All File Changes

v358_preview2 to v358_base (2017-11-13 to 2017-11-27) v358

• src/hg/cirm/cdw/cdwReallyRemoveDataset/cdwReallyRemoveDataset.c
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    f8b057d85c402f6cbe17ac2cf26723ded62f78a4 Tue Nov 21 16:49:49 2017 -0800
    Making cdwSubmit detect a bad file early (that is already a symlink to the /data/cirm/cdw/) instead of after being copied and starting a half-finished db record. This required some reworking of the code a bit.
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 1, context: html, text, full: html, text
    f8b057d85c402f6cbe17ac2cf26723ded62f78a4 Tue Nov 21 16:49:49 2017 -0800
    Making cdwSubmit detect a bad file early (that is already a symlink to the /data/cirm/cdw/) instead of after being copied and starting a half-finished db record. This required some reworking of the code a bit.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 15, context: html, text, full: html, text
    f8b057d85c402f6cbe17ac2cf26723ded62f78a4 Tue Nov 21 16:49:49 2017 -0800
    Making cdwSubmit detect a bad file early (that is already a symlink to the /data/cirm/cdw/) instead of after being copied and starting a half-finished db record. This required some reworking of the code a bit.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 6, context: html, text, full: html, text
    f8b057d85c402f6cbe17ac2cf26723ded62f78a4 Tue Nov 21 16:49:49 2017 -0800
    Making cdwSubmit detect a bad file early (that is already a symlink to the /data/cirm/cdw/) instead of after being copied and starting a half-finished db record. This required some reworking of the code a bit.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 1, context: html, text, full: html, text
    f40b940f89849de7e55a441ec1096d8b486aa395 Sat Nov 11 19:10:57 2017 -0800
    oops typo in warn mesg.
  • lines changed 127, context: html, text, full: html, text
    f8b057d85c402f6cbe17ac2cf26723ded62f78a4 Tue Nov 21 16:49:49 2017 -0800
    Making cdwSubmit detect a bad file early (that is already a symlink to the /data/cirm/cdw/) instead of after being copied and starting a half-finished db record. This required some reworking of the code a bit.
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 3, context: html, text, full: html, text
    b4ad9d17dae1670c367fac112117e3ba374b685b Tue Nov 21 17:03:42 2017 -0800
    Adding new single_cell tag. Also added csv.
• src/hg/cirm/gateway/htdocs/MISCEv1.1.pdf
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    1f084cecb1e7ea6d738d1fcbc1f20cc5a5bb7694 Tue Nov 14 14:07:39 2017 -0800
    Adding MISCE and RIGGLE info to tools page, refs #20368
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
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    4d539e0c60bcd72628200ff4194db199dd757d71 Tue Nov 14 14:33:36 2017 -0800
    Uncommenting section with help video, no redmine
• src/hg/cirm/gateway/htdocs/images/RIGGLE_demo.png
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    1f084cecb1e7ea6d738d1fcbc1f20cc5a5bb7694 Tue Nov 14 14:07:39 2017 -0800
    Adding MISCE and RIGGLE info to tools page, refs #20368
• src/hg/cirm/gateway/htdocs/images/SamplePsychicDetailedView.png
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    109176417f6395850d3380f6538730e08b7da59b Tue Nov 21 13:10:19 2017 -0800
    Adding some screenshots and detail to Sample Psychic section, refs #20368
• src/hg/cirm/gateway/htdocs/images/SamplePsychicPlot.png
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    109176417f6395850d3380f6538730e08b7da59b Tue Nov 21 13:10:19 2017 -0800
    Adding some screenshots and detail to Sample Psychic section, refs #20368
• src/hg/cirm/gateway/htdocs/images/SamplePsychicReportCard.png
  • lines changed 0, context: html, text, full: html, text
    109176417f6395850d3380f6538730e08b7da59b Tue Nov 21 13:10:19 2017 -0800
    Adding some screenshots and detail to Sample Psychic section, refs #20368
• src/hg/cirm/gateway/htdocs/style/cirmStyle.css
  • lines changed 6, context: html, text, full: html, text
    1f084cecb1e7ea6d738d1fcbc1f20cc5a5bb7694 Tue Nov 14 14:07:39 2017 -0800
    Adding MISCE and RIGGLE info to tools page, refs #20368
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 35, context: html, text, full: html, text
    1f084cecb1e7ea6d738d1fcbc1f20cc5a5bb7694 Tue Nov 14 14:07:39 2017 -0800
    Adding MISCE and RIGGLE info to tools page, refs #20368
  • lines changed 115, context: html, text, full: html, text
    109176417f6395850d3380f6538730e08b7da59b Tue Nov 21 13:10:19 2017 -0800
    Adding some screenshots and detail to Sample Psychic section, refs #20368
• src/hg/geoIp/geoIpToCountry.c
  • lines changed 1, context: html, text, full: html, text
    7564d030f4584b8f55c8a002f41f50e44deb4d11 Mon Nov 20 14:33:53 2017 -0800
    fix typo in usage statement
• src/hg/hgCustom/hgCustom.c
  • lines changed 16, context: html, text, full: html, text
    aecff87074bb35effb6ee1620132f69466807409 Tue Nov 14 11:18:57 2017 -0800
    change the variable name warn to warnMsg to avoid clash with same name function no redmine
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    e59588ca7baf37936bc6c07f9ed49a08251ed474 Wed Nov 22 09:45:17 2017 -0800
    Adding a link to hosting section to hgCustom and hgHubConnect
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    e59588ca7baf37936bc6c07f9ed49a08251ed474 Wed Nov 22 09:45:17 2017 -0800
    Adding a link to hosting section to hgCustom and hgHubConnect
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 2, context: html, text, full: html, text
    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/hg/hgSession/hgSession.c
  • lines changed 4, context: html, text, full: html, text
    e6cd762cc1e6ba7103394e13f2612198106881fc Sat Nov 18 14:16:48 2017 -0800
    copy custom composites before hub load, but copy custom tracks AFTER hub load.
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    a80fa4b47c187ea6839b195fcea07a0843f2e11f Mon Nov 20 12:49:20 2017 -0800
    move some stuff around so track hubs are loaded before new default tracks are hidden.
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 7, context: html, text, full: html, text
    74720ae3a83557093fcf0373528b24ad1d96f932 Tue Nov 14 11:33:38 2017 -0800
    hgTablesTest's countNoncommentLines was skipping blank lines which caused it to get the wrong row count when querying a field that is sometimes empty. skipLeadingSpaces skips '\n' due to isspace; check for '\n' before calling it. refs #20534
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 21, context: html, text, full: html, text
    b56aaf37a70d531c514f7ba88f3c6a73888b527e Mon Nov 20 11:59:22 2017 -0800
    hgTracks/simpleTracks.c's lookupRefNames ignores subtrack-level label settings, so don't display the refGene label settings when it's a subtrack. Also fixed up omim-detection logic for ncbiRefSeqLink. refs #19318
• src/hg/hgTracks/encode.c
  • lines changed 103, context: html, text, full: html, text
    8504d7cd72e01e7a28601edb5d4c98c7c87a7849 Thu Nov 16 20:16:51 2017 -0800
    add filtering to bigNarrowPeak
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/hg/hgVai/libifyMe.c
  • lines changed 2, context: html, text, full: html, text
    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    18271ce9eede5b6fc3b900246bf25abe002ca696 Tue Nov 14 15:29:05 2017 -0800
    Staging commented out blurbs for release prep, xenLae2, refs #17435
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    8ac66ac772755ceaefecaea8ecf2b469708d9803 Wed Nov 15 13:31:30 2017 -0800
    Releasing static docs for xenLae2, refs #17435
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 29, context: html, text, full: html, text
    18271ce9eede5b6fc3b900246bf25abe002ca696 Tue Nov 14 15:29:05 2017 -0800
    Staging commented out blurbs for release prep, xenLae2, refs #17435
  • lines changed 8, context: html, text, full: html, text
    964f4163dc0510f05e7543aef7887cedbebc3061 Tue Nov 14 15:33:42 2017 -0800
    Adding reference for xenLae2 credits, refs #17435
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    8ac66ac772755ceaefecaea8ecf2b469708d9803 Wed Nov 15 13:31:30 2017 -0800
    Releasing static docs for xenLae2, refs #17435
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 3, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 3, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 3, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 4, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigGenePred.html
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    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 4, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigNarrowPeak.html
  • lines changed 3, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigPsl.html
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    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 4, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 1, context: html, text, full: html, text
    9d4954ea3782d501377c379202f035148e3e7539 Tue Nov 21 11:28:36 2017 -0800
    Editing kent instances of wording for 'non-commercial', refs #19871
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 9, context: html, text, full: html, text
    382e272bc1d81a5ac9f89fe52884600630727ef5 Tue Nov 21 16:57:59 2017 -0800
    Adding a small section pointing to hosting section
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 4, context: html, text, full: html, text
    9d4954ea3782d501377c379202f035148e3e7539 Tue Nov 21 11:28:36 2017 -0800
    Editing kent instances of wording for 'non-commercial', refs #19871
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    32bcebae2a5213749071ed94f73e6672096d9637 Tue Nov 21 09:15:56 2017 -0800
    Adding a note about the Data Commons vs Discovery Environment at CyVerse
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 5, context: html, text, full: html, text
    4a79baa52690260168d691b52a127579ce463941 Wed Nov 22 08:42:51 2017 -0800
    Adding a link to the hosting section to each of the bigData format pages
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 39, context: html, text, full: html, text
    18271ce9eede5b6fc3b900246bf25abe002ca696 Tue Nov 14 15:29:05 2017 -0800
    Staging commented out blurbs for release prep, xenLae2, refs #17435
  • lines changed 11, context: html, text, full: html, text
    8ac66ac772755ceaefecaea8ecf2b469708d9803 Wed Nov 15 13:31:30 2017 -0800
    Releasing static docs for xenLae2, refs #17435
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    9d4954ea3782d501377c379202f035148e3e7539 Tue Nov 21 11:28:36 2017 -0800
    Editing kent instances of wording for 'non-commercial', refs #19871
  • lines changed 31, context: html, text, full: html, text
    4e30703662f46628853f5e04cc9a32a1c5eb23e1 Tue Nov 21 13:58:22 2017 -0800
    Announcing the NCBI RefSeq Gene tracks for mm10, refs #18997
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    2eae7e50194888dd23a4731c977f9c95f7814c90 Tue Nov 21 15:40:02 2017 -0800
    Minor edit to the NCBI RefSeq announcement, refs #18997
• src/hg/htdocs/indexNews.html
  • lines changed 8, context: html, text, full: html, text
    18271ce9eede5b6fc3b900246bf25abe002ca696 Tue Nov 14 15:29:05 2017 -0800
    Staging commented out blurbs for release prep, xenLae2, refs #17435
  • lines changed 9, context: html, text, full: html, text
    8ac66ac772755ceaefecaea8ecf2b469708d9803 Wed Nov 15 13:31:30 2017 -0800
    Releasing static docs for xenLae2, refs #17435
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    4e30703662f46628853f5e04cc9a32a1c5eb23e1 Tue Nov 21 13:58:22 2017 -0800
    Announcing the NCBI RefSeq Gene tracks for mm10, refs #18997
• src/hg/htdocs/training/index.html
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    cb74dda6aae145e06e1a8d82f759057363530425 Tue Nov 21 17:13:56 2017 -0800
    removing prague and ljubljana workshops
• src/hg/inc/cart.h
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    4a55fd262783e01281b132efad717b84575879cf Sat Nov 18 14:36:34 2017 -0800
    oops, left this out
• src/hg/inc/hui.h
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    8504d7cd72e01e7a28601edb5d4c98c7c87a7849 Thu Nov 16 20:16:51 2017 -0800
    add filtering to bigNarrowPeak
• src/hg/inc/versionInfo.h
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    cedef52b772e1cca44c8d8729289e50975506313 Mon Nov 27 10:06:16 2017 -0800
    New version number v358
• src/hg/js/autocomplete.js
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    7f929d20e51082fbefad6f1a482d600f3ec68ce7 Mon Nov 13 10:14:36 2017 -0800
    replace en-dash and em-dash with hyphen in hgGateway and hgTracks
• src/hg/js/hgGateway.js
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    7f929d20e51082fbefad6f1a482d600f3ec68ce7 Mon Nov 13 10:14:36 2017 -0800
    replace en-dash and em-dash with hyphen in hgGateway and hgTracks
• src/hg/js/react/lib/TextInput.jsx
  • lines changed 1, context: html, text, full: html, text
    ee4177fbf667f2eafeba46e4352075cf93e36983 Wed Nov 15 14:37:14 2017 -0800
    Using Braney's unicode em-/en-dash replacement trick in react TextInput module. refs #20517
• src/hg/lib/cart.c
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    e6cd762cc1e6ba7103394e13f2612198106881fc Sat Nov 18 14:16:48 2017 -0800
    copy custom composites before hub load, but copy custom tracks AFTER hub load.
• src/hg/lib/customFactory.c
  • lines changed 3, context: html, text, full: html, text
    7783dc22842c5459e44bc3c861800a8e7588aa77 Tue Nov 14 11:15:10 2017 -0800
    turning on limit of 50 million lines for a bed file input to a custom track to eliminate the gigantic incoming files no redmine
• src/hg/lib/hui.c
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    3fd7f765f0cdecf7248081b0ecbc1c421721d7b0 Mon Nov 13 14:48:17 2017 -0800
    Fixing broken all button on DNase hypersensitivity track, refs #20308
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    8504d7cd72e01e7a28601edb5d4c98c7c87a7849 Thu Nov 16 20:16:51 2017 -0800
    add filtering to bigNarrowPeak
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    45b4b52a4727e9aeedabcd39e011d4408f35b7e8 Wed Nov 22 16:48:32 2017 -0800
    In printDataVersion, instead of preferring hgFixed.trackVersion to trackDb setting dataVersion, prefer dataVersion because it is easier to manage pushes with a dataVersion file vs. with rows of the trackVersion table. refs #18997 note-141
• src/hg/makeDb/doc/colAng1/initialBuild.txt
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    ea289ea2ec73ce6da8c158fdb279e0f4b9881f96 Fri Nov 17 10:03:17 2017 -0800
    adding blatServers refs #18958 #17545 #18927
• src/hg/makeDb/doc/hg19.txt
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    ebb367f7a4871a28b79b667f7c6eafbe892b647c Tue Nov 14 09:05:24 2017 -0800
    lastz chainNet to gorGor5 per user request refs #20482
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    3da2c082ae7d96244d1f2c0b78334623e45240a2 Tue Nov 14 14:27:59 2017 -0800
    note featureBits for gorGor5 chainRBestHg19 refs #20482
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    102abe57743c660c975e8626136c277d0f4e5d3b Wed Nov 15 17:14:22 2017 -0800
    Cleanup build dirs and docs for GTEx eQTL tracks. refs #15646
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    009e2eaf2a289f5ea4c414afac65b1703be05ce2 Wed Nov 15 17:17:07 2017 -0800
    A bit more info.
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    b9dffc597ef24b8fe28b4f1104f85d6016ef9446 Fri Nov 17 09:34:29 2017 -0800
    Updated dbNcbiRefSeq.pl to extract genomic "rna" sequence if NCBI doesn't provide rna sequence for genes on chrM. (For human and mouse, NCBI provides only protein accessions in the GFF3.) Re-ran on hg38 and mm10. refs #18997 notes 84-88, 90-92, 96-102
• src/hg/makeDb/doc/macNem1/initialBuild.txt
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    ea289ea2ec73ce6da8c158fdb279e0f4b9881f96 Fri Nov 17 10:03:17 2017 -0800
    adding blatServers refs #18958 #17545 #18927
• src/hg/makeDb/doc/mm10.txt
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    b9dffc597ef24b8fe28b4f1104f85d6016ef9446 Fri Nov 17 09:34:29 2017 -0800
    Updated dbNcbiRefSeq.pl to extract genomic "rna" sequence if NCBI doesn't provide rna sequence for genes on chrM. (For human and mouse, NCBI provides only protein accessions in the GFF3.) Re-ran on hg38 and mm10. refs #18997 notes 84-88, 90-92, 96-102
• src/hg/makeDb/doc/rhiBie1/initialBuild.txt
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    ea289ea2ec73ce6da8c158fdb279e0f4b9881f96 Fri Nov 17 10:03:17 2017 -0800
    adding blatServers refs #18958 #17545 #18927
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    f87f9714002734ac3cb6baee1ed9288fec0a8652 Tue Nov 14 12:59:39 2017 -0800
    Adding xenLae2 to beta genbank updates, refs #17435
• src/hg/makeDb/genbank/etc/rr.dbs
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    a8a649a524d054abcd134d87922ee46c926fdfd3 Thu Nov 16 09:06:42 2017 -0800
    Adding xenLae2 to rr genebank updates, refs #17435
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
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    52f4ca22edbec229dbac490a4fc6123044dad754 Tue Nov 14 11:06:20 2017 -0800
    adding lineLimit option to error out when files are too large no redmine
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    5e941ad6b9facc9388f06ac335b9efdc6147ee4a Fri Nov 17 15:08:12 2017 -0800
    Adding to new message about tracks with over 50 million lines refs #20541
• src/hg/makeDb/outside/gtexEqtl/README.txt
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    102abe57743c660c975e8626136c277d0f4e5d3b Wed Nov 15 17:14:22 2017 -0800
    Cleanup build dirs and docs for GTEx eQTL tracks. refs #15646
• src/hg/makeDb/outside/gtexEqtl/gtexEqtlLoadTissues.csh
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    102abe57743c660c975e8626136c277d0f4e5d3b Wed Nov 15 17:14:22 2017 -0800
    Cleanup build dirs and docs for GTEx eQTL tracks. refs #15646
• src/hg/makeDb/outside/gtexEqtl/gtexEqtlMakeBeds.pl
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    102abe57743c660c975e8626136c277d0f4e5d3b Wed Nov 15 17:14:22 2017 -0800
    Cleanup build dirs and docs for GTEx eQTL tracks. refs #15646
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    c87a72d1f53485c8765e28d33592133c6a58428a Mon Nov 20 09:29:04 2017 -0800
    Fixing broken links found by the broken link report for geoFor1, no Redmine.
• src/hg/makeDb/trackDb/blatFr1.html
  • lines changed 2, context: html, text, full: html, text
    88bb9d1b77122f263417ccce39b6ba26ae5a5b3e Fri Nov 17 08:48:01 2017 -0800
    Fixing broken links for xenTro1, no Redmine.
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    47302c6d04f4ed2ae4435c0b8f3e5d29ba1b52bd Tue Nov 21 13:21:34 2017 -0800
    Fixing up chain/net track description pages, refs #19151
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    47302c6d04f4ed2ae4435c0b8f3e5d29ba1b52bd Tue Nov 21 13:21:34 2017 -0800
    Fixing up chain/net track description pages, refs #19151
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    47302c6d04f4ed2ae4435c0b8f3e5d29ba1b52bd Tue Nov 21 13:21:34 2017 -0800
    Fixing up chain/net track description pages, refs #19151
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1d89baf84a6abd434fd2cbb7782072c5ed52cb84 Mon Nov 13 11:12:47 2017 -0800
    Adding maxItems 2000 to the cosmicRegions track to help MLQ ref #19932
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
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    64b681597f2b5baa96a788e36fcdec9c3e1ba65b Wed Nov 22 11:19:55 2017 -0800
    Fixing two small links on hg38 cons100way.html refs #20573
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    3c7196ffa5e5d557a4197cfde3e9a81d30efba7b Wed Nov 22 13:20:02 2017 -0800
    Fixing a comma to a period typo on cons100way.html
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 13, context: html, text, full: html, text
    179c2a7f29fd3afd735f9a7ee882187bda48bcd1 Thu Nov 16 11:18:18 2017 -0800
    Adding comments to assemblies in cons30way not yet released #href= that can be uncommented once assemblies are released refs #20216 #20545
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
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    b15fa726528606884a2c8e50708a2f77c16c32c0 Thu Nov 16 09:06:00 2017 -0800
    Fixing indentation spacing that was lost after replacing tabs with spaces, refs #19154
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    5dcbeef58de3a608782ebe080e04e77c37b2f23b Thu Nov 16 09:20:38 2017 -0800
    Setting the Umap single read mappability tracks to squish by default. refs #19154
  • lines changed 31, context: html, text, full: html, text
    9a32fd6e37ac57e7e5b510038462f704c9a79329 Thu Nov 16 11:22:20 2017 -0800
    Removing redundant lines to the view level, refs #19154
• src/hg/makeDb/trackDb/human/hg38/mappability.html
  • lines changed 8, context: html, text, full: html, text
    8b11c5f5244d10fd4930abcbb61edbac757500a6 Thu Nov 16 07:29:24 2017 -0800
    Removing 'contact, support and questions' section since it mentions the track hub and questions should be sent to our mailing list for this native track, refs #19154
  • lines changed 17, context: html, text, full: html, text
    da939d96c13d9b444678b99dc1a10f310085dce4 Thu Nov 16 08:35:53 2017 -0800
    Adding <p> tags to the definition list to remove the need for a <br> tag. refs #19154
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    372d308c816475ce0c64f9eacd59a9ac36bba9ca Thu Nov 16 08:45:52 2017 -0800
    Removing 'we' when explaining how the bisulfite genomes were created. refs #19154
  • lines changed 23, context: html, text, full: html, text
    47f337cfa1e442d613ac7d9f5b793b702ca93fca Thu Nov 16 10:38:48 2017 -0800
    Adding Data Access section to the track description page, refs #19154
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    840fc3b5897e3a9fe37e33db03500e61399aa493 Wed Nov 22 14:56:14 2017 -0800
    Rearranging hgTracks and hgTrackUi species ordering to match 30way tree image, refs #20216
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 74, context: html, text, full: html, text
    29e1c55f50ef906b4d553446ae1f1b42d10fe92e Fri Nov 17 12:06:30 2017 -0800
    Bring ncbiRefSeq name2 and protAcc searches up from human/hg38/trackDb.ra to top-level refSeqComposite.ra and add search on product. hgFind's formatting of results is not as nice as for refGene, but at least searching works. refs #18997
• src/hg/makeDb/trackDb/human/omimAvSnp.html
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    f7c5efce7a6b1fc3f008fa88de6a2f1ec276cce6 Wed Nov 15 16:08:04 2017 -0800
    Updating OMIM AV SNPs to use snp150 on hg19 and hg38, refs #18151
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    f7ab5f57224cf66aceaef5725d64928cb3f60945 Tue Nov 21 08:44:52 2017 -0800
    Staging NCBI RefSeq Genes for mm10 on hgwbeta, refs #18997
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    33d46c92e8bc196c10a7f58ab71195c71a8962b0 Tue Nov 21 13:24:42 2017 -0800
    Releasing NCBI RefSeq Genes track for mm10, refs #18997
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c4e387173b512c619730fc1d4402886eee123367 Mon Nov 20 16:30:10 2017 -0800
    Staging NCBI RefSeq genes for mm10 on hgwbeta, refs #18997
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    33d46c92e8bc196c10a7f58ab71195c71a8962b0 Tue Nov 21 13:24:42 2017 -0800
    Releasing NCBI RefSeq Genes track for mm10, refs #18997
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    ae937fe973bedfd216bc16222a742ac359846a27 Wed Nov 15 11:01:21 2017 -0800
    Minor edit to a sentence for better flow. Adding the word 'track' after UCSC RefSeq, refs #18997
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    a6a8ebe2f7aab4ba300e0b7126f57882dad9cc3c Tue Nov 21 15:08:40 2017 -0800
    Fixing broken link in the example bigBed command, refs #18997
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 31, context: html, text, full: html, text
    06a011cb7b2170db0747a30281c2ee972286c220 Fri Nov 17 10:49:20 2017 -0800
    Fixed search specs for ncbiRefSeqCurated and ncbiRefSeqPredicted and moved them into refSeqComposite.ra. refs #18997 note 108
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    29e1c55f50ef906b4d553446ae1f1b42d10fe92e Fri Nov 17 12:06:30 2017 -0800
    Bring ncbiRefSeq name2 and protAcc searches up from human/hg38/trackDb.ra to top-level refSeqComposite.ra and add search on product. hgFind's formatting of results is not as nice as for refGene, but at least searching works. refs #18997
  • lines changed 2, context: html, text, full: html, text
    19e706ca643a4229087fb53d97e40dc165afc9df Wed Nov 22 16:43:28 2017 -0800
    Added dataVersion (from file) setting to refSeqComposite for all subtracks but refGene since that's updated by the genbank process. This setting will be ignored by v357 code because it uses hgFixed.trackVersion preferentially. I'm going to change it to prefer dataVersion, because dataVersion with a file is much easier to push out to hgwbeta and RR than rows of the hgFixed.trackVersion table. refs #18997 note 141
• src/hg/makeDb/trackDb/refSeqFuncElems.html
  • lines changed 11, context: html, text, full: html, text
    07056f88aa8c5942cc22363190db655a4f082f57 Wed Nov 15 13:13:33 2017 -0800
    Adding a missing period to the track description page. Adding a <p> tag to the Contacts section. Updating redirected URLs in the References section, refs #19638
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    07667c7505a00f60ab64a057da49ec26eb705685 Wed Nov 15 15:26:16 2017 -0800
    Renaming the 'Credits' section to 'References', refs #19638
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    06a011cb7b2170db0747a30281c2ee972286c220 Fri Nov 17 10:49:20 2017 -0800
    Fixed search specs for ncbiRefSeqCurated and ncbiRefSeqPredicted and moved them into refSeqComposite.ra. refs #18997 note 108
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
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    b6388e81f9d939cdfe35baf0a529be72f3888fb2 Tue Nov 14 08:26:38 2017 -0800
    added missing human being to gencode credits
• src/hg/makeDb/trackDb/worm/chainCe4.html
  • lines changed 1, context: html, text, full: html, text
    2ac58f7c6b428f8bc7f7c6840b210b05196f1a39 Mon Nov 27 09:45:40 2017 -0800
    Fixing broken links for caeRem1, no Redmine.
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
  • lines changed 1, context: html, text, full: html, text
    2ac58f7c6b428f8bc7f7c6840b210b05196f1a39 Mon Nov 27 09:45:40 2017 -0800
    Fixing broken links for caeRem1, no Redmine.
• src/hg/makeDb/trackDb/worm/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    529a0b2a0bdcfba12ed0ee7e8f8d44c91b7ee200 Tue Nov 21 08:36:24 2017 -0800
    Fixing broken links found by the broken link report for caePb2, no redmine.
• src/hg/makeDb/trackDb/xenTro/jgiFilteredModels.html
  • lines changed 1, context: html, text, full: html, text
    88bb9d1b77122f263417ccce39b6ba26ae5a5b3e Fri Nov 17 08:48:01 2017 -0800
    Fixing broken links for xenTro1, no Redmine.
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    e9a07097f376989db5094741ea5be83cec6e08f7 Tue Nov 14 13:27:10 2017 -0800
    Correcting matrix table for xenTro9 chains, waiting to fix priority, refs #17435
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    1db919bc746092f29774b94194155842c1cbfd42 Tue Nov 14 17:51:05 2017 -0800
    Adding chain matrix for xenLae2 assemblies, mm10,hg38,xenTro9, refs #17435
• src/hg/makeDb/trackDb/xenTro/xenLae2/description.html
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    8ac66ac772755ceaefecaea8ecf2b469708d9803 Wed Nov 15 13:31:30 2017 -0800
    Releasing static docs for xenLae2, refs #17435
• src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
  • lines changed 3, context: html, text, full: html, text
    88bb9d1b77122f263417ccce39b6ba26ae5a5b3e Fri Nov 17 08:48:01 2017 -0800
    Fixing broken links for xenTro1, no Redmine.
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 43, context: html, text, full: html, text
    cfb24cb7ed14b50c6a6ff273be7929ff345716d6 Tue Nov 14 15:29:40 2017 -0800
    fixup 11-way description refs #19151
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    da056dc54336ceda84d7c4b1444399183b649bc2 Tue Nov 21 10:23:34 2017 -0800
    linking chrPic2 to genome-preview since that browser has not been released yet, #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.11way.ra
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    2bdca3d1d4f826e05bb597abee9508d4c50c69d0 Tue Nov 14 15:31:59 2017 -0800
    correct list of species in sGroup refs #19151
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    5023731f88ef52ef71aa8d37debc639d670e8a86 Tue Nov 14 15:33:35 2017 -0800
    correct shortLabel is Conservation refs #19151
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    47302c6d04f4ed2ae4435c0b8f3e5d29ba1b52bd Tue Nov 21 13:21:34 2017 -0800
    Fixing up chain/net track description pages, refs #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra
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    eef67ffcd89a88116d32c3548a99858104743f83 Tue Nov 14 11:01:34 2017 -0800
    turn on NCBI RefSeq for evaluation refs #19151
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    626a6375905120ccf7e821f9927561d47a8a0bb9 Tue Nov 14 11:04:11 2017 -0800
    NCBI RefSeq on for only alpha make refs #19151
• src/hg/mouseStuff/chainToPsl/tests/makefile
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    88d645ebb17441000185bc5303ab1e332fea4bd7 Wed Nov 15 10:00:35 2017 -0800
    avoid gzip waiting for confirmation to overwrite refs #20479
• src/hg/utils/automation/doNcbiRefSeq.pl
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    b9dffc597ef24b8fe28b4f1104f85d6016ef9446 Fri Nov 17 09:34:29 2017 -0800
    Updated dbNcbiRefSeq.pl to extract genomic "rna" sequence if NCBI doesn't provide rna sequence for genes on chrM. (For human and mouse, NCBI provides only protein accessions in the GFF3.) Re-ran on hg38 and mm10. refs #18997 notes 84-88, 90-92, 96-102
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    6adb58474d7cf1e4669c788e417a4e28a8c20a06 Wed Nov 22 16:50:02 2017 -0800
    Store version in a file /gbdb/<db>/ncbiRefSeq/ncbiRefSeqVersion.txt instead of inserting a row into hgFixed.trackVersion -- easier to manage pushes. refs #18997 note-141
• src/hg/utils/otto/gwas/checkGwas.sh
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    efea57415b269611f9e9b44518853bfd645a08c4 Wed Nov 15 16:23:03 2017 -0800
    Updating GWAS pipeline to use snp150, refs #18151
• src/hg/utils/otto/gwas/expectedColumns.txt
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    efea57415b269611f9e9b44518853bfd645a08c4 Wed Nov 15 16:23:03 2017 -0800
    Updating GWAS pipeline to use snp150, refs #18151
• src/hg/utils/otto/gwas/makefile
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    efea57415b269611f9e9b44518853bfd645a08c4 Wed Nov 15 16:23:03 2017 -0800
    Updating GWAS pipeline to use snp150, refs #18151
• src/hg/utils/otto/omim/buildOmimTracks.sh
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    f7c5efce7a6b1fc3f008fa88de6a2f1ec276cce6 Wed Nov 15 16:08:04 2017 -0800
    Updating OMIM AV SNPs to use snp150 on hg19 and hg38, refs #18151
• src/hg/utils/otto/omim/doOmimGene2/doOmimGene2.c
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    cdad6fbfca3f0dcf14335e0dc08afe3f0147b874 Wed Nov 15 16:10:07 2017 -0800
    doOmimGene2 now uses hgFixed.refLink (its new location), and makefile has a clean target, refs #18151
• src/hg/utils/otto/omim/makefile
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    cdad6fbfca3f0dcf14335e0dc08afe3f0147b874 Wed Nov 15 16:10:07 2017 -0800
    doOmimGene2 now uses hgFixed.refLink (its new location), and makefile has a clean target, refs #18151
• src/hg/utils/tdbQuery/tdbQuery.c
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    be368a5841d9104cd9957cdb8325ae5d4ed25456 Tue Nov 21 10:26:45 2017 -0800
    tdbQuery was ignoring databases that did not have their own trackDb.ra file, in order to exclude non-assembly subdirs like cv/* and human/encodeTest. Since legit assemblies always have a description.html file, make it accept subdirs that have a description.html file even if they don't have a trackDb.ra.
• src/inc/srcVersion.h
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    b9be85ef317a960033bc2cbaadf5a9b931c20061 Tue Nov 14 12:52:17 2017 -0800
    trying out a srcVersion print in optionsInit() no redmine
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    cedef52b772e1cca44c8d8729289e50975506313 Mon Nov 27 10:06:16 2017 -0800
    New version number v358
• src/inc/windowsToAscii.h
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    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/lib/makefile
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    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
• src/lib/options.c
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    b9be85ef317a960033bc2cbaadf5a9b931c20061 Tue Nov 14 12:52:17 2017 -0800
    trying out a srcVersion print in optionsInit() no redmine
• src/lib/windowsToAscii.c
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    0c56fe6958f347b5ab7070725114c7d4c216bc87 Mon Nov 13 15:19:40 2017 -0800
    catch weird strings in position boxes
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    7d809b23986dbed1fd2132877792a7821796f0e1 Mon Nov 13 16:33:22 2017 -0800
    oops, left in a printf
• src/product/installer/browserSetup.sh
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    6f0531efc9fa0452860585dd964da592eb8c5d4b Fri Nov 17 08:29:49 2017 -0800
    Changing cse to soe in gbic, and changing help message to mention genome-euro, refs #20353
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    2425d8d4fda91af2917be39cea572f1aa2946327 Fri Nov 17 09:46:12 2017 -0800
    woops fixing typo in genome-euro-mysql name, refs #20353
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    fb5a5200ba3d42429d49a22b9bf481f32057f069 Fri Nov 17 09:53:36 2017 -0800
    Adding curl to list of programs that may not be present on a mirror after testing on debian/stretch
• src/utils/bedClip/tests/makefile
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    1c0a252fc496333382df6b391646afca45b11d2f Thu Nov 16 14:08:47 2017 -0800
    eliminate confusion from new source version printout no redmine
• src/utils/qa/updateTimesDb.sh
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    2ea1686e6e3979071cdcbc6968b000cfa1e06c65 Tue Nov 14 14:17:38 2017 -0800
    minor change to make usage message cleaner, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    0e1c30edecf67391e0260ddee07c28b565bd5f44 Mon Nov 27 10:05:32 2017 -0800
    v358 final build refs #20479
• src/utils/qa/weeklybld/updateCgiVersion.csh
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    f1d847f8a1ccfcb1c1f7267e5f87e819bdfa4a2a Tue Nov 14 13:00:04 2017 -0800
    also edit the srcVersion.h file with the versionInfo.h no redmine
• src/utils/userApps/mkREADME.sh
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    6fdd5908880d6a2fb2e4f7235679981888d8055b Tue Nov 14 13:37:59 2017 -0800
    avoid verbose argument on a few commands no redmine
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    50f1ff191f99e85d8f8ef21785fd27d142edec67 Tue Nov 14 14:17:46 2017 -0800
    a couple more programs that can not manage verbose argument no redmine
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    8621d381fa72623be321c96e4ac19e652a01147a Tue Nov 14 14:37:14 2017 -0800
    eliminate one ERROR: message no redmine
• src/utils/webSync
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    664941557f4e443e43e09d8f047b7bcbfb61a576 Mon Nov 20 16:02:36 2017 -0800
    CIRM: fix websync program to deal properly with symlinks

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