All File Changes

v357_base to v358_preview (2017-10-30 to 2017-11-06) v358

• src/hca/LICENSE
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    7fb8f954d43e80d0ac739601d017df814e3d0aff Thu Aug 3 12:27:05 2017 -0700
    Updating copyright holder per HCA request.
• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
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    54233e68e0cb7825f81de963011e83849e128f38 Thu Sep 7 15:30:13 2017 -0700
    Adapting to some changed tag names.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/hcaV2ToV3/2to3
  • lines changed 134, context: html, text, full: html, text
    f3256f82f0a5eb915068c65290675b315ee20678 Fri Sep 1 14:02:27 2017 -0700
    Adding table that describes how v2 metadata fields move to v3.
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    31139fbd0ac42c06d02e2d534831d719de4b5a0d Fri Sep 1 15:51:19 2017 -0700
    Renaming stuff for going between metadata versions.
• src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c
  • lines changed 106, context: html, text, full: html, text
    050e1358247ac10835441952c2e192613f07f834 Thu Sep 7 16:51:12 2017 -0700
    Starting to add ids if missing for protocols and donors. Protocol bits might still need some work.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c
  • lines changed 103, context: html, text, full: html, text
    822de6b51fb45bd9cea5f8c0e6e463f018e55db0 Thu Sep 7 13:20:48 2017 -0700
    Updating files[] array to lanes[] array as part of V2 -> V3 transition.
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    46ab8cdb3b6354c753c458ffba1a31a7f3bcae9b Thu Sep 7 15:18:58 2017 -0700
    Handling .1. .2. .3. output as arrays.
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    7e67a21cf569cafee3228bf6452e2e760ca7365f Thu Sep 7 15:31:01 2017 -0700
    Ooops, 'lanes' not lane.
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    233236f4f7c048d8be8cf861d047909b10e2af5a Thu Sep 7 21:43:00 2017 -0700
    Removing old V2 protocol handling. V3 doesn't need the special case.
  • lines changed 148, context: html, text, full: html, text
    40c64e7dd6319e8bba943fdfea4608e53b13ac27 Fri Sep 8 18:28:58 2017 -0700
    Removing debugging message
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    2ccd1bd9cee67dc597157a6e47d2694b93c954e6 Fri Sep 8 19:12:17 2017 -0700
    Handling another fringe case of dots in a characteristics name.
  • lines changed 14, context: html, text, full: html, text
    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/v2_v3/2to3
  • lines changed 134, context: html, text, full: html, text
    31139fbd0ac42c06d02e2d534831d719de4b5a0d Fri Sep 1 15:51:19 2017 -0700
    Renaming stuff for going between metadata versions.
  • lines changed 134, context: html, text, full: html, text
    1c61e4ebd646d8f13315dedb80affecdf9f5048e Fri Sep 1 15:51:40 2017 -0700
    Renaming stuff for going between metadata versions.
• src/hca/v2v3/2to3
  • lines changed 134, context: html, text, full: html, text
    1c61e4ebd646d8f13315dedb80affecdf9f5048e Fri Sep 1 15:51:40 2017 -0700
    Renaming stuff for going between metadata versions.
  • lines changed 4, context: html, text, full: html, text
    6f2a2d9ff2a77477878405e84f84777a04d57615 Mon Sep 4 11:56:48 2017 -0700
    Figuring out ways to modify a few less and fixing a few ontology terms.
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    442874e2a5188ef0ca1da03d42c367727f98c372 Wed Sep 6 17:21:09 2017 -0700
    Fixing a few typos and missing things.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/v2v3/hcav2v3ArraysToMidObject/hcav2v3ArraysToMidObject.c
  • lines changed 83, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
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    859c57e6d9c604e8c085f8a5c982f0f291a07ecf Sun Sep 3 11:35:58 2017 -0700
    Adding a bunch more things that are now arrays of objects.
• src/hca/v2v3/hcav2v3ArraysToMidObject/makefile
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    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hca/v2v3/hcav2v3ModifyContributors/hcav2v3ModifyContributors.c
  • lines changed 69, context: html, text, full: html, text
    a4861751824ae955f43dd60d321eb0c70620c19d Fri Sep 1 19:41:44 2017 -0700
    LIttle utility to fix up project.contributor in v2-v3 conversion seems to work.
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    7ce01a443f1fc128226f3d50455c55b5fb0b9bce Fri Sep 1 19:57:00 2017 -0700
    Unpacking more arrays.
  • lines changed 79, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hca/v2v3/hcav2v3ModifyContributors/makefile
  • lines changed 3, context: html, text, full: html, text
    a4861751824ae955f43dd60d321eb0c70620c19d Fri Sep 1 19:41:44 2017 -0700
    LIttle utility to fix up project.contributor in v2-v3 conversion seems to work.
  • lines changed 3, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hg/cirm/cdw/cdwBackup/makefile
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    d250a10d6a82f03f2852ee8e43723632ff360b9a Wed Nov 1 13:33:28 2017 -0700
    Fixing make clean for cdw/
• src/hg/cirm/cdw/cdwFindSymlinkable/cdwFindSymlinkable.c
  • lines changed 197, context: html, text, full: html, text
    91379d70225b99cfb071fd339f7f89c149e302ec Wed Nov 1 15:12:27 2017 -0700
    adding new utility to find symlinkable files for cdw.
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    961f73c71116eba96edfd213fb1b057a5cbdd0a9 Fri Nov 3 13:28:31 2017 -0700
    Adding some more handy double-checking to the cdw symlinker.
• src/hg/cirm/cdw/cdwFindSymlinkable/makefile
  • lines changed 4, context: html, text, full: html, text
    91379d70225b99cfb071fd339f7f89c149e302ec Wed Nov 1 15:12:27 2017 -0700
    adding new utility to find symlinkable files for cdw.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 26, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
• src/hg/cirm/cdw/cdwReallyRemoveDataset/cdwReallyRemoveDataset.c
  • lines changed 4, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 3, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 19, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
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    a69e35d913d0c9bc99b2d1814635467e7c062ecd Wed Nov 1 15:20:00 2017 -0700
    oops, need to ren-enable pipeline call
• src/hg/cirm/cdw/cdwSummary/makefile
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    d250a10d6a82f03f2852ee8e43723632ff360b9a Wed Nov 1 13:33:28 2017 -0700
    Fixing make clean for cdw/
• src/hg/cirm/cdw/cdwUnlockSubmittedFile/cdwUnlockSubmittedFile.csh
  • lines changed 19, context: html, text, full: html, text
    79196cfbc8d6c9140569d96fb0e8f699301001b5 Wed Nov 1 17:29:35 2017 -0700
    Adding cdwUnlockSubmittedFile.csh to allow wranglers to change a submitted file in the wrangle dir back to an file they can edit again. After checking that the symlink is valid, it removes it and makes a copy of its target that is writeable.
• src/hg/cirm/cdw/cdwUnlockSubmittedFile/makefile
  • lines changed 13, context: html, text, full: html, text
    79196cfbc8d6c9140569d96fb0e8f699301001b5 Wed Nov 1 17:29:35 2017 -0700
    Adding cdwUnlockSubmittedFile.csh to allow wranglers to change a submitted file in the wrangle dir back to an file they can edit again. After checking that the symlink is valid, it removes it and makes a copy of its target that is writeable.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 86, context: html, text, full: html, text
    30aecb6730202593ae34967fe4ce07647d9acdaa Mon Oct 30 11:29:38 2017 -0700
    Making pie charts have an 'other' slice that collects together the pieces that are really too small to label.
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    68468b245eab143bdd55fc4781c187b875ab38cd Mon Oct 30 17:08:19 2017 -0700
    CIRM: fixing download instructions for cirm public site
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    195a8f91ef9142b437a126f7a25634408f65f12c Wed Nov 1 15:24:20 2017 -0700
    Bumping cdwWebBrowse version number since it's changed a bit.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 13, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 166, context: html, text, full: html, text
    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
• src/hg/cirm/cdw/makefile
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    be508ea1e3d9043b295ee9b8826f89dc300a3851 Mon Sep 4 11:58:02 2017 -0700
    Using kentSrc define one more place to avoid future edits.
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    8877724b8354227a11c7702ac006931881107e74 Wed Nov 1 15:05:52 2017 -0700
    cdw changes to support symlinks instead of copying to save space.
  • lines changed 1, context: html, text, full: html, text
    79196cfbc8d6c9140569d96fb0e8f699301001b5 Wed Nov 1 17:29:35 2017 -0700
    Adding cdwUnlockSubmittedFile.csh to allow wranglers to change a submitted file in the wrangle dir back to an file they can edit again. After checking that the symlink is valid, it removes it and makes a copy of its target that is writeable.
• src/hg/cirm/cdw/utils/cdwVcfStats/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    d250a10d6a82f03f2852ee8e43723632ff360b9a Wed Nov 1 13:33:28 2017 -0700
    Fixing make clean for cdw/
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/makefile
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    9fb246d429b86813fbd87b2032fddc2814e22102 Wed Nov 1 17:36:03 2017 -0700
    fixing some minor makefile issues.
• src/hg/cirm/cdw/wrangle/makefile
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    9fb246d429b86813fbd87b2032fddc2814e22102 Wed Nov 1 17:36:03 2017 -0700
    fixing some minor makefile issues.
• src/hg/cirm/cdw/wrangle/matrixFilter/makefile
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    d250a10d6a82f03f2852ee8e43723632ff360b9a Wed Nov 1 13:33:28 2017 -0700
    Fixing make clean for cdw/
• src/hg/hgCollection/hgCollection.c
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    3155ab7933aae3bf9e111c826290f2605e560b16 Tue Oct 31 15:46:51 2017 -0700
    fixes from code review #20441
• src/hg/htdocs/FAQ/FAQreleases.html
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    834be433496b216c7afacca3032bc78936c2fb5e Thu Nov 2 09:32:04 2017 -0700
    Static docs and announcements for danRer11 release, refs #19459
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    19750d78ffc25bac333e50c3efc3c1850db79938 Wed Nov 1 17:23:52 2017 -0700
    Adding criGriChoV1 credits, refs #19228
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    834be433496b216c7afacca3032bc78936c2fb5e Thu Nov 2 09:32:04 2017 -0700
    Static docs and announcements for danRer11 release, refs #19459
  • lines changed 1, context: html, text, full: html, text
    98921d613964fa58f7e4d96c8377f339dd323aa8 Thu Nov 2 15:09:57 2017 -0700
    Minor edits to static docs for criGriChoV1 staged release, refs #19228
• src/hg/htdocs/goldenPath/newsarch.html
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    f506da5e2427a0638dd18128f5991126bf65041f Wed Nov 1 16:55:14 2017 -0700
    Staging news release for criGriChoV1, refs #19228
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    834be433496b216c7afacca3032bc78936c2fb5e Thu Nov 2 09:32:04 2017 -0700
    Static docs and announcements for danRer11 release, refs #19459
  • lines changed 1, context: html, text, full: html, text
    98921d613964fa58f7e4d96c8377f339dd323aa8 Thu Nov 2 15:09:57 2017 -0700
    Minor edits to static docs for criGriChoV1 staged release, refs #19228
• src/hg/htdocs/images/phylo/hg38_30way.png
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    b100844ac8b7327846d5fb5729c1cc7c0537c810 Thu Nov 2 10:21:35 2017 -0700
    phylo diagram for hg38 30-way with 27 primates refs #20216
• src/hg/htdocs/indexNews.html
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    834be433496b216c7afacca3032bc78936c2fb5e Thu Nov 2 09:32:04 2017 -0700
    Static docs and announcements for danRer11 release, refs #19459
• src/hg/js/autocomplete.js
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    7134b10231edfae04fc73a035dfe9710102d1ba1 Tue Oct 31 10:52:03 2017 -0700
    nit: use !== not != to avoid JS type coercion
• src/hg/js/hgCollection.js
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    3155ab7933aae3bf9e111c826290f2605e560b16 Tue Oct 31 15:46:51 2017 -0700
    fixes from code review #20441
• src/hg/js/jquery.watermarkinput.js
  • lines changed 2, context: html, text, full: html, text
    6ff8ed264eb9c9679749cab9722e23f39a88c5ac Tue Oct 31 11:42:12 2017 -0700
    Don't insert watermark if the input is in focus, i.e. the user is already trying to type something there. refs #20426
• src/hg/lib/cart.c
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    4aa211ce6d56df70ecd7f54a08a1dcab7ee539a3 Thu Nov 2 12:06:22 2017 -0700
    Add database to page title (appears in tab).
• src/hg/lib/jksql.c
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    5481476932dcbcff3c36b1b77633f699cb0d7a85 Mon Oct 30 13:21:53 2017 -0700
    Code review feedback.
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 93, context: html, text, full: html, text
    442a79795fc882e76b13d9742294a8e444f0a52a Tue Oct 31 11:34:19 2017 -0700
    catching up with loading recip best and syntenic net chainNet tracks refs #20216
• src/hg/makeDb/doc/hg38/multiz30way.txt
  • lines changed 1947, context: html, text, full: html, text
    8f9caed5af1a271e07fd7e103a8e4c09391947d6 Fri Nov 3 11:20:07 2017 -0700
    working on 4d phylo tree generation refs #20216
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    7215c43bdfbdc83776a93ccb82c3b47456ab1381 Wed Nov 1 09:38:52 2017 -0700
    Adding danRer11 to hgwbeta updates
• src/hg/makeDb/genbank/etc/rr.dbs
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    71fdc11dc0ee37e9d5fbdbab978383152f48a588 Wed Nov 1 13:55:38 2017 -0700
    Turning genbank updates on for danRer11 on the rr, refs #19459
• src/hg/makeDb/hgFindSpec/hgFindSpec.c
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    105f7e89a0d83816b557eb3015a7d1360fe41db7 Wed Nov 1 11:31:22 2017 -0700
    we don't check for table presence for bigBed searchType because bigBed tracks may not have a table
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    a1332cc6646a330ddc31eaefd0ff773a8a37b45c Thu Nov 2 10:52:47 2017 -0700
    correct case on primate titles refs #20440
• src/hg/makeDb/trackDb/human/hg38/bismap.html
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    7a5a1bc7f5c6dde9c33608b168f59c5e7c86024a Thu Nov 2 11:21:35 2017 -0700
    Removing the title tag in the bismap and umap track description page, refs #19154
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    435fb9f7f51427fff5b9a4a8678da8d36a1a62f2 Fri Nov 3 15:59:18 2017 -0700
    Making each line less than 100 characters long, refs #19154
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 529, context: html, text, full: html, text
    9e204233faaca3e0b0c0b61ed0fb8864c17ee434 Thu Nov 2 10:54:56 2017 -0700
    adding 30-way trackDb refs #20216
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 35, context: html, text, full: html, text
    1ceeb27d91a0bb273b350c58e3b08fa6fe36b167 Mon Oct 30 14:19:57 2017 -0700
    Removing html lines now that the track names are the same as the HTML names and empty lines, refs #19154
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    d70238e645300cf185298f6d885678cfcf2b7561 Fri Nov 3 14:28:11 2017 -0700
    Creating a super track with a bismap and umap composite tracks. Within these composite tracks, I create two views: Single-read (all bigBeds) and Multi-read (all bigWigs), refs #19154
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    676a2e173bcbd9fd7e713ba6f6a4a6c9f04265cf Fri Nov 3 15:07:31 2017 -0700
    Grouping the negative strand tracks and positive strand tracks together in the bismap composite, refs #19154
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
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    9e204233faaca3e0b0c0b61ed0fb8864c17ee434 Thu Nov 2 10:54:56 2017 -0700
    adding 30-way trackDb refs #20216
• src/hg/makeDb/trackDb/human/hg38/trackDb.4way.ra
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    40efc61aa54e97424fa4f21f87f39c10caf8ca53 Mon Oct 30 14:48:12 2017 -0700
    default off no redmine
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    9e204233faaca3e0b0c0b61ed0fb8864c17ee434 Thu Nov 2 10:54:56 2017 -0700
    adding 30-way trackDb refs #20216
• src/hg/makeDb/trackDb/human/hg38/umap.html
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    7a5a1bc7f5c6dde9c33608b168f59c5e7c86024a Thu Nov 2 11:21:35 2017 -0700
    Removing the title tag in the bismap and umap track description page, refs #19154
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    435fb9f7f51427fff5b9a4a8678da8d36a1a62f2 Fri Nov 3 15:59:18 2017 -0700
    Making each line less than 100 characters long, refs #19154
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    f6da34d674a2e44506e63eb5c0f2fc3b7bc5c833 Wed Nov 1 11:26:57 2017 -0700
    Turning off wgEncodeRegTfbsClusteredV3 as a default track in hg38, no redmine
• src/hg/makeDb/trackDb/human/lovd.html
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    fe6b78d957e9356656d4b5d8b8c2d17fded18b3d Tue Oct 31 11:01:43 2017 -0700
    updating LOVD to include variant effect, refs #15525
• src/hg/makeDb/trackDb/human/trackDb.ra
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    71edd894df6ba44f37637940c7d9b891df607b1b Wed Nov 1 14:34:56 2017 -0700
    Adding an alpha release tag so cosmic searching is not broken on beta and the rr, refs #20430
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    cb2ad13e0e81966bf2bdb4f26ffba0656178b822 Tue Oct 31 15:20:04 2017 -0700
    Adding danRer11 to mm10 vertebrate composite chain track, refs #19459
• src/hg/makeDb/trackDb/refSeqComposite.html
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    4166792b097b510fbaea9a841e8e5c682dabeeff Thu Nov 2 16:21:59 2017 -0700
    Adding target=_blank to links so they open in a new tab, refs #18997
• src/hg/makeDb/trackDb/snp138.shared.html
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    929416c233ad25872e8847072735d5e4033dfc4a Mon Oct 30 09:32:19 2017 -0700
    Fixing broken links found by the broken link report for galGal4, no Redmine
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
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    82935abba4a62221acfa13016876373f246f6990 Thu Nov 2 08:43:25 2017 -0700
    Fixing broken links found by the broken link report for taeGut1, no Redmine
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.chainNet.ra
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    65c4bb6e7869b71a5c83a67184d0e6d156d1994d Tue Oct 31 13:30:40 2017 -0700
    Adding overrides for zebrafish chain net scores, refs #19459
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    65c4bb6e7869b71a5c83a67184d0e6d156d1994d Tue Oct 31 13:30:40 2017 -0700
    Adding overrides for zebrafish chain net scores, refs #19459
• src/hg/oneShot/freen/freen.c
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    018ef2c233c992fbbc573da09f9d7a01799828ad Tue Jul 18 16:45:54 2017 -0700
    Testing jsonWriteDouble();
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    de453283f2c66364b952d5e1745652fb37027008 Mon Sep 4 12:04:57 2017 -0700
    Testing some stuff for tagStorm array support.
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    ec4cc6c85b75e159916f9051de61e602c3cfc575 Tue Sep 5 12:33:28 2017 -0700
    Freen tests a function that is a little tricky used in building up tagStorm schemas involving arrays.
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    4929a9a5c8d7170a976fb2189f6dbee664be7790 Tue Sep 5 16:04:39 2017 -0700
    Testing some of the tag storm array processing stuff for tagStormCheck
• src/hg/utils/otto/lovd/download.sh
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    fe6b78d957e9356656d4b5d8b8c2d17fded18b3d Tue Oct 31 11:01:43 2017 -0700
    updating LOVD to include variant effect, refs #15525
• src/hg/utils/transMapPslToGenePred/tests/expected/cds2InsertTest.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/expected/fill30Test.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/input/chimp.mapped.psl
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/tests/input/chimp.src.gp
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    7c174ad59b22b2628e55dea4cd641e714c7d7d0a Wed Nov 1 16:59:09 2017 -0700
    fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly
• src/inc/tagSchema.h
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    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
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    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/inc/tagToSql.h
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    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
• src/lib/jsonWrite.c
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    165743602ab381693f1f340dd7c3693e6f662343 Tue Jul 18 16:46:34 2017 -0700
    Changing jsonWriteDouble printf format from %lf to %g for jsonWriteDouble.
• src/lib/tagSchema.c
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    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
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    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/lib/tagToJson.c
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    b16f8d69be2fe49227f2a1d72214228763bc53b6 Tue Jul 18 16:48:16 2017 -0700
    Making ttjMakeSubObj() handle null and empty prefix parameters.
• src/lib/tagToSql.c
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    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
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    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tabFile/tabQuery/tabQuery.c
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    857a84306ccc2fc4f6147edd822d1153dba507da Mon Sep 4 12:08:25 2017 -0700
    Adding another verbose(2) level for debugging.
• src/tagStorm/tagSchemaToJson/tagSchemaToJson.c
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    f959d4aeea0c00a3116be9a62648a0d70a775fb8 Wed Sep 6 11:45:21 2017 -0700
    Adding shortcuts option
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    f42040eda7ad73e000510a0c3750f42b55a60c83 Wed Sep 6 12:24:54 2017 -0700
    Improving shortcut handling.
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    f3fb971b8bb28090c5d0f8a72f4063dde9e67280 Thu Sep 7 11:02:00 2017 -0700
    Making descriptions work better with subobjects, and arrays of subobjects work better.
• src/tagStorm/tagSchemaToJson/test.schema
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    aff5997f4c5ffa408b6be5de0a94a2bee8ccb2d6 Wed Sep 6 17:22:00 2017 -0700
    Updating test.schema to reflect HCA V3 more closely.
• src/tagStorm/tagStormCheck/tagStormCheck.c
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    4e1c6cfbdfa69c61a2a02be485297e786e0a0c9c Mon Sep 4 14:10:31 2017 -0700
    Adapting tagStormCheck for internal arrays.
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    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tagStorm/tagStormCheck/test.schema
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    d931a2f62577733ea2db68a37d8e31bc2160edf6 Tue Sep 5 16:03:30 2017 -0700
    Updating test set for new functionality.
• src/tagStorm/tagStormCheck/test.tags
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    d931a2f62577733ea2db68a37d8e31bc2160edf6 Tue Sep 5 16:03:30 2017 -0700
    Updating test set for new functionality.
• src/tagStorm/tagStormInfo/tagStormInfo.c
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    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
  • lines changed 1, context: html, text, full: html, text
    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tagStorm/tagStormInfo/tests/expected.counts
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    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.out
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    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.schema
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    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.vals
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    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/test.in
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    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
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    6b6763ede646c2be8b8929c2a8700a4a68565cf1 Mon Jul 10 09:58:08 2017 -0700
    Creating a json output option.
• src/utils/qa/weeklybld/buildEnv.csh
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    5ecde213875b916cdf763baf0cd17552c5520cfc Mon Nov 6 09:53:44 2017 -0800
    v358 preview1 refs #20479

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