All File Changes

v342_base to v343_preview (2016-12-05 to 2016-12-19) v343

• LICENSE
  • lines changed 29, context: html, text, full: html, text
    10bfc8ee7b8aab034feed51fba8eeaa8d4b2e899 Thu Dec 8 15:02:41 2016 -0800
    adding top level LICENSE file refs #13978
  • lines changed 1, context: html, text, full: html, text
    3337edf8a4b51ed5171aad467e664341a2e0f833 Thu Dec 8 15:07:55 2016 -0800
    fixing typo in dir in LICENSE file refs #13978
• README
  • lines changed 8, context: html, text, full: html, text
    381f721e9b949828dce20fe816447a434dee155b Thu Dec 8 14:57:07 2016 -0800
    adding info about LICENSE file refs #13978
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    93924ceb49da8ca93c1f57922fdb99f016d5305c Sun Dec 18 01:11:48 2016 -0800
    Installing updated hg.conf files from UCSC servers
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 15, context: html, text, full: html, text
    b84bb83ec3c69ff8dfe3b90f5b3385796d914de8 Thu Dec 8 08:58:19 2016 -0800
    qaGbTracks now uses the runBits.csh script to calculate coverage as well as find overlaps with undbridged gaps. All results are still written to the log file. Coverage amounts are extracted from runBits output and written to summary file as before. refs #18054
• python/lib/ucscGb/qa/tables/pslQa.py
  • lines changed 43, context: html, text, full: html, text
    2250228e5a62ab129d2c0a671c907c9b204b2543 Thu Dec 8 08:55:19 2016 -0800
    Changing the way pslCheck is run by qaGbTracks based on markd recommendation that it run a more comprehensive check. Now qaGbTracks will run this comprehensive check for those psl tracks that use the baseColorUseSequence setting and have this set to table or extFile. For all others the standard pslCheck that we have been using is run. refs #17753
• src/LICENSE
  • lines changed 29, context: html, text, full: html, text
    0ad422da3deea55bcfefa713d0d2921eeb6fb6c2 Thu Dec 8 15:13:51 2016 -0800
    copy of top-level LICENSE for this dir, refs #13978
• src/README
  • lines changed 15, context: html, text, full: html, text
    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
  • lines changed 1, context: html, text, full: html, text
    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
  • lines changed 15, context: html, text, full: html, text
    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/browserbox/README.txt
  • lines changed 15, context: html, text, full: html, text
    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
  • lines changed 1, context: html, text, full: html, text
    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
  • lines changed 13, context: html, text, full: html, text
    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/hg/README
  • lines changed 15, context: html, text, full: html, text
    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
  • lines changed 1, context: html, text, full: html, text
    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
  • lines changed 12, context: html, text, full: html, text
    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/hg/cartDump/cartDump.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
  • lines changed 16, context: html, text, full: html, text
    b8ad24053540b0671424d324770e314a408b4bac Wed Dec 7 12:31:35 2016 -0800
    Adding -id option.
• src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
  • lines changed 1, context: html, text, full: html, text
    ea3f30667f13b3dd9adda8db59d97fb0204797f4 Wed Dec 14 10:20:16 2016 -0800
    Removing a useless function call spotted by Angie, refs #18487
• src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
  • lines changed 21, context: html, text, full: html, text
    ec0f405c412524b4db6ca1363285b7195f571261 Wed Dec 7 12:32:06 2016 -0800
    Adding -id option.
  • lines changed 1, context: html, text, full: html, text
    7953d348a47ca2566d13b9decfe3cf510af971b1 Mon Dec 12 15:14:47 2016 -0800
    oops, vf->id should have been vf->fileId!
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 43, context: html, text, full: html, text
    171885f8c06eea0da831433ddafc194712798449 Wed Dec 7 12:28:30 2016 -0800
    Making meta.txt and manifest.txt get their file permissions and groups set.
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 170, context: html, text, full: html, text
    68db9a72ddef3feeebab3128efb1b3b3818ea76e Mon Dec 5 11:28:40 2016 -0800
    Pulling out static javascript into cdwSummaryJs.js, moving the graphs around and updating the R function names, had to switch a 9 to a 4 to get it to work on the test case, Max has suggested this should be reverted for other cases. Refs #16300
  • lines changed 5, context: html, text, full: html, text
    c94ff9d1a1b45a433ab06d67531e7b005ef83566 Mon Dec 5 14:01:24 2016 -0800
    Putting the fix Max pushed in, back in, oops. Refs #16300
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 5, context: html, text, full: html, text
    080f3b1ad5610d709b20dad37ada05da41d23700 Tue Dec 6 17:57:52 2016 -0800
    Removing an unused parameter, and adding datasetId to label on dataset page list.
  • lines changed 96, context: html, text, full: html, text
    ea3f30667f13b3dd9adda8db59d97fb0204797f4 Wed Dec 14 10:20:16 2016 -0800
    Removing a useless function call spotted by Angie, refs #18487
  • lines changed 1, context: html, text, full: html, text
    850f2f7ad54c98fd3cba9d966dc353cff00f343c Wed Dec 14 15:34:00 2016 -0800
    Bumping version #refs 17870
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 6, context: html, text, full: html, text
    a7cca5a01f084ce82e1bc73009fde0c5601d6814 Wed Dec 7 12:30:57 2016 -0800
    Decribing recent changes.
  • lines changed 2, context: html, text, full: html, text
    850f2f7ad54c98fd3cba9d966dc353cff00f343c Wed Dec 14 15:34:00 2016 -0800
    Bumping version #refs 17870
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 15, context: html, text, full: html, text
    aee231ceb577134cf8df8af1a5385be3629cd248 Wed Dec 14 18:54:27 2016 -0800
    Adding subcellular_localization tag and controlled vocab.
• src/hg/cirm/cdw/oneShot/cdwFixFrazer3/cdwFixFrazer3.c
  • lines changed 127, context: html, text, full: html, text
    0cf014f5ff559c705ef8dd96cca5e637e02ef305 Wed Dec 14 18:50:40 2016 -0800
    A program to massage Frazer metadata tree by moving solo meta stanzas up and adding a sample_label tag.
• src/hg/cirm/cdw/oneShot/cdwFixFrazer3/makefile
  • lines changed 3, context: html, text, full: html, text
    0cf014f5ff559c705ef8dd96cca5e637e02ef305 Wed Dec 14 18:50:40 2016 -0800
    A program to massage Frazer metadata tree by moving solo meta stanzas up and adding a sample_label tag.
• src/hg/cirm/cdw/oneShot/cdwFixFrazerControls2/cdwFixFrazerControls2.c
  • lines changed 106, context: html, text, full: html, text
    009bf8a5c3cd3a699fdcd236119ad69e1924dd8e Wed Dec 14 12:16:07 2016 -0800
    A little program to fix some issues with the ChIP-seq controls and assays tags in the second Frazer lab submission.
• src/hg/cirm/cdw/oneShot/cdwFixFrazerControls2/makefile
  • lines changed 3, context: html, text, full: html, text
    009bf8a5c3cd3a699fdcd236119ad69e1924dd8e Wed Dec 14 12:16:07 2016 -0800
    A little program to fix some issues with the ChIP-seq controls and assays tags in the second Frazer lab submission.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c
  • lines changed 12, context: html, text, full: html, text
    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
• src/hg/encode3/importEncode2/encodeCvToDb/encodeCvToDb.c
  • lines changed 10, context: html, text, full: html, text
    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
  • lines changed 23, context: html, text, full: html, text
    be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800
    some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
  • lines changed 1, context: html, text, full: html, text
    09a44b13b888eb07a70a0baef7717dac5a9caed4 Tue Dec 13 11:02:22 2016 -0800
    some more changes per Hiram to get the trash cleaner to like BLAT result custom tracks.
  • lines changed 3, context: html, text, full: html, text
    9b2bccae0dced3d04c3edb7a263437407586e1ff Tue Dec 13 11:28:53 2016 -0800
    more changes for Hiram
• src/hg/hgConvert/hgConvert.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgGenome/hgGenome.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgGetAnn/hgGetAnn.c
  • lines changed 30, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
  • lines changed 30, context: html, text, full: html, text
    4e6bf605e30e69005f567883b9423c50b9dab1dd Wed Dec 14 16:22:03 2016 -0800
    backed out mistaked commit
• src/hg/hgGetAnn/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
  • lines changed 8, context: html, text, full: html, text
    4e6bf605e30e69005f567883b9423c50b9dab1dd Wed Dec 14 16:22:03 2016 -0800
    backed out mistaked commit
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
  • lines changed 79, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
• src/hg/hgLogin/hgLogin.h
  • lines changed 1, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
  • lines changed 54, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    752a606718a481777bc8d503fc2a69a64a754063 Wed Dec 7 14:44:01 2016 -0800
    increasing maximum extra bigBed fields number to 1024 fields. One of my bigBed files mysteriously failed. no redmine.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    4ef05a371988c817b2a22fc22d3bcc0f18cb9ba5 Mon Dec 5 14:01:51 2016 -0800
    Small edit with hgTracks.c done when sitting next to Max refs #18367
  • lines changed 2, context: html, text, full: html, text
    5941524ea9c4f355fa2710761b0149b3219bc009 Tue Dec 13 14:24:15 2016 -0800
    make track hub tracks respond to URL visibility settings even if they don't have the hub_#_ prefix #18544
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    0291671251a9d06afd8d1fe62c67c6fd3eb58a94 Fri Dec 9 16:54:41 2016 -0800
    Fix missing gene labels bug #18528. pgSnp tracks in full mode were leaving the drawing machine in a non-default state
• src/hg/hgTracks/transMapTracks.c
  • lines changed 5, context: html, text, full: html, text
    6e41e8a48a74cb10e8d1455a51169f1ea8e2662a Thu Dec 15 20:05:29 2016 -0800
    updated transmap trackDb in prep for new bigTransMap
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/hgc/gencodeClick.c
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    cf56097b1e6a5f61ba03b882cdf885a913c08c48 Wed Dec 14 11:29:32 2016 -0800
    remove status field from gencode hgc display; this is being dropped by gencode and ensembl
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
  • lines changed 1, context: html, text, full: html, text
    6e41e8a48a74cb10e8d1455a51169f1ea8e2662a Thu Dec 15 20:05:29 2016 -0800
    updated transmap trackDb in prep for new bigTransMap
• src/hg/htdocs/FAQ/FAQcustom.html
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    78ff49e62c6d858a1c07cc2636c32315f7b91ed8 Tue Dec 13 11:03:06 2016 -0800
    changed wording on FAQcustom per refs #18481
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    165c9a8ac99f7ae113cb4071f3995af8c6bcc593 Mon Dec 5 13:29:29 2016 -0800
    Minor typo on downloads FAQ page, no refs
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    ae27469e7ad72496effe3303e8f278c9acec9f52 Thu Dec 15 12:57:18 2016 -0800
    added data access faq, refs #17960
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    1cd565728c591cc740ac91e3731573531673dde1 Thu Dec 15 13:03:12 2016 -0800
    fixed a few formatting issues
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    c7e7ce2475786bfc9d477c2e546502c2042400ce Thu Dec 15 13:06:12 2016 -0800
    added missing br tag
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    79e17e97e27e47a524742dfbf92facb9fb4e528a Thu Dec 15 13:46:28 2016 -0800
    made changes to link
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    b1f4e52212483f56ce1adab472aec4ced33f93e5 Thu Dec 15 13:50:48 2016 -0800
    removed extra periods
• src/hg/htdocs/FAQ/FAQreleases.html
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    f5f2768d876513bb515b14b81a3908e73ccf7f06 Mon Dec 12 09:39:47 2016 -0800
    updating FAQreleases page per refs# 18532
• src/hg/htdocs/goldenPath/credits.html
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    697c34dc6d79c1d3ab833d7dbefb9fea4e5303db Thu Dec 15 10:42:25 2016 -0800
    Fixing green monkey credits as per Steve's ML suggestion
• src/hg/htdocs/goldenPath/help/bigMaf.html
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    3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800
    more changes to support the new big* formats
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 1, context: html, text, full: html, text
    3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800
    more changes to support the new big* formats
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 9, context: html, text, full: html, text
    a22173c4332fe37e8cf9a901122138d2e2330488 Thu Dec 15 14:12:37 2016 -0800
    Small updates to track line 'track_primary_table_name' documentation. Linking to Bobs video on finding this table name, refs #7380
  • lines changed 16, context: html, text, full: html, text
    9573b42e19b9ae4aca83585428135110af07aea2 Fri Dec 16 10:25:01 2016 -0800
    Edited customTrackText to include track hubs per refs #18535
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
  • lines changed 6, context: html, text, full: html, text
    bad1835abf867ee3f3e9821d68c4bdd5dc0c6b96 Tue Dec 13 16:57:32 2016 -0800
    Staging commits to bump the trackDbHub.html to v2
• src/hg/htdocs/goldenPath/help/trackDb/makefile
  • lines changed 3, context: html, text, full: html, text
    bad1835abf867ee3f3e9821d68c4bdd5dc0c6b96 Tue Dec 13 16:57:32 2016 -0800
    Staging commits to bump the trackDbHub.html to v2
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 1, context: html, text, full: html, text
    bad1835abf867ee3f3e9821d68c4bdd5dc0c6b96 Tue Dec 13 16:57:32 2016 -0800
    Staging commits to bump the trackDbHub.html to v2
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 234, context: html, text, full: html, text
    eb855900d2bd4af4bc981eb2b299b0edf7d31566 Wed Dec 7 15:06:56 2016 -0800
    update trackDbHub doc to know about bigGenePred, bigPsl, bigChain, and bigMaf #17741
  • lines changed 25, context: html, text, full: html, text
    3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800
    more changes to support the new big* formats
  • lines changed 259, context: html, text, full: html, text
    e0b62e855333978ca76854071d471ffa1d5fb245 Tue Dec 13 16:23:21 2016 -0800
    Bumping trackDbHub.v1.html back to before additions of bigPsl,bigMaf,bigChain,bigGenePred,refUrl to Max commit where bigDataIndex added (git checkout 0c1d13ef4e32 trackDbHub.v1.html) to set stage for a trackDbHub.v2.html
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 934, context: html, text, full: html, text
    bad1835abf867ee3f3e9821d68c4bdd5dc0c6b96 Tue Dec 13 16:57:32 2016 -0800
    Staging commits to bump the trackDbHub.html to v2
  • lines changed 14, context: html, text, full: html, text
    e5afe1edc175c6769db72180a90f316ea64d22c6 Fri Dec 16 13:34:39 2016 -0800
    Staging the v2 for the TrackDbHub Doc, where any status in v1 that was new -is-now-> full in v2. Also setting some introduced required settings to full as they are not truly required refs #17741
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 73, context: html, text, full: html, text
    eb855900d2bd4af4bc981eb2b299b0edf7d31566 Wed Dec 7 15:06:56 2016 -0800
    update trackDbHub doc to know about bigGenePred, bigPsl, bigChain, and bigMaf #17741
  • lines changed 1, context: html, text, full: html, text
    e6acda1ce5512cffb02839f7fd690391d980bdff Thu Dec 8 07:13:02 2016 -0800
    Minor grammar correction to baseColorUseSequence section, no redmine
  • lines changed 21, context: html, text, full: html, text
    3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800
    more changes to support the new big* formats
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 17, context: html, text, full: html, text
    a9e7108a5d9188ead684415c5481303714d7c9f1 Tue Dec 6 15:47:32 2016 -0800
    Adding 1-start coordinate info for wiggle files, refs #17963
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 17, context: html, text, full: html, text
    b51f4f8b6833dd3ee0ec6e98bad07d5eceb6f769 Fri Dec 9 15:17:02 2016 -0800
    adding announcement of new video. added new vid to training and training/vids pages. made links on training page go directly to YouTube
  • lines changed 8, context: html, text, full: html, text
    92c42017dc716168377378aeec4036a97d07cdf4 Mon Dec 12 09:19:24 2016 -0800
    rewording announcement of new viedo
  • lines changed 37, context: html, text, full: html, text
    884c5fd87a8659a0928640c99a4ba257e67bb5df Tue Dec 13 16:54:24 2016 -0800
    Adding GTEx announcements refs #17369
  • lines changed 0, context: html, text, full: html, text
    ef6fdf3973ac02bb54def8d0b69f5a324859ecf8 Wed Dec 14 17:05:11 2016 -0800
    Fixing date target link for GTEx announcement refs #17369
  • lines changed 2, context: html, text, full: html, text
    a6ed58c32d630fcc04c5309c1804eea83b88fd4e Wed Dec 14 17:41:17 2016 -0800
    Adding lost hr tag, no rm
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 4, context: html, text, full: html, text
    8e164fdef0d2ba0cf0ccdad06f00c25ca01d06fa Tue Dec 6 15:46:22 2016 -0800
    Removing et al to show all authors in 2017 NAR, no RM
• src/hg/htdocs/images/gtexBodyMap.svg
  • lines changed 9, context: html, text, full: html, text
    64a4f61177497c19ccd120244cb3eeee79ba5e1e Mon Dec 5 10:30:58 2016 -0800
    Remove bones -- they are not GTEx tissues, and were grouped with Muscle (artist likely thought 'Muscle-Skeletal' included skeleton) and caused muscle to highlight on mouseover. Response to QA note #45. refs #17369
• src/hg/htdocs/images/training/vidTitle10.jpg
  • lines changed 0, context: html, text, full: html, text
    38cbf9147d045ba909b0136d1a7c536494020d9d Fri Dec 9 14:03:16 2016 -0800
    adding new video and rearranging vid index page to two-column format. adding thumbnail for new vid
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    b51f4f8b6833dd3ee0ec6e98bad07d5eceb6f769 Fri Dec 9 15:17:02 2016 -0800
    adding announcement of new video. added new vid to training and training/vids pages. made links on training page go directly to YouTube
  • lines changed 11, context: html, text, full: html, text
    884c5fd87a8659a0928640c99a4ba257e67bb5df Tue Dec 13 16:54:24 2016 -0800
    Adding GTEx announcements refs #17369
  • lines changed 1, context: html, text, full: html, text
    ef6fdf3973ac02bb54def8d0b69f5a324859ecf8 Wed Dec 14 17:05:11 2016 -0800
    Fixing date target link for GTEx announcement refs #17369
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    59aac91f981f2934cee8937aa5e65379bf0976b6 Mon Dec 5 13:28:03 2016 -0800
    Add boostrap css file for Body Map. refs #17369
  • lines changed 1, context: html, text, full: html, text
    d1df06ffe92964fa00103bf3efdd01c8fafceec9 Mon Dec 5 13:33:55 2016 -0800
    Add boostrap css file for Body Map. refs #17369
• src/hg/htdocs/training/index.html
  • lines changed 28, context: html, text, full: html, text
    b51f4f8b6833dd3ee0ec6e98bad07d5eceb6f769 Fri Dec 9 15:17:02 2016 -0800
    adding announcement of new video. added new vid to training and training/vids pages. made links on training page go directly to YouTube
  • lines changed 2, context: html, text, full: html, text
    4b1f601439d2392446afa716201d64ba834b3443 Fri Dec 9 16:31:15 2016 -0800
    fixing broken link to youtube
• src/hg/htdocs/training/vids/index.html
  • lines changed 221, context: html, text, full: html, text
    38cbf9147d045ba909b0136d1a7c536494020d9d Fri Dec 9 14:03:16 2016 -0800
    adding new video and rearranging vid index page to two-column format. adding thumbnail for new vid
  • lines changed 16, context: html, text, full: html, text
    b51f4f8b6833dd3ee0ec6e98bad07d5eceb6f769 Fri Dec 9 15:17:02 2016 -0800
    adding announcement of new video. added new vid to training and training/vids pages. made links on training page go directly to YouTube
• src/hg/inc/autoUpgrade.h
  • lines changed 2, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
• src/hg/inc/gpFx.h
  • lines changed 3, context: html, text, full: html, text
    40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
    If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    c9cff716524000d6b44e520bbfe0026685fdbbb0 Thu Dec 15 14:35:38 2016 -0800
    making the gbic mirrors identify itself to phoneHome with a distinct string, refs #14399
• src/hg/inc/trashDir.h
  • lines changed 3, context: html, text, full: html, text
    be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800
    some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
• src/hg/inc/wikiLink.h
  • lines changed 19, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
  • lines changed 2, context: html, text, full: html, text
    fba55c7cdca98634dd406e5a0b58ce09f98593d3 Mon Dec 12 16:46:03 2016 -0800
    Having absolutely no new security is a bummer, so for now, by default, check incoming cookie vs. gbMembers.idx, but add a setting login.acceptAnyId that we can enable in case there is a problem with checking idx. Also add a new setting login.acceptIdx that can be disabled (along with login.acceptAnyId) in order to absolutely require a login.cookieSalt match for better security. refs #17327
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    b4b68f5f9cd0ce68dd8c94c4fc8a1ca0dbbcfe10 Mon Dec 12 17:18:01 2016 -0800
    changing autocomplete box text for DNA sequence quick jump, refs #16950
  • lines changed 2, context: html, text, full: html, text
    6d01ac5f9d5e585990537e6146beb591a9170436 Tue Dec 13 14:35:56 2016 -0800
    backing out the documentation of the quick BLAT on the position box again. May lead to more trouble than it's worth for now, refs #16950
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    d86e271296446bd244d4165ca60e2368a079998c Thu Dec 8 09:25:18 2016 -0800
    fix focus problem in hgTrackUi popup for custom tracks #18500
  • lines changed 10, context: html, text, full: html, text
    6637c305d27006f311f212614841153ce4aadc98 Mon Dec 12 17:15:27 2016 -0800
    allow a DNA sequence in the position box, refs# 16950
  • lines changed 7, context: html, text, full: html, text
    6d01ac5f9d5e585990537e6146beb591a9170436 Tue Dec 13 14:35:56 2016 -0800
    backing out the documentation of the quick BLAT on the position box again. May lead to more trouble than it's worth for now, refs #16950
• src/hg/lib/.gitignore
  • lines changed 1, context: html, text, full: html, text
    4feb01b9f78ef5fb72b83e9b86522dacaa47af08 Tue Nov 29 12:16:32 2016 -0800
    Ignore new automatically generated .h file.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 48, context: html, text, full: html, text
    40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
    If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
• src/hg/lib/annoStreamDb.c
  • lines changed 11, context: html, text, full: html, text
    3668909bc45cf722a9b69e2dafbf5e161a6a87a6 Wed Dec 14 16:36:45 2016 -0800
    annoStreamDb should not be hardcoded to find all.joiner in the current directory. Now, if env var ALL_JOINER_FILE exists, it will be used instead. vai.pl can now look for all.joiner in hgVai's parent directory (.../cgi-bin) and use ALL_JOINER_FILE if there is no ./all.joiner. refs #12216 note-28
• src/hg/lib/bigMaf.as
  • lines changed 8, context: html, text, full: html, text
    eb855900d2bd4af4bc981eb2b299b0edf7d31566 Wed Dec 7 15:06:56 2016 -0800
    update trackDbHub doc to know about bigGenePred, bigPsl, bigChain, and bigMaf #17741
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
  • lines changed 12, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
  • lines changed 5, context: html, text, full: html, text
    1363e178b292e47349dfbc7b5158ac5c1ceb0e2a Wed Dec 14 14:13:46 2016 -0800
    Instead of requiring that loginValidateCookies() be called before wikiLinkUserName is called, just call it if necessary in wikiLinkUserName. Avoids clashes with other squirrelly paths to wikiLinkUserName. refs #17327, #12216#note-28
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    4cc51edbbb70a41e84029fc8d5334c3d3d9d2ef2 Tue Dec 6 11:39:42 2016 -0800
    An unintended side effect of adding plain VCF recognition to customTrackTypeFromBigFile was that customTrackIsBigData started returning true for plain VCF, which tripped up customPp and customFactory code. Fix by excluding plain VCF from customTrackIsBigData. fixes #18503
• src/hg/lib/gpFx.c
  • lines changed 1, context: html, text, full: html, text
    40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
    If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
• src/hg/lib/hdb.c
  • lines changed 10, context: html, text, full: html, text
    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
  • lines changed 2, context: html, text, full: html, text
    6d01ac5f9d5e585990537e6146beb591a9170436 Tue Dec 13 14:35:56 2016 -0800
    backing out the documentation of the quick BLAT on the position box again. May lead to more trouble than it's worth for now, refs #16950
  • lines changed 3, context: html, text, full: html, text
    a803fd1b4604a2a90f26f92a2eecd77677c7e7f2 Tue Dec 13 14:55:21 2016 -0800
    fixing a buffer overflow that appears when one is pasting a long text into the positionbox. This has come up before but I cannot find the redmine now.
  • lines changed 6, context: html, text, full: html, text
    c9cff716524000d6b44e520bbfe0026685fdbbb0 Thu Dec 15 14:35:38 2016 -0800
    making the gbic mirrors identify itself to phoneHome with a distinct string, refs #14399
• src/hg/lib/hubConnect.c
  • lines changed 2, context: html, text, full: html, text
    1d7247f0e72ce7c7ee1543bb31e6e71b4f2d771d Fri Dec 9 16:15:13 2016 -0800
    trying to fix an error that is thrown only in newer mysql versions. The fields in hubStatus are defined as not being NULL but have NULL as their default value. In addition, in the INSERT statement in hubConnect.c, they are not specified. Newer Mysql versions refuse to set them to NULL if NULL is not allowed. No redmine. This came up on the CIRM server but will come up everywhere in the future.
• src/hg/lib/hui.c
  • lines changed 6, context: html, text, full: html, text
    c85802ccef6bba0d6159c20950a01094e817c56c Thu Dec 15 11:15:23 2016 -0800
    Add env var UDC_CACHEDIR to override hg.conf udc.cacheDir for command-line use of CGI. Add -udcCache option to vai.pl using UDC_CACHEDIR. refs #12216 note-32
• src/hg/lib/trashDir.c
  • lines changed 21, context: html, text, full: html, text
    be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800
    some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
  • lines changed 1, context: html, text, full: html, text
    09a44b13b888eb07a70a0baef7717dac5a9caed4 Tue Dec 13 11:02:22 2016 -0800
    some more changes per Hiram to get the trash cleaner to like BLAT result custom tracks.
  • lines changed 1, context: html, text, full: html, text
    c65d1d60bacfcd3531bee6f3be302b5c30a131b1 Wed Dec 14 11:17:38 2016 -0800
    keep the day of year directory name to 3 digits refs #2811
• src/hg/lib/wikiLink.c
  • lines changed 281, context: html, text, full: html, text
    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
  • lines changed 33, context: html, text, full: html, text
    0c450818052cb799efeab3d7d49c800378bcf3ab Mon Dec 12 13:57:55 2016 -0800
    Without login.cookieSalt, don't even check ID cookie vs. gbMembers.idx because that could vary from system to system. refs #17327
  • lines changed 52, context: html, text, full: html, text
    fba55c7cdca98634dd406e5a0b58ce09f98593d3 Mon Dec 12 16:46:03 2016 -0800
    Having absolutely no new security is a bummer, so for now, by default, check incoming cookie vs. gbMembers.idx, but add a setting login.acceptAnyId that we can enable in case there is a problem with checking idx. Also add a new setting login.acceptIdx that can be disabled (along with login.acceptAnyId) in order to absolutely require a login.cookieSalt match for better security. refs #17327
  • lines changed 1, context: html, text, full: html, text
    1363e178b292e47349dfbc7b5158ac5c1ceb0e2a Wed Dec 14 14:13:46 2016 -0800
    Instead of requiring that loginValidateCookies() be called before wikiLinkUserName is called, just call it if necessary in wikiLinkUserName. Avoids clashes with other squirrelly paths to wikiLinkUserName. refs #17327, #12216#note-28
• src/hg/liftOver/README.txt
  • lines changed 15, context: html, text, full: html, text
    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
  • lines changed 1, context: html, text, full: html, text
    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
  • lines changed 12, context: html, text, full: html, text
    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/hg/makeDb/doc/hg38/hg38Patch9.txt
  • lines changed 918, context: html, text, full: html, text
    512facd3554fb1943a0debdcc424e3af752ef7ce Mon Dec 5 15:00:12 2016 -0800
    running up hg38Patch9 refs #18274
• src/hg/makeDb/doc/mm10.txt
  • lines changed 39, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/doc/mm9.txt
  • lines changed 4, context: html, text, full: html, text
    09a173fa38faa9e18e03adef7cd98e2489e1d191 Thu Dec 15 14:57:15 2016 -0800
    adding mm9, refs #17235
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    53ffc1510b9aae25ada3af08937eaee731e8bd20 Thu Dec 15 15:07:03 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    bd1541312993bbccb160cb805896d35c44230e4d Thu Dec 15 15:07:03 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    16d1fef33888328cafb7364e3db38022ee597caa Thu Dec 15 15:07:04 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    2e37e2d9bebb1fbcd5e9ccae2c22ba6f4b8d9463 Thu Dec 15 15:07:05 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.trackDb.txt
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    9c1b62c1487a7563ff0b02253f71089688229c0c Thu Dec 15 15:07:06 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.trackDb.txt
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    787663b916f5b3f740d3fc1eeca578ccbb7e1b93 Thu Dec 15 15:07:07 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.trackDb.txt
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    9fd446f8fbe4cc86f0b558bc4e2d7f207f30edd6 Thu Dec 15 15:07:08 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt
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    b8e1bc656e5965d2cf04c7efb38f7da9a0fbd63a Thu Dec 15 15:07:09 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt
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    b534a50640fa7c89eccb4c8070e711b033c37c52 Thu Dec 15 15:07:10 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.trackDb.txt
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    c816846b559ff41c484068f54d919e507f72ccc7 Thu Dec 15 15:07:11 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.trackDb.txt
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    f530058c0a7ee043b91cb39586d4f0f55f9b07e1 Thu Dec 15 15:07:13 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt
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    4b787d7053f66e72a53f7039ac9afca234ccf8a6 Thu Dec 15 15:07:15 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.trackDb.txt
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    2b249c5b1893cdb28d4efa0336a51315e0e5f3bf Thu Dec 15 15:07:16 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt
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    a535d0f45a4bb8e4c518d0589aa016fd4ae6cd8a Thu Dec 15 15:07:17 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.trackDb.txt
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    8a852d389dded9e22f2e2c3486d125cd6edf5f02 Thu Dec 15 15:07:17 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.trackDb.txt
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    0986a2c022f2058c1dbb37d9ff7b53f8f736ed31 Thu Dec 15 15:07:18 2016 -0800
    adding cactus.trackDb to the trackDb
• src/hg/makeDb/doc/mouseStrains/makefile
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    14520408afbbb396717415c7ace90fff7a400bde Thu Dec 15 15:22:54 2016 -0800
    single install location for the rnaSeqStar.html and mouseStrains.html descriptions
• src/hg/makeDb/doc/mouseStrains/mouseStrains.html
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    ff63cc15374d62de5c7488ddf0f9a16038931aa4 Thu Dec 15 15:09:29 2016 -0800
    html description for cactus snake track
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/schema/all.joiner
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    dccf1cf20c81862bcdc8337958383e08e7dc2409 Tue Dec 6 11:47:48 2016 -0800
    adding rules for hg38Patch9 refs #18274
• src/hg/makeDb/trackDb/chimp/bacEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/dog/canFam1/bacEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/dog/canFam2/bacEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/drosophila/dm3/bacEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/fosEndPairs.html
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    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/human/chainNetGorGor3.ra
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    7d1d12c78f54d880b0a34e3d9fd6d3fdd3dbef86 Fri Dec 9 11:37:01 2016 -0800
    Adding gorGor3 chain/net tracks into primate group on beta
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 2, context: html, text, full: html, text
    4d300325b7e11e6f2a8c75135cd0aa0a639d9725 Wed Dec 7 09:46:02 2016 -0800
    Adding panTro4 back to hg19
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    7d1d12c78f54d880b0a34e3d9fd6d3fdd3dbef86 Fri Dec 9 11:37:01 2016 -0800
    Adding gorGor3 chain/net tracks into primate group on beta
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 1, context: html, text, full: html, text
    9d36b6e00627698ffd2e4d35b8b2f6ffb0430cd2 Mon Dec 12 09:08:08 2016 -0800
    Removing uneeded 'the' based on CR, refs #18479
• src/hg/makeDb/trackDb/human/hg38/hg38Patch9.html
  • lines changed 521, context: html, text, full: html, text
    ec1e1a8658a50bbaeb99edb3d042833d9745419e Tue Dec 6 11:39:23 2016 -0800
    adding hg38Patch9 definitions refs #18274
• src/hg/makeDb/trackDb/human/hg38/hg38Patch9.ra
  • lines changed 118, context: html, text, full: html, text
    ec1e1a8658a50bbaeb99edb3d042833d9745419e Tue Dec 6 11:39:23 2016 -0800
    adding hg38Patch9 definitions refs #18274
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    ec1e1a8658a50bbaeb99edb3d042833d9745419e Tue Dec 6 11:39:23 2016 -0800
    adding hg38Patch9 definitions refs #18274
• src/hg/makeDb/trackDb/human/hg38Patch9/description.html
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    aac4d652ce81983b8107fc22a8f86a09193d81d9 Tue Dec 6 11:24:44 2016 -0800
    adding hg38Patch9 to the build refs #18274
• src/hg/makeDb/trackDb/human/hg38Patch9/gap.html
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    aac4d652ce81983b8107fc22a8f86a09193d81d9 Tue Dec 6 11:24:44 2016 -0800
    adding hg38Patch9 to the build refs #18274
• src/hg/makeDb/trackDb/human/hg38Patch9/gold.html
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    aac4d652ce81983b8107fc22a8f86a09193d81d9 Tue Dec 6 11:24:44 2016 -0800
    adding hg38Patch9 to the build refs #18274
• src/hg/makeDb/trackDb/human/hg38Patch9/trackDb.ra
  • lines changed 38, context: html, text, full: html, text
    aac4d652ce81983b8107fc22a8f86a09193d81d9 Tue Dec 6 11:24:44 2016 -0800
    adding hg38Patch9 to the build refs #18274
• src/hg/makeDb/trackDb/makefile
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    aac4d652ce81983b8107fc22a8f86a09193d81d9 Tue Dec 6 11:24:44 2016 -0800
    adding hg38Patch9 to the build refs #18274
• src/hg/makeDb/trackDb/marmoset/calJac3/bacEnds.html
  • lines changed 2, context: html, text, full: html, text
    744c31bb741d3e625673da2ee6ed4cd39859bc23 Fri Dec 9 14:14:46 2016 -0800
    Fixing bad url for CHORI no RM
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.html
  • lines changed 321, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
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    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM12.html
  • lines changed 343, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM12.ra
  • lines changed 272, context: html, text, full: html, text
    23470c9be7d5744390cefef23563e3d1109db14a Wed Dec 14 11:13:53 2016 -0800
    load of GENCODE VM12 (not being pushed to RR)
• src/hg/makeDb/trackDb/mouseStrains.html
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    cd9fdf441b73c9497c8d4d80c98c8cd936a9100e Mon Dec 5 10:49:00 2016 -0800
    updated references refs #18440
• src/hg/makeDb/trackDb/spAnnot.html
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    a70e445b2f90b417c5dcc8bc448c895f453f45c9 Thu Dec 8 12:39:54 2016 -0800
    Replacing ascii quote character with html-name ", refs #18451
• src/hg/makeDb/trackDb/spMut.html
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    22e4f21218e37fb63a33d497db246541bb7048c1 Fri Dec 16 09:09:15 2016 -0800
    Adding Data Access section to track description pages. Changing example bigBedToBed command chromosome region to a location that generates output
• src/hg/makeDb/trackDb/spUniprot.html
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    a70e445b2f90b417c5dcc8bc448c895f453f45c9 Thu Dec 8 12:39:54 2016 -0800
    Replacing ascii quote character with html-name ", refs #18451
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    22e4f21218e37fb63a33d497db246541bb7048c1 Fri Dec 16 09:09:15 2016 -0800
    Adding Data Access section to track description pages. Changing example bigBedToBed command chromosome region to a location that generates output
• src/hg/makeDb/trackDb/trackDb.ra
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    6e41e8a48a74cb10e8d1455a51169f1ea8e2662a Thu Dec 15 20:05:29 2016 -0800
    updated transmap trackDb in prep for new bigTransMap
• src/hg/makeDb/trackDb/trackDb.transMap.ra
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    6e41e8a48a74cb10e8d1455a51169f1ea8e2662a Thu Dec 15 20:05:29 2016 -0800
    updated transmap trackDb in prep for new bigTransMap
• src/hg/mouseStuff/README
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    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
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    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
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    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/hg/near/hgNear/hgNear.c
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    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/oneShot/freen/freen.c
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    a1ee3cb0f0574ac88b3e35681706d61fff5f3b75 Wed Dec 7 12:32:52 2016 -0800
    Checking error messages we get from overloading library function names.
• src/hg/phyloPng/phyloPng.c
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    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/hg/ratStuff/README
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    9c0f463152095051a207201ce8d28eec87a1aaaa Tue Dec 6 13:39:52 2016 -0800
    per Jim request, adding copyright information to a couple README files refs #13978
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    b40b82a00950316bb7c5eb1d92b2a6c68c503ab7 Thu Dec 8 14:02:21 2016 -0800
    fixed typo
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    87e7961d71523fd532a5cac11b5dae5a81587520 Thu Dec 8 15:28:10 2016 -0800
    removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978
• src/hg/utils/hubCheck/hubCheck.c
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    29b62babe31abb529c19a265923eafc873c10616 Thu Dec 8 12:12:57 2016 -0800
    fixing an unnecessary NULL bug in hubCheck found by braney
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    3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800
    more changes to support the new big* formats
• src/hg/utils/hubCheck/makefile
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
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    761c35e2360dc7d1c0d15132296c0d601ccd6d4b Sat Dec 10 10:40:29 2016 -0800
    clean up test output
• src/hg/utils/hubCheck/tests/expected/output1.txt
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
• src/hg/utils/hubCheck/tests/expected/output2.txt
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
• src/hg/utils/hubCheck/tests/input/hub1.txt
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
• src/hg/utils/hubCheck/tests/makefile
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
• src/hg/utils/makefile
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    d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800
    rudimentary tests for hubCheck.
• src/hg/utils/vai.pl
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    b546eecd8adb64a42547ccd39ae436b09d0bd167 Fri Dec 9 15:44:46 2016 -0800
    Use cgi-bin by default, not cgi-bin-angie! Thanks Christopher Lee. refs #12216
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    4a1540ff08c68fd435e71eeefe579e368ad8211a Wed Dec 14 14:51:15 2016 -0800
    Doh, an early extra close() on a filehandle... refs #12216 note-27
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    3668909bc45cf722a9b69e2dafbf5e161a6a87a6 Wed Dec 14 16:36:45 2016 -0800
    annoStreamDb should not be hardcoded to find all.joiner in the current directory. Now, if env var ALL_JOINER_FILE exists, it will be used instead. vai.pl can now look for all.joiner in hgVai's parent directory (.../cgi-bin) and use ALL_JOINER_FILE if there is no ./all.joiner. refs #12216 note-28
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    b0b401942ab87c2208fec5bfbeeeb4a1cb1bc326 Wed Dec 14 16:48:38 2016 -0800
    If HGDB_CONF is not set and hg.conf is not in the usual places, look for it in hgVai's parent dir and set HGDB_CONF if found. refs #12216 note-32
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    0239643d97af85334bfeb84c9e9732c19ae6682f Thu Dec 15 10:40:53 2016 -0800
    Oops, an overly restrictive regex was preventing vai.pl from accepting --position=chrX (without the range). refs #12216 note-20
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    c85802ccef6bba0d6159c20950a01094e817c56c Thu Dec 15 11:15:23 2016 -0800
    Add env var UDC_CACHEDIR to override hg.conf udc.cacheDir for command-line use of CGI. Add -udcCache option to vai.pl using UDC_CACHEDIR. refs #12216 note-32
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
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    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/inc/common.h
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    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
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    be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800
    some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
• src/inc/tagStorm.h
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    749dadba2cba56c5cc7b64425048093cee380713 Wed Dec 14 18:52:16 2016 -0800
    Renaming tagStormUpdateTag to tagStanzaUpdateTag for consistency, and adding a new tagStanzaDeleteTag.
• src/lib/annoStreamTab.c
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    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
• src/lib/basicBed.c
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    be313e01c1c762665d07df3691b4bbee56771e44 Sat Dec 10 11:51:20 2016 -0800
    fix problem with creating bigPsl files with more than 10240 blocks
• src/lib/blastParse.c
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    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
• src/lib/common.c
  • lines changed 12, context: html, text, full: html, text
    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
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    e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
    Better cookies and validation for hgLogin: instead of sending gbMembers.idx as the login cookie and then never checking the value of the incoming cookie, use a salted hash. The salt is a secret text value specified by login.cookieSalt in hg.conf.private. For remote login, both hosts' hg.conf.private files must specify the same login.cookieSalt. In order to avoid logging out all users, for now the correct value of gbMembers.idx is accepted in place of the salted hash for local logins. For remote logins without login.cookieSalt, there is still no way to check the incoming cookie. For local logins without login.cookieSalt, the correct gbMembers.idx is accepted. refs #17327
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    be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800
    some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
• src/lib/tagStorm.c
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    749dadba2cba56c5cc7b64425048093cee380713 Wed Dec 14 18:52:16 2016 -0800
    Renaming tagStormUpdateTag to tagStanzaUpdateTag for consistency, and adding a new tagStanzaDeleteTag.
• src/lib/wormdna.c
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    1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
    Libifying isAllDigits from a handful of places into common.c.
• src/makefile
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    751228a4d6d75d72ae2407231ece2651e9f8de4d Mon Dec 12 16:05:41 2016 -0800
    fix up cgi-alpha and cgi-beta targets to copy bedToBigBed into the CGI loader directory
• src/product/ex.hg.conf
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    89a44e5c387d7b75c46c45f84729f11a70d57597 Mon Dec 12 15:28:15 2016 -0800
    Document new hg.conf(.private) setting login.cookieSalt in ex.hg.conf. refs #17327
• src/product/installer/README.md
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    72085932f3a35662f7445168802b13d86a25c343 Fri Dec 16 16:25:06 2016 -0800
    update to GBIC mirror docs. This commit was approved by Chris L.
• src/product/installer/browserSetup.sh
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    c6d2a00e29c9874544eca28b9b5c25deb08e694d Mon Dec 5 12:05:32 2016 -0800
    adding r-base-core to gbic script, email from cmalee
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    c9cff716524000d6b44e520bbfe0026685fdbbb0 Thu Dec 15 14:35:38 2016 -0800
    making the gbic mirrors identify itself to phoneHome with a distinct string, refs #14399
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    199db02e8d247ce16b1384100b5058a7e10e0cf2 Fri Dec 16 10:58:42 2016 -0800
    fixing a bug in gbic found in the source code by Chris L, refs #18553
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    d3cb61d5bd1304565bab0443c8b73269c7e95ee7 Fri Dec 16 12:07:33 2016 -0800
    fixing a bugfix for a bug in gbic found in the source code by Chris L. (What would I do without ChrisL?) refs #18553
• src/product/mirrorDocs/staticPage.lua
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    72085932f3a35662f7445168802b13d86a25c343 Fri Dec 16 16:25:06 2016 -0800
    update to GBIC mirror docs. This commit was approved by Chris L.
• src/tagStorm/tagStormHoist/tagStormHoist.c
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    749dadba2cba56c5cc7b64425048093cee380713 Wed Dec 14 18:52:16 2016 -0800
    Renaming tagStormUpdateTag to tagStanzaUpdateTag for consistency, and adding a new tagStanzaDeleteTag.
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    fc1eaa85ad365f4e1eb76372da4189b3b038ddf2 Thu Dec 15 08:01:52 2016 -0800
    Added -one option to hoist just a single tag.
• src/tagStorm/tagStormToHtml/tagStormToHtml.c
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    530f3e6a088dee15b6ef77d89ab7ea9f8bb70245 Tue Dec 6 17:56:11 2016 -0800
    Simplifying look and reducing number of DOM objects.
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    f41fc48aa625075782b67ef8e41f4538aeedae2f Fri Dec 9 09:25:35 2016 -0800
    Put in code to check for IE, and put up simpler non-javascript page if that is the case. Removed tabs since they are interpreted as 4 spaces not 8 under web browsers javascript debuggers, and so code looks off.
• src/utils/columnsToGrid.sh
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    f04cdaf3e9e0f7a2d3aba45cc5736b4b2ccadd05 Wed Dec 7 12:38:30 2016 -0800
    Adding a new utility which takes columns (delimiter can be specified) and displays them as blocks in a grid.
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    8bbb5dcbd2177f8bb63a9408b7990cbbceec4315 Wed Dec 7 15:54:08 2016 -0800
    fixed tab stop to tab 8 shiftwidth 4 on columnsToGrid.sh.
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    8fc01f4dc649740449c56f2ab0b997b0171a4480 Wed Dec 7 16:25:30 2016 -0800
    Testing. New to this, excited to learn conventions
• src/utils/makefile
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    e0b5992e43c58605f0079aa6710d988de58d5001 Wed Dec 7 14:33:35 2016 -0800
    sorting the script list in alphabetical order for easier future maintenance.
• src/utils/newProg/newProg.c
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    1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
    Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
• src/utils/qa/makefile
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    4e729f995f1748a128c557b56c439ba5c22cbd39 Fri Dec 9 10:41:43 2016 -0800
    Adding new public hub contact info scraper to makefile, refs #18316
• src/utils/qa/weeklybld/buildEnv.csh
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    a73a283efc30de413d6d040531a98bb111b3a2c5 Mon Dec 19 10:08:23 2016 -0800
    v343 preview1 refs #18555

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• files changed: 259