All File Changes

v347_preview to v347_preview2 (2017-03-20 to 2017-03-27) v347

• confs/hgwdev.hg.conf
  • lines changed 12, context: html, text, full: html, text
    8a517dbde81136ae75107ba8d5dc8dc7e8e613c8 Sun Mar 26 01:11:45 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwManiFastqToPeaks/cdwManiFastqToPeaks
  • lines changed 139, context: html, text, full: html, text
    5c192b951f65115371250c7a2addb231569e6234 Thu Mar 23 15:31:05 2017 -0700
    Script to run MACS2 on CIRM chip-seq data
• src/hg/cirm/cdw/cdwManiFastqToPeaks/makefile
  • lines changed 6, context: html, text, full: html, text
    5c192b951f65115371250c7a2addb231569e6234 Thu Mar 23 15:31:05 2017 -0700
    Script to run MACS2 on CIRM chip-seq data
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 4, context: html, text, full: html, text
    8b1679d3f01d3b16731cdaaf78474db303853746 Tue Mar 21 12:28:34 2017 -0700
    adding in the csv option for meta data on the data set pages, refs #17870
• src/hg/cirm/cdw/wrangle/maniMani/maniMani
  • lines changed 27, context: html, text, full: html, text
    c5c24e3631bfae258c1afdc994d64049c8139b3b Thu Mar 23 15:29:11 2017 -0700
    fixing an error spotted by kate in refs #19104
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 3, context: html, text, full: html, text
    f2a4ac793ad34d9f25a7dc184b9c785c476d98e1 Fri Mar 24 15:50:50 2017 -0700
    Changing http to https for pubs url, refs #19135
• src/hg/hgLogin/hgLogin.c
  • lines changed 23, context: html, text, full: html, text
    263daca0593f4d67610f2466cdcdb262f27d6a67 Thu Mar 23 10:22:32 2017 -0700
    Changing your password now automatically logs you in; also fixed a javascript type error, refs #8351
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    48123b8bfcac353f062a5a03d4c361720628850b Thu Mar 23 09:44:53 2017 -0700
    fix code that wasn't grabbing trackDb settings correctly
  • lines changed 3, context: html, text, full: html, text
    aecb77f1983b836e929cb00c825e1d947fe47421 Thu Mar 23 10:34:57 2017 -0700
    small tweak to coverage wiggle support so default values are the same in hgTracks and they are in hgTrackUi
  • lines changed 11, context: html, text, full: html, text
    6b833bddf059affee05eb0ddb1b2d4e06554ca6b Thu Mar 23 14:28:05 2017 -0700
    DECIPHER track now displays correct mean ratio and pathogenicity, refs #19129
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    3ceeebfd0424d1e80bf9b9b320565d6e2875dbd1 Mon Mar 20 14:38:24 2017 -0700
    make the bigDataUrl in custom BLAT tracks point directly to ../trash so symbolic links will work
  • lines changed 7, context: html, text, full: html, text
    6b833bddf059affee05eb0ddb1b2d4e06554ca6b Thu Mar 23 14:28:05 2017 -0700
    DECIPHER track now displays correct mean ratio and pathogenicity, refs #19129
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 7, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 95, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 23, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 14, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ENCODE/pilot.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ENCODE/search.html
  • lines changed 2, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 4, context: html, text, full: html, text
    1c30c208e0c142a42e063a2a7e8de073611771b6 Thu Mar 23 13:51:26 2017 -0700
    Adding 'code' styling to utility reference in FAQ, refs #19100
  • lines changed 1, context: html, text, full: html, text
    264b58682befda515eb5c717ffecbfabf045bb75 Fri Mar 24 13:05:36 2017 -0700
    Changing MySQL url from cse to soe, no RM
  • lines changed 12, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/Neandertal/index.html
  • lines changed 197, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/admin/mirror.html
  • lines changed 336, context: html, text, full: html, text
    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
  • lines changed 4, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/admin/mirrorManual.html
  • lines changed 15, context: html, text, full: html, text
    631c995e82e53c5413caa7c0bf47be4c49162137 Wed Mar 22 17:08:10 2017 -0700
    Documentation changes to add new proxy settings. refs #19124
  • lines changed 993, context: html, text, full: html, text
    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
  • lines changed 6, context: html, text, full: html, text
    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
  • lines changed 279, context: html, text, full: html, text
    8ae3277c2dcbae99c1058939bfcd004625765e28 Thu Mar 23 16:46:25 2017 -0700
    merge conflict resolved.
  • lines changed 9, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/datorg.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 47, context: html, text, full: html, text
    c048bc2c54c13ca3fb37ed28f60ce2917ad89e64 Wed Mar 22 12:02:05 2017 -0700
    Removing 2 obsolete files gbdDescriptions, refs #17656
• src/hg/htdocs/goldenPath/gbdDescriptionsOld.html
  • lines changed 5865, context: html, text, full: html, text
    c048bc2c54c13ca3fb37ed28f60ce2917ad89e64 Wed Mar 22 12:02:05 2017 -0700
    Removing 2 obsolete files gbdDescriptions, refs #17656
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 4, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 5, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 5, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 6, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 5, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 5, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 11, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 8, context: html, text, full: html, text
    631c995e82e53c5413caa7c0bf47be4c49162137 Wed Mar 22 17:08:10 2017 -0700
    Documentation changes to add new proxy settings. refs #19124
  • lines changed 6, context: html, text, full: html, text
    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
  • lines changed 2, context: html, text, full: html, text
    264b58682befda515eb5c717ffecbfabf045bb75 Fri Mar 24 13:05:36 2017 -0700
    Changing MySQL url from cse to soe, no RM
  • lines changed 2, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 204, context: html, text, full: html, text
    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 1, context: html, text, full: html, text
    264b58682befda515eb5c717ffecbfabf045bb75 Fri Mar 24 13:05:36 2017 -0700
    Changing MySQL url from cse to soe, no RM
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/hgTextHelp.html
  • lines changed 1232, context: html, text, full: html, text
    fa7d26e86c79a3171d2a32bcfd02afeb11ca0132 Wed Mar 22 12:10:41 2017 -0700
    Removing 5 obsolete files: hgTextHelp.html, trackDescriptions.html definitions.html, jobs.html, knownIssues.html, refs #17656
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 6, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 2, context: html, text, full: html, text
    0e07a2ebb8a7ac9126f182a77314bb59df3f7564 Wed Mar 22 13:34:21 2017 -0700
    Adding section about apply button to graph config page, refs #19031
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 3, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 5, context: html, text, full: html, text
    264b58682befda515eb5c717ffecbfabf045bb75 Fri Mar 24 13:05:36 2017 -0700
    Changing MySQL url from cse to soe, no RM
  • lines changed 1, context: html, text, full: html, text
    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/README.txt
  • lines changed 33, context: html, text, full: html, text
    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/aa.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/aaAnom.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/aa_abund2.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/cys.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/cys_occur.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/exon.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/exonCntDist.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/exon_distrib.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/hydro.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/hydrophobic.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/makefile
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/mol_wt.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/mw.jpg
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pI_large.gif
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbNglyDisc.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaScale.shtml
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaScale.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaScaleDisc.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaSeq.shtml
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaSeq.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbaaSeqDisc.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbcCnt.shtml
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbcCnt.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbcCntDisc.txt
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/pbcCntTr.shtml
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    667387691f729b537617017740db75bd55327a9d Wed Mar 22 11:48:29 2017 -0700
    Removing obsolete files in dir pbTracksHelpFiles from old Proteome Browser guide, refs #17656
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    1c975a71eba4419f677101b30648cf196fa4dcd7 Wed Mar 22 09:07:56 2017 -0700
    Adding links to new hubCheck help doc section based on CR, refs #19099
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    ad60de6c8589ba542d6b11b4584c3f3e4c7ee390 Wed Mar 22 10:03:15 2017 -0700
    Adding missing word to sentence, no redmine
• src/hg/htdocs/goldenPath/help/trackDescriptions.html
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    fa7d26e86c79a3171d2a32bcfd02afeb11ca0132 Wed Mar 22 12:10:41 2017 -0700
    Removing 5 obsolete files: hgTextHelp.html, trackDescriptions.html definitions.html, jobs.html, knownIssues.html, refs #17656
• src/hg/htdocs/goldenPath/help/trix.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/help/twoBit.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/newsarch.html
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    8a1f0134a1569d3351c4d4ec517956dcf2eb5689 Mon Mar 20 15:26:43 2017 -0700
    Adding announcement for the new 20-way conservation track on rn6, refs #19064
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    1c975a71eba4419f677101b30648cf196fa4dcd7 Wed Mar 22 09:07:56 2017 -0700
    Adding links to new hubCheck help doc section based on CR, refs #19099
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/releaseLogOld.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/goldenPath/statistics/definitions.html
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    fa7d26e86c79a3171d2a32bcfd02afeb11ca0132 Wed Mar 22 12:10:41 2017 -0700
    Removing 5 obsolete files: hgTextHelp.html, trackDescriptions.html definitions.html, jobs.html, knownIssues.html, refs #17656
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    c95a5def0f83a4c3c6b8c2a6fe33bc385a0dea8c Tue Mar 21 10:51:52 2017 -0700
    quick peek at a 4-way on Chinese tree shrew no redmine
• src/hg/htdocs/images/training/thumbCloud.jpg
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    d0e6935e0d2a557c15040f363d7643d7ac40428a Fri Mar 17 15:12:17 2017 -0700
    adding GBiC video to top of vids page. dropped some stuff at the bottom that related to adding new material at the end of the file. Will wait to push til QA has a look at it
• src/hg/htdocs/inc/encode.custTracks.topbar.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/inc/encode.topbar_pilot.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/indexNews.html
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    8a1f0134a1569d3351c4d4ec517956dcf2eb5689 Mon Mar 20 15:26:43 2017 -0700
    Adding announcement for the new 20-way conservation track on rn6, refs #19064
• src/hg/htdocs/jobs.html
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    fa7d26e86c79a3171d2a32bcfd02afeb11ca0132 Wed Mar 22 12:10:41 2017 -0700
    Removing 5 obsolete files: hgTextHelp.html, trackDescriptions.html definitions.html, jobs.html, knownIssues.html, refs #17656
• src/hg/htdocs/knownIssues.html
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    fa7d26e86c79a3171d2a32bcfd02afeb11ca0132 Wed Mar 22 12:10:41 2017 -0700
    Removing 5 obsolete files: hgTextHelp.html, trackDescriptions.html definitions.html, jobs.html, knownIssues.html, refs #17656
• src/hg/htdocs/template.html
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    101f86c57afe42985c19adaf21b8987921671af7 Wed Mar 22 10:46:38 2017 -0700
    adding a line about removing broders from tables
• src/hg/htdocs/training/ashg2009/sidebar.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/htdocs/training/index.html
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    8f5af154dffee1df39e7398ff907cc67e8a201c2 Wed Mar 22 11:14:54 2017 -0700
    adding UT San Antonio workshop and place-saver for SouthwesternU. adding &list= syntax to video links, so all our vids show up when user goes to YouTube
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    390af8b1e5b0c84f0ff89e42adfdfbc7c42f7938 Wed Mar 22 11:35:46 2017 -0700
    reversing addition to &list= to GBiC link because it breaks
• src/hg/htdocs/training/vids/index.html
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    d0e6935e0d2a557c15040f363d7643d7ac40428a Fri Mar 17 15:12:17 2017 -0700
    adding GBiC video to top of vids page. dropped some stuff at the bottom that related to adding new material at the end of the file. Will wait to push til QA has a look at it
• src/hg/htdocs/util.html
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    2f0bc369147f52829fc7984a50a1b4e8fa78c260 Fri Mar 24 14:44:40 2017 -0700
    Changing hgdownload urls from cse to soe, refs #19134
• src/hg/lib/bigBedFind.c
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    f2a08138a81d43b03a6fd6bd805b4a2ceb609139 Mon Mar 20 13:51:11 2017 -0700
    fail silently if a bigBed is missing and there is a search rule for it.
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    46d3135f90e8e5255fd8996dea33c1413460fee8 Wed Mar 22 09:30:34 2017 -0700
    fix NULL dereference in bigBed trix search on track hubs
• src/hg/lib/cart.c
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
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    417d09f28ac6349b73cbde88a4379962d195fec9 Wed Mar 22 15:28:58 2017 -0700
    fixing some minor details for no_proxy.
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    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
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    10ed5851072ff7a4c8ab8021f0baa1dd578feef4 Thu Mar 23 22:56:06 2017 -0700
    added logProxy=on setting to hg.conf to help confirm that the proxy is actually doing the expected thing. Not meant to be left on in production. refs #19124
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    0b073cd9000113cdb5e48ef772449ede60e1dea0 Fri Mar 24 01:31:59 2017 -0700
    little fix to cart.c so definitions happen before cartNew called.
• src/hg/lib/customFactory.c
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    3ceeebfd0424d1e80bf9b9b320565d6e2875dbd1 Mon Mar 20 14:38:24 2017 -0700
    make the bigDataUrl in custom BLAT tracks point directly to ../trash so symbolic links will work
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    2420bd05a82e3be4af0b4d186b9890b469403794 Mon Mar 20 16:01:23 2017 -0700
    use trashDir() instead of "../trash"
• src/hg/lib/hAnno.c
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    e52b9728905070e9979662928bccd604db61d8f4 Thu Mar 23 00:16:08 2017 +0000
    Commit 6072cb04b (#18445) introduced a bug: when hReplaceGbdb changes a path into a URL, fileExists() is no longer a sufficient test. Using hDbDbNibPath was unnecessarily complicated -- we have standardized on /gbdb/$db/$db.2bit for 2bit files. fixes #19113
• src/hg/lib/hdb.c
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    861e6f43bdfd6fd801c12200f44631a204655064 Tue Mar 21 14:47:29 2017 -0700
    Yet another place where we need the all_ prefix for the table. fixes #19111
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    4c9e841fc4f0b1c8664e8b44ed889e38b5a3ad97 Thu Mar 23 11:40:36 2017 -0700
    Yet another place where we need the all_ prefix for the table (again, thanks Jairo!). fixes #19111
• src/hg/makeDb/doc/bisBis1/initialBuild.txt
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    bf201e01e0bdda16197a3ad1f0fefdfc2f4fbb93 Wed Mar 22 10:13:59 2017 -0700
    blat server setups and default position established refs #15056 #15388 #15515
• src/hg/makeDb/doc/hg19.txt
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    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    eceae68b803365df1db9560ec075e3089f32c7bc Mon Mar 20 13:53:29 2017 -0700
    adding lastz/chain/net for manPen1 aquChr2 bisBis1 refs #15515 #15096 #15388
• src/hg/makeDb/doc/hg38/variation.txt
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    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/doc/manPen1/initialBuild.txt
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    bf201e01e0bdda16197a3ad1f0fefdfc2f4fbb93 Wed Mar 22 10:13:59 2017 -0700
    blat server setups and default position established refs #15056 #15388 #15515
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
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    bf201e01e0bdda16197a3ad1f0fefdfc2f4fbb93 Wed Mar 22 10:13:59 2017 -0700
    blat server setups and default position established refs #15056 #15388 #15515
• src/hg/makeDb/schema/all.joiner
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    485b8d1a5b85c64f08d1f4db88b7782a6ca24b3f Wed Mar 22 14:21:59 2017 -0700
    adding cioSav2 chainNet refs #16628
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    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 17, context: html, text, full: html, text
    3ce9513e52c3e0eb899cb6dba5f570eb3f047fb8 Tue Mar 21 13:31:01 2017 -0700
    adding bisBis1 chainNet definitions refs #15388
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    96a905b7edc9270b666464d710e8d793760caa66 Tue Mar 21 14:25:49 2017 -0700
    adding manPen1 chainNet definitions refs #15515
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 21, context: html, text, full: html, text
    c5d418bf992f9372bd42a95ca03bb036460b54f3 Fri Mar 24 12:59:37 2017 -0700
    Updating data display notice for DECIPHER track in accordance with agreement
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    b701f7d66e6f90b4b91062ebda452d5b634de89f Fri Mar 24 13:10:04 2017 -0700
    Fixing a couple of typos in the DECIPHER data display notice
• src/hg/makeDb/trackDb/human/snp149.html
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    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149.shared.html
  • lines changed 484, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Common.html
  • lines changed 28, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Flagged.html
  • lines changed 29, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/snp149Mult.html
  • lines changed 25, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 111, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    3ce9513e52c3e0eb899cb6dba5f570eb3f047fb8 Tue Mar 21 13:31:01 2017 -0700
    adding bisBis1 chainNet definitions refs #15388
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    96a905b7edc9270b666464d710e8d793760caa66 Tue Mar 21 14:25:49 2017 -0700
    adding manPen1 chainNet definitions refs #15515
• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
  • lines changed 19, context: html, text, full: html, text
    65be6694c8e19b34d837f0668ea112444666ecdb Fri Mar 24 13:24:24 2017 -0700
    Clarifying that while Zimin et al. is the source of the very useful table, it is not a reference for rheMac8 itself.
• src/hg/makeDb/trackDb/trackDb.chainNet.other.ra
  • lines changed 119, context: html, text, full: html, text
    7e016783aa23fc41598e2c1c3136286033e81cef Wed Mar 22 14:19:05 2017 -0700
    adding ci3 and cioSav2 chainNet definitions refs #16628
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 52, context: html, text, full: html, text
    3ce9513e52c3e0eb899cb6dba5f570eb3f047fb8 Tue Mar 21 13:31:01 2017 -0700
    adding bisBis1 chainNet definitions refs #15388
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    96a905b7edc9270b666464d710e8d793760caa66 Tue Mar 21 14:25:49 2017 -0700
    adding manPen1 chainNet definitions refs #15515
• src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
  • lines changed 58, context: html, text, full: html, text
    d9e42884ec51af52682c0738ba79c9c695166c29 Tue Mar 21 14:10:34 2017 -0700
    add nanPar1 chainNet refs #15056
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    7e016783aa23fc41598e2c1c3136286033e81cef Wed Mar 22 14:19:05 2017 -0700
    adding ci3 and cioSav2 chainNet definitions refs #16628
• src/hg/makeDb/trackDb/transMapRefSeqV4.html
  • lines changed 12, context: html, text, full: html, text
    df3166892562946df38aecb57279a74002afcfc7 Sat Mar 25 13:14:37 2017 -0700
    fixed name of transMap V4 html file
• src/hg/makeDb/trackDb/transMapRefseqV4.html
  • lines changed 12, context: html, text, full: html, text
    df3166892562946df38aecb57279a74002afcfc7 Sat Mar 25 13:14:37 2017 -0700
    fixed name of transMap V4 html file
• src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.chainNet.ra
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    d9e42884ec51af52682c0738ba79c9c695166c29 Tue Mar 21 14:10:34 2017 -0700
    add nanPar1 chainNet refs #15056
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
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    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 62, context: html, text, full: html, text
    42fd1b9f372ffefa7afc0696539f429bc2e02ae7 Wed Mar 15 12:36:59 2017 -0700
    snp149 tracks (dbSNP b149) for hg19 and hg38. refs #18330 Pipeline tweaks: - doDbSnp.pl: separate the fasta part of the translate step into its own step catFasta so that repeating the translate step doesn't waste time on unchanging fasta. - snpNcbiToUcsc: - Turn phys_pos_from mismatch from error into warning if on Un/random/alt -- dbSNP seems to be using real-chrom coords for some of these (patch placements??) - Some insertions are now coming up with ncbiStart==ncbiEnd (the base to the left of the insertion) instead of the old ncbiEnd = ncbiStart+1 2-base range; accept those instead of erroring out.
• src/hg/utils/automation/makePushQSql.pl
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    dc25e3fec2c61b58e296023dc63ec8b48daac29d Tue Mar 21 09:49:56 2017 -0700
    adding db to table names refs #17545
• src/hg/utils/automation/makefile
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    57c6f2c734ab1bcd357cc1b673b14aeb8770767d Mon Mar 20 14:46:47 2017 -0700
    update assHub script file list refs #13553
• src/htslib/knetfile.c
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
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    4fdbee9b0b51fa1a9d8da8e366a27e9abf306b80 Wed Mar 22 16:00:15 2017 -0700
    too much hassle to bother with for now. needs code from kent stuff.
• src/inc/common.h
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
• src/inc/https.h
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
• src/inc/net.h
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
• src/lib/common.c
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
• src/lib/https.c
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
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    cfd72459cd19002cba98f593d9e83003b64ad1ea Wed Mar 22 18:19:22 2017 -0700
    fixing compiler complaints.
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    0af1ab08a87d41f37c7e04185be43abd55c1c8de Wed Mar 22 18:27:16 2017 -0700
    just for improved consistency
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    10ed5851072ff7a4c8ab8021f0baa1dd578feef4 Thu Mar 23 22:56:06 2017 -0700
    added logProxy=on setting to hg.conf to help confirm that the proxy is actually doing the expected thing. Not meant to be left on in production. refs #19124
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    4d7dee6cf2f288286da304fb82d4f379cc45c5b1 Thu Mar 23 23:36:08 2017 -0700
    avoid errAbort in https.c
• src/lib/net.c
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
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    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
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    10ed5851072ff7a4c8ab8021f0baa1dd578feef4 Thu Mar 23 22:56:06 2017 -0700
    added logProxy=on setting to hg.conf to help confirm that the proxy is actually doing the expected thing. Not meant to be left on in production. refs #19124
• src/product/README.proxy
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    3b7af84b7d8ebe9d30811103accd61584add9d9a Sun Mar 19 22:24:29 2017 -0700
    Initial check-in of proxy stuff. Added support for https_proxy for configuring https proxy. Added no_proxy for configuring domain suffixes which should be excluded from proxying. src/product/README.proxy updated. There are probably some documentation pages that will still need updating.
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    417d09f28ac6349b73cbde88a4379962d195fec9 Wed Mar 22 15:28:58 2017 -0700
    fixing some minor details for no_proxy.
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    631c995e82e53c5413caa7c0bf47be4c49162137 Wed Mar 22 17:08:10 2017 -0700
    Documentation changes to add new proxy settings. refs #19124
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    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
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    10ed5851072ff7a4c8ab8021f0baa1dd578feef4 Thu Mar 23 22:56:06 2017 -0700
    added logProxy=on setting to hg.conf to help confirm that the proxy is actually doing the expected thing. Not meant to be left on in production. refs #19124
• src/product/README.txt
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/ex.hg.conf
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    631c995e82e53c5413caa7c0bf47be4c49162137 Wed Mar 22 17:08:10 2017 -0700
    Documentation changes to add new proxy settings. refs #19124
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    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
• src/product/installer/README.md
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/installer/staticPage.html
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/mirrorDocs/makefile
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/mirrorDocs/staticPage.html
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/mirrorDocs/staticPage.lua
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    77a479f336905a0215cac7278ea32370a70c82a8 Thu Mar 23 15:58:38 2017 -0700
    Modifying html writers to use new static doc style and updating the appropriate gbic and mirror pages to bring them up to the new style. Also got the markdown formatted files in line with the html since they had become out of sync.
• src/product/mirrorManual.txt
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    631c995e82e53c5413caa7c0bf47be4c49162137 Wed Mar 22 17:08:10 2017 -0700
    Documentation changes to add new proxy settings. refs #19124
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    36071edc0403574d51170357bab076e39d076826 Thu Mar 23 16:42:09 2017 -0700
    Adds ftp proxy capability to system. Works with Squid 3.5 ftp_port at least. refs #19124
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    10ed5851072ff7a4c8ab8021f0baa1dd578feef4 Thu Mar 23 22:56:06 2017 -0700
    added logProxy=on setting to hg.conf to help confirm that the proxy is actually doing the expected thing. Not meant to be left on in production. refs #19124
• src/utils/qa/weeklybld/buildEnv.csh
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    d88ed49afc8a2ccbd24afa9c52d5854bca03686c Mon Mar 27 09:58:23 2017 -0700
    v347 preview2 refs #18964

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