All File Changes

v370_preview2 to v370_base (2018-08-13 to 2018-08-20) v370

• confs/preview.hg.conf
  • lines changed 244, context: html, text, full: html, text
    320ffaf706be3ac10810765b5f686f6049dbaa66 Sun Aug 19 01:12:20 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/altSplice/affySplice/altHtmlPages.c
  • lines changed 5, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/affySplice/altProbes.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/altSplice/altAnalysis.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/altSplice/altPaths.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/altSplice/altSummary.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/altSplice/correlateWithExpression.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/altSplice/altSplice/spliceStats.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/autoDtd/test/chado/in.xml
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 254, context: html, text, full: html, text
    02dae03050cceb57036aba4d3681bac6e15c9bb9 Mon Aug 20 09:30:09 2018 -0700
    Adding new publications funded by CESCG to page. Updating references for bioRxiv papers that have now been published. no redmine
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 10, context: html, text, full: html, text
    293253c859ae5b3c204c83894608d92a79ebb536 Mon Aug 20 09:31:26 2018 -0700
    Updating page to use coloring classes for section header bars, no redmine
• src/hg/das/das.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/encode/hgEncodeSubmit/app/views/layouts/account.rhtml
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/encode/hgEncodeSubmit/app/views/layouts/main.rhtml
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/encode/hgEncodeSubmit/app/views/layouts/standard.rhtml
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/encode3/eap/eapFreen/eapFreen.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgBlat/hgBlat.c
  • lines changed 6, context: html, text, full: html, text
    3ffc9f5979986da9c3b6d4094959890bab59fa9e Tue Aug 14 12:37:12 2018 -0700
    fixing unmatched html tags in hgBlat
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 9, context: html, text, full: html, text
    e254e37d2d9aa6011480785602a9091746bff5d7 Wed Aug 15 15:12:59 2018 -0700
    adding an error message to hgGeneGraph, no redmine
• src/hg/hgGtexApi/hgGtexApi.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgTracks/gbrowseTest.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/hgc/lowelab.c
  • lines changed 3, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
  • lines changed 3, context: html, text, full: html, text
    3f2e6792566fd91a20c9c892e3c29ca487c1616c Tue Aug 14 13:56:52 2018 -0700
    last minute lowelab fix. cse domain is going away.
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 8, context: html, text, full: html, text
    2fb182c651848e063d4d998b126ebe9c061da7b5 Thu Aug 16 15:01:23 2018 +0200
    forgot to add the html versions of the mirror manual, no redmine
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 11, context: html, text, full: html, text
    23c925b8257fa23fd6ec14c0158e17ee365a4603 Tue Aug 14 11:22:10 2018 +0200
    documenting a few more position box options, no redmine
• src/hg/htdocs/training/index.html
  • lines changed 30, context: html, text, full: html, text
    15b15438261195b9f4bb4697e2406c5876f817ef Tue Aug 14 14:50:41 2018 -0700
    adding ashg appearances, adding new feature: list of events beyond the few given in details
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    6ad507c36972b05ffc53c857a9aef43304859c68 Mon Aug 20 09:57:38 2018 -0700
    New version number v370
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/lib/customFactory.c
  • lines changed 15, context: html, text, full: html, text
    ee8e9e0ec936192990ec856e319a3c253a352bbc Fri Aug 17 14:37:19 2018 -0700
    move some code around so it executes BEFORE some memory it uses gets free'd (see 21889 note 7)
• src/hg/lib/fileUi.c
  • lines changed 6, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
  • lines changed 156, context: html, text, full: html, text
    3c13015353004b4de688ff6c7d6225e8941f1da7 Tue Aug 14 16:28:52 2018 -0700
    add <column>FilterValues tdb statemnt allowing for filtering on values
• src/hg/lib/wigAsciiToBinary.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/lib/wigDataStream.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/logCrawl/dbTrackAndSearchUsage/README.txt
  • lines changed 29, context: html, text, full: html, text
    33f3851ffc8aeb5d0902f3c8abadfa0c769341f9 Fri Aug 17 13:42:51 2018 -0700
    Changes based on feedback in code review. generateUsageStats and generateSearchUse now automaitcally identify gzipped files and automatically create directories if one isn't specified. Trailing slash is not needed on input dirs. Expand examples in README. refs #21760
• src/hg/logCrawl/dbTrackAndSearchUsage/generateSearchUse.py
  • lines changed 68, context: html, text, full: html, text
    33f3851ffc8aeb5d0902f3c8abadfa0c769341f9 Fri Aug 17 13:42:51 2018 -0700
    Changes based on feedback in code review. generateUsageStats and generateSearchUse now automaitcally identify gzipped files and automatically create directories if one isn't specified. Trailing slash is not needed on input dirs. Expand examples in README. refs #21760
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 78, context: html, text, full: html, text
    33f3851ffc8aeb5d0902f3c8abadfa0c769341f9 Fri Aug 17 13:42:51 2018 -0700
    Changes based on feedback in code review. generateUsageStats and generateSearchUse now automaitcally identify gzipped files and automatically create directories if one isn't specified. Trailing slash is not needed on input dirs. Expand examples in README. refs #21760
• src/hg/logCrawl/dbTrackAndSearchUsage/makeLogSymLinks.sh
  • lines changed 2, context: html, text, full: html, text
    33f3851ffc8aeb5d0902f3c8abadfa0c769341f9 Fri Aug 17 13:42:51 2018 -0700
    Changes based on feedback in code review. generateUsageStats and generateSearchUse now automaitcally identify gzipped files and automatically create directories if one isn't specified. Trailing slash is not needed on input dirs. Expand examples in README. refs #21760
• src/hg/logCrawl/hgAccessCrawl/hgAccessCrawl.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/makeDb/makefile
  • lines changed 2, context: html, text, full: html, text
    b1e4dd29fa59c88bcf14965ba55513c7300155bb Wed Aug 15 10:09:20 2018 -0700
    Adding hgGoldGapGl to userapps, refs #21887
• src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    6a4330e20a410e9c3bf2d2040c8331ee1fff0d79 Fri Aug 17 13:20:43 2018 -0700
    Updating the chainMinScore for the hg38 and panTro6 chain/net tracks, refs #20979
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/crispr.html
  • lines changed 218, context: html, text, full: html, text
    272254a50b57013c8ecc0b843539db61c63d7ddf Sun Aug 19 22:03:01 2018 -0700
    copied crispr.html file to green monkey directory to add Regeneron acknowledgement
• src/hg/makeDb/trackDb/dog/canFam2/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    8f2b633bbc2f15eb4e7497f9c0c46deb49410bbd Thu Aug 16 07:50:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 4, context: html, text, full: html, text
    8f2b633bbc2f15eb4e7497f9c0c46deb49410bbd Thu Aug 16 07:50:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/dog/canFam2/phastConsElements4way.html
  • lines changed 5, context: html, text, full: html, text
    8f2b633bbc2f15eb4e7497f9c0c46deb49410bbd Thu Aug 16 07:50:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/dog/canFam2/polyASeqSites.html
  • lines changed 1, context: html, text, full: html, text
    8f2b633bbc2f15eb4e7497f9c0c46deb49410bbd Thu Aug 16 07:50:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/affyTxnPhase3Super.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChipBut.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg18/encodeUppsalaChipBut.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSignal.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSites.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSuper.html
  • lines changed 0, context: html, text, full: html, text
    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    75dda910966085b00702ecf378c953d5fbe3108f Wed Aug 15 11:19:50 2018 -0700
    Removing the two pennantIcons from hg19 posted on June 21st (gnomAD)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    2d48615505e3ce3fd2e4cca41146eefd3263106b Wed Aug 15 03:53:23 2018 -0700
    adding mastermind, refs #21635
  • lines changed 1, context: html, text, full: html, text
    4a389a8ac5b680fd4d3d4466ad43d777e5c05953 Wed Aug 15 06:05:08 2018 -0700
    oops forgot release tag in last commit
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    7d222cca6278e161f02f7ecd3e27690df5bb008b Mon Aug 13 12:21:01 2018 -0700
    Updating the makefile to point to the new hgwdev machine, refs #21876
  • lines changed 1, context: html, text, full: html, text
    8b7524b18fbe764e3775a9982c4aa8e4fcf7d7a4 Wed Aug 15 18:20:04 2018 -0700
    change the name of hgwbeta to include soe instead of cse
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    4e04399749f1b2ad436b5f4a7219ce89884c8aea Mon Aug 13 14:23:34 2018 -0700
    Add settings for native track version. refs #21109
• src/hg/mouseStuff/chainBridge/chainBridge.c
  • lines changed 5, context: html, text, full: html, text
    47c6bc793c8690cfe95f80006aa8d9fd46d0b4ef Wed Aug 15 15:15:36 2018 -0700
    Bug fix: canTrivialExtend was forgetting to reset retFromStart and retFromEnd for single-sided gap.
• src/hg/orthoMap/orthoPickIntron.c
  • lines changed 3, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/qaPushQ/README
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 8, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/sageVisCGI/sageVisCGI.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/README.txt
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/gatewayPage.js
  • lines changed 4, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/gatewayPage.pl
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/hubIndexNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/ncbiPartitionedHubIndexNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/automation/genbank/rmskDescription.pl
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/bedExtendRanges/bedExtendRanges.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 40, context: html, text, full: html, text
    6faeebd03bcc35c7df35f73e18ba19c9e4d247c6 Tue Aug 14 10:28:55 2018 -0700
    Strip versions from NM IDs to avoid trouble when hg38.ncbiRefSeq updates -- except for NM_002111.6 because we already expected that to fail. These are all c.'s, and CDS coords are generally stable enough across version updates (which usually tweak UTR boundaries) to get away with ignoring version.
• src/hg/utils/hgvsToVcf/tests/input/clinVarChanges.txt
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    6faeebd03bcc35c7df35f73e18ba19c9e4d247c6 Tue Aug 14 10:28:55 2018 -0700
    Strip versions from NM IDs to avoid trouble when hg38.ncbiRefSeq updates -- except for NM_002111.6 because we already expected that to fail. These are all c.'s, and CDS coords are generally stable enough across version updates (which usually tweak UTR boundaries) to get away with ignoring version.
• src/hg/utils/hubCheck/hubCheck.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/utils/otto/omim/parseGeneMap.pl
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    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    40b936c66dcfc2979c7568c82d0ebc3a769d59ef Tue Aug 14 10:33:22 2018 -0700
    Updating accession version numbers and n. coord changes because hg38.ncbiRefSeq updated.
• src/hg/visiGene/hgVisiGene/README
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    bcbc5e6ebd4cf680201145e774b6e2e2dd7d192f Mon Aug 13 23:38:17 2018 -0700
    fix .cse.ucsc.edu url in hgVisigine README
• src/hg/visiGene/vgLoadAllen/vgLoadAllen.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/visiGene/vgLoadJax/vgLoadJax.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/hg/xmlToSql/test/chado/in.xml
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    8423b66ad3d5d5a16913bef44f0c2e219418d4de Wed Aug 15 11:15:33 2018 -0700
    convert some legacy files from DOS to UNIX lf standards. These weren't noticed on the old dev because the file command didn't flag them because there were HTML, xml, or perl.
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    55d5adaedccc1c67ce8a8a155ef36acf79c1ed2f Tue Aug 14 02:04:59 2018 -0700
    changing to default librt (static glibc part provided by centos), refs #21906
• src/inc/common.mk.galt
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    a4c0a9f4b48c074daec96559640b76ab2d9db488 Mon Aug 13 16:03:28 2018 -0700
    experiment finished.
• src/inc/srcVersion.h
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    6ad507c36972b05ffc53c857a9aef43304859c68 Mon Aug 20 09:57:38 2018 -0700
    New version number v370
• src/jkOwnLib/gfInternal.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/lib/psl.c
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    24fb9ffd97320b3969abf5e430889907f365d4ce Wed Aug 15 14:30:04 2018 -0700
    fix brain-dead error that only just now bit us.
• src/lib/tests/htmlMimeTest.c
  • lines changed 2, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/lib/tests/makefile
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/lib/tests/udcTest.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
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    d275a14297f5d9a04c124b8ed6e6880ee0f65345 Wed Aug 15 16:44:42 2018 -0700
    Removing unused constant.
• src/product/mirrorManual.txt
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    36c19c05822766c8805fab2fba90320b1118efe0 Wed Aug 15 23:49:16 2018 +0200
    adding python mysqldb to install instructions, no redmine, this came up through hgwdev-new
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    2fb182c651848e063d4d998b126ebe9c061da7b5 Thu Aug 16 15:01:23 2018 +0200
    forgot to add the html versions of the mirror manual, no redmine
• src/tracks/tracks.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/utils/bedClip/bedClip.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/utils/bedToBigBed/bedToBigBed.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/utils/git-reports/git-reports.c
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    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876
• src/utils/qa/weeklybld/buildEnv.csh
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    0764d78c0b3a4599b8a2f9d5ec22c121f9d12dc5 Mon Aug 20 09:55:55 2018 -0700
    v370 final build, refs #NNNNN
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 1, context: html, text, full: html, text
    110f5e12a634db49ea9aa1ea23ff4965f1c2befe Tue Aug 14 13:48:57 2018 -0700
    changing cse to soe in domains, sometimes gi. ref #21876

• lines changed: 1814
• files changed: 106