2, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html
  • lines changed 2, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/nucleosomeControlCoverage.html
  • lines changed 2, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/nucleosomeDensity.html
  • lines changed 2, context: html, text, full: html, text
    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/nucleosomeStringency.html
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    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/makeDb/trackDb/worm/rmsk.html
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    248937189aa9eb847686b2a904348d6485b59294 Wed Jan 31 09:35:43 2018 -0800
    Fixing broken links for ce4, no Redmine.
• src/hg/mouseStuff/chainToPsl/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/automation/dbAssemblyEquivalents.tab
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    2351b871084ddfbe26c56812d625b9ba3d6f9c47 Mon Jan 29 10:25:37 2018 -0800
    exact equivalents UCSC db to NCBI RefSeq assembly refs #20215
• src/hg/utils/automation/doNcbiRefSeq.pl
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    3fe082c78f89149e7a35da9dd5f2a79066797e6a Thu Feb 1 13:28:16 2018 -0800
    fixing up to work with ce11 wormbase links refs #20215
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    b1245af3744adb9af6943f93b5671d33af2bbe20 Mon Feb 5 09:49:37 2018 -0800
    could be an empty psl file from the gff3 refs #20215
• src/hg/utils/automation/gff3ToRefLink.pl
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    da64eb14ea6dd47c3caf5631e06712172834ea8c Thu Feb 1 13:26:39 2018 -0800
    recognize wormbase links and substitute into hgnc link refs #20215
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
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    f3e8212eceff94cb37f76470649f908c899c6ed3 Thu Feb 1 13:27:37 2018 -0800
    use WormBase identifiers when present refs #20215
• src/hg/utils/automation/ncbiRefSeqOtherIxIxx.pl
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    36e2ae1f6f1df801b6d35a89272687d353a16ffb Thu Feb 1 11:39:59 2018 -0800
    smart indexing of ncbiRefSeqOther.bed extra names refs #20215
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    50a9e60e0b628bf6c083499a8cd1c234ec982a20 Thu Feb 1 13:29:04 2018 -0800
    add noSuffix names and remove xxx: prefixes refs #20215
• src/hg/utils/genePredFilter/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/genePredToProt/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
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    c1652a35737e2110ab747d6acd85f5709624655f Sun Feb 4 19:50:49 2018 -0800
    fixed stupid bug in unlinking child with multiple parents from one of thoses parents
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.out
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.out
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/gff3ToGenePred/tests/input/ncbiProblems.gff3
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/gff3ToGenePred/tests/makefile
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    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
• src/hg/utils/hubCheck/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/pslRc/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/pslToBigPsl/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/transMapPslToGenePred/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/visiGene/hgVisiGene/visiSearch.c
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    7e88d971aeed23ac14b271ba65bbc2d0514d0378 Tue Jan 30 01:19:50 2018 -0800
    little cleanup.
• src/inc/gff3.h
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    c1652a35737e2110ab747d6acd85f5709624655f Sun Feb 4 19:50:49 2018 -0800
    fixed stupid bug in unlinking child with multiple parents from one of thoses parents
• src/lib/gff3.c
  • lines changed 3, context: html, text, full: html, text
    e5268a564b983a211baf36b7df298e54e2d189f3 Mon Jan 29 16:14:25 2018 -0800
    allow skip more types of gff3ToGenePred conversions errors with -warnAndContinue to support other NCBI GFF3 files
  • lines changed 22, context: html, text, full: html, text
    c1652a35737e2110ab747d6acd85f5709624655f Sun Feb 4 19:50:49 2018 -0800
    fixed stupid bug in unlinking child with multiple parents from one of thoses parents
• src/lib/htmshell.c
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    a9a8194dc4202814c36699790576ab7cc3a4535d Fri Feb 2 11:53:37 2018 -0800
    Fixed bug in hex encoding for non-ascii high-bit characters.
• src/lib/tagToSql.c
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    d484e0663d0fb0e8ada6a0bf84dde4ddeb5c4d9e Mon Jan 29 19:44:34 2018 -0800
    Added some reminders that sqlSafef functions are not available in tabToSql.c because of its location.
• src/lib/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/utils/bamToPsl/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/utils/bedClip/tests/makefile
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    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/utils/qa/weeklybld/buildEnv.csh
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    837fb343b0b0c433ff6baf30e75968b7febb001e Mon Feb 5 10:01:14 2018 -0800
    v361 preview2 refs #20889
• src/utils/qa/weeklybld/doNewBranch.csh
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    564f68b47e3af193949fc5b9af194601a4badc83 Mon Jan 29 18:27:46 2018 -0800
    add cath email to reporting listings no redmine
• src/utils/qa/weeklybld/doNewReview.csh
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    564f68b47e3af193949fc5b9af194601a4badc83 Mon Jan 29 18:27:46 2018 -0800
    add cath email to reporting listings no redmine
• src/utils/qa/weeklybld/doNewReview2.csh
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    564f68b47e3af193949fc5b9af194601a4badc83 Mon Jan 29 18:27:46 2018 -0800
    add cath email to reporting listings no redmine

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