All File Changes

v349_base to v350_preview (2017-05-15 to 2017-05-22) v350

• confs/hgwbeta.hg.conf
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    21ee06cfcbe0ae90887eb7d8944306ee1fe83ed0 Sun May 21 01:11:56 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
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    f7848b9aa7b5d5a786ed49c64ee0f24e6ad3777d Tue May 16 18:11:55 2017 -0700
    CIRM: fixing loading bug that appears only with very old VCF files
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    e1c83946159b3b16797cb9cd91ca52d24f73883a Mon May 15 16:21:22 2017 -0700
    CIRM: making the logout button work with HTTP Basic Auth
  • lines changed 10, context: html, text, full: html, text
    23b0b620b9584c3fabecb98028183474094708b0 Tue May 16 17:47:43 2017 -0700
    CIRM: fixing missing permissions to files when login is email address
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 23, context: html, text, full: html, text
    e1c83946159b3b16797cb9cd91ca52d24f73883a Mon May 15 16:21:22 2017 -0700
    CIRM: making the logout button work with HTTP Basic Auth
  • lines changed 11, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
  • lines changed 2, context: html, text, full: html, text
    20bf8d47b6351e8406d616f91380dab4c2b3e896 Tue May 16 17:30:48 2017 -0700
    CIRM: fixing a bug in auth detection
  • lines changed 2, context: html, text, full: html, text
    23b0b620b9584c3fabecb98028183474094708b0 Tue May 16 17:47:43 2017 -0700
    CIRM: fixing missing permissions to files when login is email address
• src/hg/cirm/cdw/lib/cdwLogoutJs.h
  • lines changed 26, context: html, text, full: html, text
    e1c83946159b3b16797cb9cd91ca52d24f73883a Mon May 15 16:21:22 2017 -0700
    CIRM: making the logout button work with HTTP Basic Auth
  • lines changed 26, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
• src/hg/hgComposite/hgComposite.c
  • lines changed 3, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
  • lines changed 4, context: html, text, full: html, text
    d9979532689e2d49aa15e6062458617878551a87 Sat May 20 18:50:32 2017 -0700
    changes in response to code review
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 3, context: html, text, full: html, text
    03babf928b4b69bce4c86dcf5d0abab9a435e336 Mon May 15 13:08:09 2017 -0700
    fixing strange error when showing only 0 or 1 gene in hgGeneGraph, refs #18626
  • lines changed 4, context: html, text, full: html, text
    cd9e9bc3bea3e5438c2da40e57ffcb69c8fa2672 Fri May 19 13:35:52 2017 -0700
    adding all.joiner for the interactions track, refs #13634
• src/hg/hgLogin/hgLogin.c
  • lines changed 9, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    3c556eed91140fc152600a25bdccdc72cf9dc6b4 Mon May 15 12:55:38 2017 -0700
    fixing error message 'no value specified for field "settings"' by newer Mysql versions that do not accept missing fields in INSERT statements, This is another bug of the type previously fixed in refs #18626
  • lines changed 19, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
  • lines changed 3, context: html, text, full: html, text
    ec74b71d82b5ee60aa2641765969e0ee86210e0c Thu May 18 09:02:46 2017 -0700
    fixing URL bug I introduced yesterday with my hgSession change. refs #19430
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    c96d86d2466368820ee4ca92f8c6b43f2bdec249 Mon May 22 09:58:10 2017 -0700
    Invoke GTEx UI from supertrack added to package new GTEx Transcript track with existing GTEx Gene track. refs #19350
  • lines changed 4, context: html, text, full: html, text
    15c8d30b5344d0b2214f4f5f9260b889560b5c61 Mon May 22 09:58:57 2017 -0700
    Ws cleanup
• src/hg/hgTracks/barChartTrack.c
  • lines changed 3, context: html, text, full: html, text
    aa675de1a849fe445eb1924f7f26707810df1c89 Mon May 15 15:48:22 2017 -0700
    Better error checking for hubs and custom tracks. refs #18736
• src/hg/hgTracks/extTools.c
  • lines changed 5, context: html, text, full: html, text
    f8cbb9d40119d1b7fd52578e08c4148e39e10ce4 Tue May 16 17:19:56 2017 -0700
    removing external tools link when on alternate chromosomes, e.g. on hg38, refs #16619
• src/hg/hgTracks/hgTracks.c
  • lines changed 38, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
  • lines changed 1, context: html, text, full: html, text
    f8cbb9d40119d1b7fd52578e08c4148e39e10ce4 Tue May 16 17:19:56 2017 -0700
    removing external tools link when on alternate chromosomes, e.g. on hg38, refs #16619
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/imageV2.c
  • lines changed 4, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/imageV2.h
  • lines changed 1, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/makefile
  • lines changed 3, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/makefile.hgRenderTracks
  • lines changed 1, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/multiWig.c
  • lines changed 15, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/sortWig.c
  • lines changed 138, context: html, text, full: html, text
    5f037d70130d40df64b477c1fef293d5876f9e32 Mon May 15 13:06:19 2017 -0700
    oops, left out the most important file for sorting!
• src/hg/hgTracks/wigCommon.h
  • lines changed 9, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgTracks/wigTrack.c
  • lines changed 30, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    e91ede5d7c99da66098240cc7b2e9d2fe1ca74c3 Mon May 15 14:00:27 2017 -0700
    Updating COSMIC code so it is backwards compatible, refs #14461
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    11b6402543489d909b52a5554f7877e7e10e6a6a Tue May 16 09:48:03 2017 -0700
    Announcing aquChr2 (golden eagle) initial release, refs #15096
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 56, context: html, text, full: html, text
    11b6402543489d909b52a5554f7877e7e10e6a6a Tue May 16 09:48:03 2017 -0700
    Announcing aquChr2 (golden eagle) initial release, refs #15096
  • lines changed 1, context: html, text, full: html, text
    15f17c1dd7bb39f477bfd2d8b89b05ef7bc9727a Tue May 16 12:37:00 2017 -0700
    Fixing link to the rhiRox1 gateway page in the credits.html page, no redmine
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 314, context: html, text, full: html, text
    65f64f58e28ffe1256fcea31b1ec8e673234b86d Fri May 19 13:15:24 2017 -0700
    First pass at barChart track format page. needs grammar edits but most of the content should be there. Still need to add references to pre-existing pages about this new format, refs #18736
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 1, context: html, text, full: html, text
    b6800dfb9d96efbcfba301b1dc2d09b81c2bcdf3 Mon May 15 14:16:35 2017 -0700
    Adding in missing quote, refs #13634
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    b39d30af743bb5436622a5a8114e9d3437046e8f Tue May 16 10:55:23 2017 -0700
    some minor grammer and readability tweaks
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    df5f2572b22b45a0f5f7455f4f81032db5748189 Thu May 18 10:51:39 2017 -0700
    Mostly whitespace formatting changes based on Donna's feedback about how we indent 'li' lists, refs #13634
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    11b6402543489d909b52a5554f7877e7e10e6a6a Tue May 16 09:48:03 2017 -0700
    Announcing aquChr2 (golden eagle) initial release, refs #15096
  • lines changed 31, context: html, text, full: html, text
    731dba3f018f3deb9ec63a1c60b3fc2c086d125f Wed May 17 16:28:45 2017 -0700
    Minor edits, Donna's feedback, refs #19370
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 22, context: html, text, full: html, text
    d36b64cbb2d5e431b2ed722ad7eb348da6f32344 Wed May 17 14:51:21 2017 -0700
    Adding new publication for Braney, no RM
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    85bd10da37f403d155c4434d90edcd146e682948 Mon May 15 13:03:32 2017 -0700
    add sorting to composite wiggles.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    11b6402543489d909b52a5554f7877e7e10e6a6a Tue May 16 09:48:03 2017 -0700
    Announcing aquChr2 (golden eagle) initial release, refs #15096
  • lines changed 2, context: html, text, full: html, text
    731dba3f018f3deb9ec63a1c60b3fc2c086d125f Wed May 17 16:28:45 2017 -0700
    Minor edits, Donna's feedback, refs #19370
• src/hg/inc/wikiLink.h
  • lines changed 15, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
• src/hg/lib/barChartBed.c
  • lines changed 17, context: html, text, full: html, text
    0df623bc76a0c81c38aed0ea9945808a605935b6 Thu May 18 17:01:41 2017 -0700
    Protect against bad barChart files (where #expScores doesn't match expCount. refs #18736
• src/hg/lib/barChartUi.c
  • lines changed 2, context: html, text, full: html, text
    e746fa8cd0ad323ba549ddb3ea05825f2927cec1 Mon May 15 15:47:13 2017 -0700
    Cleanup some comments. refs #18736
• src/hg/lib/customFactory.c
  • lines changed 25, context: html, text, full: html, text
    aa675de1a849fe445eb1924f7f26707810df1c89 Mon May 15 15:48:22 2017 -0700
    Better error checking for hubs and custom tracks. refs #18736
  • lines changed 11, context: html, text, full: html, text
    91362f97f8284e8b4c42c158f2652111ee03625f Thu May 18 14:23:59 2017 -0700
    Error checking on barChart custom track first line. Reject if #expScores != expCount. refs #18736
  • lines changed 2, context: html, text, full: html, text
    d6153bc5e077a19003043e8a85a36ad32f711513 Thu May 18 17:02:14 2017 -0700
    Protect against bad barChart files (where #expScores doesn't match expCount. refs #18736
• src/hg/lib/ggEventDb.as
  • lines changed 1, context: html, text, full: html, text
    c131ed83cd627d80bd614262fc7d03e8f6d48ea6 Fri May 19 13:54:04 2017 -0700
    improving gene graph .as files a little
• src/hg/lib/ggEventText.as
  • lines changed 1, context: html, text, full: html, text
    c131ed83cd627d80bd614262fc7d03e8f6d48ea6 Fri May 19 13:54:04 2017 -0700
    improving gene graph .as files a little
• src/hg/lib/ggGeneClass.as
  • lines changed 1, context: html, text, full: html, text
    c131ed83cd627d80bd614262fc7d03e8f6d48ea6 Fri May 19 13:54:04 2017 -0700
    improving gene graph .as files a little
• src/hg/lib/ggGeneName.as
  • lines changed 1, context: html, text, full: html, text
    c131ed83cd627d80bd614262fc7d03e8f6d48ea6 Fri May 19 13:54:04 2017 -0700
    improving gene graph .as files a little
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    e746fa8cd0ad323ba549ddb3ea05825f2927cec1 Mon May 15 15:47:13 2017 -0700
    Cleanup some comments. refs #18736
• src/hg/lib/hgHgvs.c
  • lines changed 77, context: html, text, full: html, text
    8de038378e49e6e1ba6b2de24bddc334c8b75d99 Tue May 9 11:51:59 2017 -0700
    Adding support for HGVS m. and n. terms in position/search. refs #19423
• src/hg/lib/logoutJs.h
  • lines changed 26, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
• src/hg/lib/trackHub.c
  • lines changed 12, context: html, text, full: html, text
    aa675de1a849fe445eb1924f7f26707810df1c89 Mon May 15 15:48:22 2017 -0700
    Better error checking for hubs and custom tracks. refs #18736
• src/hg/lib/wikiLink.c
  • lines changed 116, context: html, text, full: html, text
    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
  • lines changed 1, context: html, text, full: html, text
    cf8cec85220443d790c83cb54adac5515989d40f Tue May 16 15:54:38 2017 -0700
    fixing an esoteric GCC warning, thanks Hiram
• src/hg/makeDb/doc/chrPic2.txt
  • lines changed 210, context: html, text, full: html, text
    899b390be2ea230d0372dcb5f3ac9ab8d36f933c Thu May 18 10:45:58 2017 -0700
    catching up a few stray tracks to prepare for release refs #13166
• src/hg/makeDb/doc/criGri1.txt
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    f3671e97ff62b9133727a4d32093c7dd6882d2d2 Thu May 18 11:01:03 2017 -0700
    adding chainNet/lastz mm10 criGri1 to catch up criGri1 with standard lastz/chainNet refs #19228
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 13, context: html, text, full: html, text
    1cd4732b626618fdaf77313ceb19cc0ce2e139bc Tue May 16 10:33:26 2017 -0700
    Updating the doc for Hoffman lab mappability hub, refs #19154
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    5c4a0bd130a63e03576c7bff7d5dde5b41d8ea23 Wed May 17 15:27:47 2017 -0700
    Files for the tcga expression supertrack, refs #19155
• src/hg/makeDb/doc/micMur1.txt
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    96f7d63e0f50c7bdce4072e4b4bb91efd435f57a Thu May 18 10:50:05 2017 -0700
    liftOver to micMur3 refs #18984
• src/hg/makeDb/doc/micMur2/initialBuild.txt
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    d59c89099d4cb7380e79d27c480b38249011c00a Thu May 18 10:54:31 2017 -0700
    liftOver to micMur3 refs #18984
• src/hg/makeDb/doc/mm10.txt
  • lines changed 57, context: html, text, full: html, text
    f3671e97ff62b9133727a4d32093c7dd6882d2d2 Thu May 18 11:01:03 2017 -0700
    adding chainNet/lastz mm10 criGri1 to catch up criGri1 with standard lastz/chainNet refs #19228
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
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    a9b8b1f4f61861850714790a26097dfcf1d49a7e Thu May 18 11:04:57 2017 -0700
    adding assembly info comment data from NCBI references refs #15056
• src/hg/makeDb/doc/oxyTri2/initialBuild.txt
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    47440f5d8fba85a17d4afed0df71f37db01f6678 Thu May 18 11:06:15 2017 -0700
    catching up outstanding procedures refs #16535
• src/hg/makeDb/doc/worms/ancCey1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/burXyl1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/caeAng2.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/caeSp51.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/dirImm1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/melInc2.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/necAme1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/priExs1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/priPac3.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/strRat1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/strRat2.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/triSpi1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/worms/triSui1.txt
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    ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700
    catching up build procedures, no redmine
• src/hg/makeDb/doc/xenLae2/initialBuild.txt
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    cc4f3f178daaf46cf06567a6f29ee0b4e261dd71 Thu May 18 11:12:43 2017 -0700
    running makePushQ with the redmine listings refs #19151
• src/hg/makeDb/doc/xenTro9/initialBuild.txt
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    cc4f3f178daaf46cf06567a6f29ee0b4e261dd71 Thu May 18 11:12:43 2017 -0700
    running makePushQ with the redmine listings refs #19151
• src/hg/makeDb/doc/xenTro9/lastzRuns.txt
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    0645c47bfe34098da9797bc094067b54b93fd20b Tue May 16 16:12:38 2017 -0700
    completed xenLae2 recip best refs #19151
• src/hg/makeDb/schema/all.joiner
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    cd9e9bc3bea3e5438c2da40e57ffcb69c8fa2672 Fri May 19 13:35:52 2017 -0700
    adding all.joiner for the interactions track, refs #13634
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
• src/hg/makeDb/trackDb/human/hg38/Bismap.html
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    7d78b481f793ff4ef8fda4f7d17f4ac11b565495 Tue May 16 10:26:24 2017 -0700
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    7d78b481f793ff4ef8fda4f7d17f4ac11b565495 Tue May 16 10:26:24 2017 -0700
    Track.db changes and html files for mappability tracks, refs #19154
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    5c4a0bd130a63e03576c7bff7d5dde5b41d8ea23 Wed May 17 15:27:47 2017 -0700
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
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    7d78b481f793ff4ef8fda4f7d17f4ac11b565495 Tue May 16 10:26:24 2017 -0700
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    9482d69065d2b6d7fed214fbdbe72e83088756af Wed May 17 08:23:06 2017 -0700
    Adding release alpha to super track substanzas, refs #19154
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    5c4a0bd130a63e03576c7bff7d5dde5b41d8ea23 Wed May 17 15:27:47 2017 -0700
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    5c4a0bd130a63e03576c7bff7d5dde5b41d8ea23 Wed May 17 15:27:47 2017 -0700
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
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    b0a46939927bd741962bd0d6db48cf9713c39ef9 Fri May 19 13:19:52 2017 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1SuperTrack.ra
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    7586739d1a3921d25f55dcc466b2ee5ce54fa6ef Wed May 17 14:28:01 2017 -0700
    Fixing the order of the SNP tracks by having the newest track first in the Variation and Repeats group on mm10, refs #19187
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    a854a79c60bc78ef6571bc5919252b2f8e7eabbc Wed May 17 13:21:52 2017 -0700
    Setting the default display of the Conservation track to full by default on mm10, refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    be3cc3e70a0b4b4d7cd81b495e2d8d9e3ecae43d Wed May 17 09:07:23 2017 -0700
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    7586739d1a3921d25f55dcc466b2ee5ce54fa6ef Wed May 17 14:28:01 2017 -0700
    Fixing the order of the SNP tracks by having the newest track first in the Variation and Repeats group on mm10, refs #19187
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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    d086e7eaf8689ddf0117260cf4a12f49fa58580c Fri May 19 15:07:34 2017 -0700
    Changing some defaults for human/mouse based on Jim's feedback. GTEx now default for hg19/hg38. dgvMerged now default for hg19. Turned off mRNAs by default in hg19, hg38, mm10, mm9. no redmine
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra
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    81765a9713ec8020330790a0fb445431de0afc9f Thu May 18 11:16:31 2017 -0700
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    22740c40dcb1f2cc493c0fa2774d0ea32e23de69 Tue May 16 10:29:13 2017 -0700
    A python utility written to import the Hoffman lab mappability hub, refs #19154
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    a694e0a184fd207b5ca389e1b8697e5564b000a0 Thu May 18 22:31:55 2017 -0700
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    a694e0a184fd207b5ca389e1b8697e5564b000a0 Thu May 18 22:31:55 2017 -0700
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    a694e0a184fd207b5ca389e1b8697e5564b000a0 Thu May 18 22:31:55 2017 -0700
    adding tandem dup procedure refs #13553
• src/hg/utils/automation/ucscToINSDC.sh
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    862daf89620592b91269007bc40b9ae536c64969 Thu May 18 10:06:21 2017 -0700
    correctly recognize _ in unlocalized scaffold names for galGal5 refs #17168
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    49b315a9a902659d3d47e353fbb5fd907588b558 Tue May 16 08:57:20 2017 -0700
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    49b315a9a902659d3d47e353fbb5fd907588b558 Tue May 16 08:57:20 2017 -0700
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    b0879b9b7a1fffb44a187b7c56507ab862cf581b Thu May 18 11:37:03 2017 -0700
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    69b103ed65e09747f59b59e8cca624ef68976b0d Thu May 18 10:41:58 2017 -0700
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    c8623d4f6f811ad58339d934f1d37142ab5ba9d9 Thu May 18 10:42:55 2017 -0700
    adding comment about key for hash no redmine
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    36c1354e6104862b2ee276f419dcdcca05712136 Mon May 22 06:03:38 2017 -0700
    made error messages a bit more specific
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    0df623bc76a0c81c38aed0ea9945808a605935b6 Thu May 18 17:01:41 2017 -0700
    Protect against bad barChart files (where #expScores doesn't match expCount. refs #18736
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    e2316d8ff89ed1beb085f9169c4c7ca344affb20 Tue May 16 14:55:40 2017 -0700
    Changes to hgLogin and hgSession to replace hgLogin with Apache's Basic authentication system, refs #19424, primarily motivated by CIRM but hopefully useful in other contexts
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    b1a99b763d15ce616e7c3d712f5d87a0de88548c Mon May 15 15:00:56 2017 -0700
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    e3ed5309131999cbb6d837720d5e49d460d15838 Tue May 16 15:01:07 2017 -0700
    making HTTPHOST the default in ex.hg.conf
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    7a0a5b8714e42c126e2673f73d336d95c79633b2 Mon May 15 15:48:03 2017 -0700
    fixing bug reported by email to ChrisL, from John Chen. thanks Chris., no redmine (yet)
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    16d99600473977053f8052c7e827a22ac5324c74 Wed May 17 13:42:30 2017 -0700
    fixing GBIC for systemd, no redmine yet
• src/utils/bamToPsl/bamToPsl.c
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    a5baef17b79d806a60d886cec056f0991a4eee14 Thu May 18 11:30:12 2017 -0700
    add noSequenceVerify option to speed up procedure refs #13673
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    allow xenoRefGene table to be used refs #18969
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    catch up checkin no redmine
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