All File Changes

v341_base to v342_preview (2016-11-07 to 2016-11-14) v342

• README
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
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    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 1, context: html, text, full: html, text
    0b80133a4247fe337090f0d92b0b4d5550a72690 Tue Nov 8 11:22:17 2016 -0800
    Adding Content-Length: tag to http header. Seems it is required for udc and hence track hubs to work.
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    4ec7a642d90b0877ff26c2ba48f9f97adc833925 Tue Nov 8 13:31:31 2016 -0800
    Adding support for jpg and pdf Content-type.
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
  • lines changed 56, context: html, text, full: html, text
    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
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    9c1d574ebfc2eba73c7999133e8462684cf1223a Tue Nov 8 12:19:24 2016 -0800
    Renaming printMatchingStanzas to cdwPrintMatchingStanzas, putting declaration of it in inc/cdwLib.h.
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
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    fc3ea13605d209284b5c555b51f2e7b150d83597 Wed Nov 2 18:06:56 2016 -0700
    Refactoring code to be shorter in the ignored formats, and adding text and html to the ignored list
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 22, context: html, text, full: html, text
    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
  • lines changed 22, context: html, text, full: html, text
    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
  • lines changed 231, context: html, text, full: html, text
    a8fff85a54441b2e938c2202005abd6633f58c10 Thu Nov 10 22:21:29 2016 -0800
    CIRM: adding vcf option to cdwSummary
  • lines changed 26, context: html, text, full: html, text
    9b2ed714d434316bc052e4473fd52c7f77516468 Fri Nov 11 00:50:53 2016 -0800
    CIRM: fixing merge conflict in cdwSummary
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 53, context: html, text, full: html, text
    39776a6084cfea5605f90b053a066e7458c6b16a Tue Nov 8 11:24:03 2016 -0800
    Fixing it so that links to genome browser and direct html and pdf file browse links go through cdwGetFile rather than using the now nonexisting link to htdocs/cdw. This fixes bugs that resulted from removing that link, which we needed to do for security reasons.
  • lines changed 1, context: html, text, full: html, text
    9c1d574ebfc2eba73c7999133e8462684cf1223a Tue Nov 8 12:19:24 2016 -0800
    Renaming printMatchingStanzas to cdwPrintMatchingStanzas, putting declaration of it in inc/cdwLib.h.
  • lines changed 1, context: html, text, full: html, text
    fddc333f0f9c9248f037747a980d60d1474bfcc5 Tue Nov 8 12:20:10 2016 -0800
    Bumping version number.
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
  • lines changed 13, context: html, text, full: html, text
    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 5, context: html, text, full: html, text
    9521430396e78ea99f63258a1d399b5343870acc Mon Nov 7 14:25:34 2016 -0800
    Starting to document version changes in web site.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    9c1d574ebfc2eba73c7999133e8462684cf1223a Tue Nov 8 12:19:24 2016 -0800
    Renaming printMatchingStanzas to cdwPrintMatchingStanzas, putting declaration of it in inc/cdwLib.h.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 1, context: html, text, full: html, text
    9c1d574ebfc2eba73c7999133e8462684cf1223a Tue Nov 8 12:19:24 2016 -0800
    Renaming printMatchingStanzas to cdwPrintMatchingStanzas, putting declaration of it in inc/cdwLib.h.
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    e367d1148b0c1c61e6881a2d1e9d9684421c1a0b Wed Nov 9 15:23:09 2016 -0800
    Eliminating a crash on old files that didn't validate by adding a null check.
• src/hg/hgGtexTrackSettings/README.txt
  • lines changed 56, context: html, text, full: html, text
    1707e42ef82fc3d38811178598bc3e0b31e0b794 Thu Oct 20 11:43:29 2016 -0700
    Draft 4 illustration export, with post-processing as in hgGtexTrackSettings/README.txt. refs #17369
  • lines changed 3, context: html, text, full: html, text
    f9cbf216c6f273ff4403779d1fe40c5605c5f7f4 Thu Oct 20 17:00:48 2016 -0700
    More SVG cleanup. refs #17369
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    ead07b2aa201b1b7dbc812dd98ef155e1714f23c Tue Oct 25 14:19:32 2016 -0700
    Draft 05 from Jeff West, with corrections found during animation of Draft 04. Exported and post-processed as described in hgGtexTrackSettings/README.txt. refs #17369
  • lines changed 4, context: html, text, full: html, text
    194a6dd93807d0100740f324e6a3fe5837847199 Tue Oct 25 16:57:20 2016 -0700
    Correct id problems in draft 5. refs #17369
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    f380603812bf58efc0b6314f1a61b55416a758b0 Wed Oct 26 15:44:07 2016 -0700
    Fade out leader line color, as we are now keeping visible (not just on mouseover). refs #17369
  • lines changed 1, context: html, text, full: html, text
    d4a2892366004d7f58c232ab93bd46c37bc95e0d Thu Nov 3 16:09:58 2016 -0700
    Tweak SVG processing. refs #17369
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    4282fb2d1cb60a12f8b70a9c9524d92828a485df Sat Nov 12 17:23:24 2016 -0800
    Fix truncated label by widening viewport. refs #17369
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    c83b730a18186bcddc4fe008a48317ac577d9bde Sat Nov 12 20:17:41 2016 -0800
    Fix twitchy highlights. refs #17369
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 110, context: html, text, full: html, text
    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • lines changed 4, context: html, text, full: html, text
    cbbb309fcbc6b5a8709f42c8ace1280f1a2c3cd3 Tue Oct 4 14:08:18 2016 -0700
    Support JWest page design w/o banner. Per JK suggestion reviewing GTEx track settings page with body map. refs #17639
  • lines changed 54, context: html, text, full: html, text
    38fe0330488867c168c817169bbf1c49806c5cfb Fri Oct 7 15:32:40 2016 -0700
    Move tissue table to code for flexibility/maintenance. refs #17369
  • lines changed 24, context: html, text, full: html, text
    624776f628c3257193e39187f02b5624d3b58b53 Mon Oct 17 16:36:51 2016 -0700
    Add track description. refs #17369
  • lines changed 9, context: html, text, full: html, text
    8658c9d49e2b66327b4bfcdb39cbf39c35cb8903 Mon Oct 17 18:33:55 2016 -0700
    Add navigation to track description and back to top. refs #17369
  • lines changed 14, context: html, text, full: html, text
    4d1bafe4de39413f4ab1a9cd7183c64655b01e0a Mon Oct 24 14:59:31 2016 -0700
    Temporarily hardcode hg19 for review purposes. refs #17369
  • lines changed 288, context: html, text, full: html, text
    cfed2e78dcef652dc85360454f81d7558aa1b678 Thu Oct 27 18:05:04 2016 -0700
    Implement config panel cart vars. Moved from .html mockup to C code. refs #17369
  • lines changed 7, context: html, text, full: html, text
    578933212e6c900f4cda77f4d9cd1e7d01b9ace1 Thu Nov 3 16:09:25 2016 -0700
    Initialize tissues from cart. refs #17369
  • lines changed 7, context: html, text, full: html, text
    11db7ea49d8fb79b428a1add7e21ace39c7aac73 Thu Nov 3 16:46:29 2016 -0700
    Get score filter form cart. refs #17369
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    9a3d804d4836f8508ed10a5372e3cc50c4c5ff64 Thu Nov 3 20:50:16 2016 -0700
    Finish connection to hgTracks; create form and submit button, and get tissues into cart. refs #17369
  • lines changed 4, context: html, text, full: html, text
    4275e302d217370b4eb756d45842f03e1ada9ae1 Tue Nov 8 11:50:38 2016 -0800
    Changes to colorPatch in tissue table to better distinguish selected tissues: switch to white patch with tissue color border. Also fix to problem with select/deselect of tissues from SVG. refs #17369
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
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    58f75643f74cae771b15e359a322a4bb93933f60 Sat Nov 12 20:18:10 2016 -0800
    Fix double label. refs #17369
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html
  • lines changed 184, context: html, text, full: html, text
    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • lines changed 8, context: html, text, full: html, text
    cbbb309fcbc6b5a8709f42c8ace1280f1a2c3cd3 Tue Oct 4 14:08:18 2016 -0700
    Support JWest page design w/o banner. Per JK suggestion reviewing GTEx track settings page with body map. refs #17639
  • lines changed 88, context: html, text, full: html, text
    135c5c06f4aa65c8d660b621f682ef88559c5f59 Thu Oct 6 14:19:39 2016 -0700
    Improvements to visual layout of tissue table, using design from Jeff West (DRAFT03c_BodyMapBrowserPage.pdf). refs #17639
  • lines changed 4, context: html, text, full: html, text
    1b6890714b9e09a3cba18068f5e3b726484548b1 Thu Oct 6 16:03:13 2016 -0700
    Crop whitespace and remove cruft from illustration. Related layout tweaks. refs #17369
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    89de213f460f60dcc7fcf7d6e0370401d7c3ed25 Thu Oct 6 16:37:33 2016 -0700
    More small layout tweaks. refs #17369
  • lines changed 88, context: html, text, full: html, text
    38fe0330488867c168c817169bbf1c49806c5cfb Fri Oct 7 15:32:40 2016 -0700
    Move tissue table to code for flexibility/maintenance. refs #17369
  • lines changed 2, context: html, text, full: html, text
    ea41056f39eb940ef5ce1ad4e83512e2550bb647 Sat Oct 8 16:43:44 2016 -0700
    First steps to animage tissue selection panel that includes bodymap and table. Hover and click over tissue names and set all/clear all mostly working. Also some corrections to svg (missing colon sub-tissues, oddity in aorta id naming). refs 17369
  • lines changed 2, context: html, text, full: html, text
    def53e877b0ec5eaa779e540bd0568c10104688e Mon Oct 10 10:18:11 2016 -0700
    Remove search box. Would require significant work to implement and adds little value. refs #17369
  • lines changed 1, context: html, text, full: html, text
    16a124688058c010d943b185944e5ae795583b43 Mon Oct 10 13:27:06 2016 -0700
    Header change, suggested by Cath. refs #17369
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    1a8f6f1c1791b0d2b48bbea782cd7ee390159418 Mon Oct 10 18:23:09 2016 -0700
    More streamlining, for Cath's review. #17369
  • lines changed 4, context: html, text, full: html, text
    3813a7e3eea7f27539bc67db740579af4b4806ac Mon Oct 10 18:48:01 2016 -0700
    Add sub-panel labels as per Cath suggestion. Early commit (not yet complete). refs #17639
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    918bf07cb0a69e5a45192639b6d868cc056e494b Tue Oct 11 12:18:14 2016 -0700
    Layout with panel labels for body map and tissue table, as per Cath suggestion. refs #17369
  • lines changed 54, context: html, text, full: html, text
    fbccbe8c3660e3021e5e9d5e1418de0ab81766b4 Mon Oct 17 14:41:41 2016 -0700
    Another layout. Moves config into side panel. Preferred by Cath and Jeff W. refs #17369
  • lines changed 9, context: html, text, full: html, text
    8658c9d49e2b66327b4bfcdb39cbf39c35cb8903 Mon Oct 17 18:33:55 2016 -0700
    Add navigation to track description and back to top. refs #17369
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    8ff13070d2da7a7b709da2bbb8c1043d99ecd8c9 Thu Oct 20 12:33:07 2016 -0700
    Style tweaks. refs #17369
• src/hg/hgGtexTrackSettings/makefile
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    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • lines changed 9, context: html, text, full: html, text
    cfed2e78dcef652dc85360454f81d7558aa1b678 Thu Oct 27 18:05:04 2016 -0700
    Implement config panel cart vars. Moved from .html mockup to C code. refs #17369
• src/hg/hgTables/bam.c
  • lines changed 3, context: html, text, full: html, text
    7bc26524a7cd5a31d65b7a092f8ae0d835710efc Mon Nov 7 16:30:52 2016 -0800
    Fixes #18300. Added a missing popAbortHandler in cart.c. Trying to deal with early warnings in hgTables. In our current code, early warnings do not actually work -- instead they usually just produce a duplicate page header. But early aborts do work. So we have decided to convert the hgTables resource output exceeded warnings to errAbort.
• src/hg/hgTables/longRange.c
  • lines changed 3, context: html, text, full: html, text
    7bc26524a7cd5a31d65b7a092f8ae0d835710efc Mon Nov 7 16:30:52 2016 -0800
    Fixes #18300. Added a missing popAbortHandler in cart.c. Trying to deal with early warnings in hgTables. In our current code, early warnings do not actually work -- instead they usually just produce a duplicate page header. But early aborts do work. So we have decided to convert the hgTables resource output exceeded warnings to errAbort.
• src/hg/hgTables/vcf.c
  • lines changed 3, context: html, text, full: html, text
    7bc26524a7cd5a31d65b7a092f8ae0d835710efc Mon Nov 7 16:30:52 2016 -0800
    Fixes #18300. Added a missing popAbortHandler in cart.c. Trying to deal with early warnings in hgTables. In our current code, early warnings do not actually work -- instead they usually just produce a duplicate page header. But early aborts do work. So we have decided to convert the hgTables resource output exceeded warnings to errAbort.
• src/hg/hgTables/wiggle.c
  • lines changed 1, context: html, text, full: html, text
    7bc26524a7cd5a31d65b7a092f8ae0d835710efc Mon Nov 7 16:30:52 2016 -0800
    Fixes #18300. Added a missing popAbortHandler in cart.c. Trying to deal with early warnings in hgTables. In our current code, early warnings do not actually work -- instead they usually just produce a duplicate page header. But early aborts do work. So we have decided to convert the hgTables resource output exceeded warnings to errAbort.
• src/hg/hgTracks/cds.c
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    96f933be7215c92173bbf2dbb8dc1cedbe23b1c1 Wed Nov 9 11:36:42 2016 -0800
    Fixing buffer overflow with bigger buffer, refs #18369
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    46cde8738a468e47a7d39a988dde632eb533aca2 Thu Nov 3 17:22:33 2016 -0700
    Hook new GTEx body map track settings in to browser, in place of hgTrackUi. refs #17369
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    9e064b7c08551b56508ae9f7e0b0573d7be7101b Tue Nov 8 11:03:09 2016 -0800
    adding keyboard shortcuts for zoom to x bp, no redmine. This message was approved by cmalee and mspeir
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    66e096cba6f2b2da5feaf6fd270f74da61ab64b6 Thu Nov 10 16:17:17 2016 -0800
    Add hg.conf setting to enable new GTEx trackUI. For removal when new CGI is fully released. refs #17369
• src/hg/hgTracks/simpleTracks.c
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    7f51a5729d96af40876b1639eccfa57eaa96c72b Thu Nov 10 13:55:58 2016 -0800
    Turning codon numbers on by default for GenePred tracks, refs #15459
• src/hg/hgTracks/snakeTrack.c
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    49d55b9f5352a988c08588424eb2e256cbb301a7 Thu Nov 10 15:33:48 2016 -0800
    allow chrom trix file index to change chr names from hal file into chr names in ucsc browser refs #13553
• src/hg/hgVai/hgVai.c
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/htdocs/goldenPath/credits.html
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    9ee3d539cc378fbb1864bfcf7defe26bad2bd272 Mon Nov 7 14:27:09 2016 -0800
    edits to credits.html per refs #18347
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    ef9f61894b551c92a60be79c27bd371114ad17aa Mon Nov 7 14:42:19 2016 -0800
    adding changes to credits.html per refs #18347
• src/hg/htdocs/goldenPath/newsarch.html
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    72da8bf1ec6a9946062a974396a0fe277e992106 Mon Nov 7 16:38:46 2016 -0800
    Staging crispr announcement, refs #17235
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    ccb2e7d6fc99b36e9f5c0ffd7c68c9c3c678f7ad Tue Nov 8 07:19:55 2016 -0800
    Fixing typo in crispr announcement, refs #17235
• src/hg/htdocs/images/bodyMap.svg
  • lines changed 977, context: html, text, full: html, text
    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • lines changed 1331, context: html, text, full: html, text
    1b6890714b9e09a3cba18068f5e3b726484548b1 Thu Oct 6 16:03:13 2016 -0700
    Crop whitespace and remove cruft from illustration. Related layout tweaks. refs #17369
  • lines changed 116, context: html, text, full: html, text
    d702c482f45bd3f97716f555bdf11caef9491252 Fri Oct 7 10:06:28 2016 -0700
    Added ids and font list. refs #17369
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    ea41056f39eb940ef5ce1ad4e83512e2550bb647 Sat Oct 8 16:43:44 2016 -0700
    First steps to animage tissue selection panel that includes bodymap and table. Hover and click over tissue names and set all/clear all mostly working. Also some corrections to svg (missing colon sub-tissues, oddity in aorta id naming). refs 17369
  • lines changed 2589, context: html, text, full: html, text
    1707e42ef82fc3d38811178598bc3e0b31e0b794 Thu Oct 20 11:43:29 2016 -0700
    Draft 4 illustration export, with post-processing as in hgGtexTrackSettings/README.txt. refs #17369
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    9da293adea7360f6521ce9e6d07317aa038d3c32 Thu Oct 20 11:44:22 2016 -0700
    Corrections to ID's (some mis-spellings, some missing ids). Jeff W notified so he can incorporate in his original. refs #17369
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    bb14db8215e66c2848385af6442f6e76dcb13f9f Thu Oct 20 13:56:22 2016 -0700
    1. Fix some identifier naming errors (notified Jeff). Tweaked fonts to match GB (revisit this later). refs #17369
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    a812abb853ad86bf636d934f1394c2473735cc6f Thu Oct 20 17:01:26 2016 -0700
    More SVG cleanup. refs #17369
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    ead07b2aa201b1b7dbc812dd98ef155e1714f23c Tue Oct 25 14:19:32 2016 -0700
    Draft 05 from Jeff West, with corrections found during animation of Draft 04. Exported and post-processed as described in hgGtexTrackSettings/README.txt. refs #17369
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    359363b36f72d88528e47cb067935b61e964e23f Tue Oct 25 16:56:00 2016 -0700
    Correct id problems in draft 5. refs #17369
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    f380603812bf58efc0b6314f1a61b55416a758b0 Wed Oct 26 15:44:07 2016 -0700
    Fade out leader line color, as we are now keeping visible (not just on mouseover). refs #17369
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    4282fb2d1cb60a12f8b70a9c9524d92828a485df Sat Nov 12 17:23:24 2016 -0800
    Fix truncated label by widening viewport. refs #17369
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    c83b730a18186bcddc4fe008a48317ac577d9bde Sat Nov 12 20:17:41 2016 -0800
    Fix twitchy highlights. refs #17369
• src/hg/htdocs/indexNews.html
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    72da8bf1ec6a9946062a974396a0fe277e992106 Mon Nov 7 16:38:46 2016 -0800
    Staging crispr announcement, refs #17235
• src/hg/htdocs/style/hgGtexTrackSettings.css
  • lines changed 166, context: html, text, full: html, text
    771b3b9d95995491d03e9d543609ac5e3e3f4bfd Thu Oct 6 12:30:33 2016 -0700
    Add UCSC logo to menu bar. Improve appearance (layout, margins). CSS/HTML cleanup to follow. refs #17369
  • lines changed 19, context: html, text, full: html, text
    135c5c06f4aa65c8d660b621f682ef88559c5f59 Thu Oct 6 14:19:39 2016 -0700
    Improvements to visual layout of tissue table, using design from Jeff West (DRAFT03c_BodyMapBrowserPage.pdf). refs #17639
  • lines changed 10, context: html, text, full: html, text
    1b6890714b9e09a3cba18068f5e3b726484548b1 Thu Oct 6 16:03:13 2016 -0700
    Crop whitespace and remove cruft from illustration. Related layout tweaks. refs #17369
  • lines changed 3, context: html, text, full: html, text
    89de213f460f60dcc7fcf7d6e0370401d7c3ed25 Thu Oct 6 16:37:33 2016 -0700
    More small layout tweaks. refs #17369
  • lines changed 21, context: html, text, full: html, text
    ea41056f39eb940ef5ce1ad4e83512e2550bb647 Sat Oct 8 16:43:44 2016 -0700
    First steps to animage tissue selection panel that includes bodymap and table. Hover and click over tissue names and set all/clear all mostly working. Also some corrections to svg (missing colon sub-tissues, oddity in aorta id naming). refs 17369
  • lines changed 15, context: html, text, full: html, text
    453c5a463c5d2c1dcd85cf018c7c8912a48a28b8 Tue Oct 11 11:38:29 2016 -0700
    Layout tweaks, input from Cath. refs #17369
  • lines changed 12, context: html, text, full: html, text
    a8eae0028b061e668072852bbc0fe2072f34229a Tue Oct 11 12:22:42 2016 -0700
    Layout with panel labels for body map and tissue table, as per Cath suggestion. refs #17369
  • lines changed 31, context: html, text, full: html, text
    fbccbe8c3660e3021e5e9d5e1418de0ab81766b4 Mon Oct 17 14:41:41 2016 -0700
    Another layout. Moves config into side panel. Preferred by Cath and Jeff W. refs #17369
  • lines changed 31, context: html, text, full: html, text
    624776f628c3257193e39187f02b5624d3b58b53 Mon Oct 17 16:36:51 2016 -0700
    Add track description. refs #17369
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    13b15ae7d313d66a036d1e291796178f9d79e888 Mon Oct 17 16:39:14 2016 -0700
    Change hg19 'badge' to look as on Gateway page. refs #17369
  • lines changed 22, context: html, text, full: html, text
    8658c9d49e2b66327b4bfcdb39cbf39c35cb8903 Mon Oct 17 18:33:55 2016 -0700
    Add navigation to track description and back to top. refs #17369
  • lines changed 5, context: html, text, full: html, text
    8ff13070d2da7a7b709da2bbb8c1043d99ecd8c9 Thu Oct 20 12:33:07 2016 -0700
    Style tweaks. refs #17369
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    e04944e2ed12d0ad5a722755bb9a7fd0f2a3ba2d Thu Oct 20 17:02:39 2016 -0700
    Click handling on individual tissues and set all/clear all now works with DRAFT 04. refs #17369
  • lines changed 4, context: html, text, full: html, text
    b1b6338b01cffb734c6e1694f7120855d024c0fa Wed Oct 26 15:37:55 2016 -0700
    Display tweaks; 1. Leader lines visible always, highlighted on mouseover (JK request). Border highlights on tissue table color patches on mouseover. refs #17369
  • lines changed 2, context: html, text, full: html, text
    9a3d804d4836f8508ed10a5372e3cc50c4c5ff64 Thu Nov 3 20:50:16 2016 -0700
    Finish connection to hgTracks; create form and submit button, and get tissues into cart. refs #17369
  • lines changed 6, context: html, text, full: html, text
    4275e302d217370b4eb756d45842f03e1ada9ae1 Tue Nov 8 11:50:38 2016 -0800
    Changes to colorPatch in tissue table to better distinguish selected tissues: switch to white patch with tissue color border. Also fix to problem with select/deselect of tissues from SVG. refs #17369
  • lines changed 5, context: html, text, full: html, text
    ad2c455833e131ab3fcfb22889803e88f6cadb96 Wed Nov 9 17:03:34 2016 -0800
    Major JS code cleanup and refactor. Also fixed some event handling. refs #17369
• src/hg/htdocs/style/makefile
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    771b3b9d95995491d03e9d543609ac5e3e3f4bfd Thu Oct 6 12:30:33 2016 -0700
    Add UCSC logo to menu bar. Improve appearance (layout, margins). CSS/HTML cleanup to follow. refs #17369
• src/hg/htdocs/training/index.html
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    e77a663fadc3e405fb362e8511a515ddd8ef094e Thu Nov 10 14:11:03 2016 -0800
    removed completed workshop. added petter link to PAG workshop
• src/hg/inc/cart.h
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    578933212e6c900f4cda77f4d9cd1e7d01b9ace1 Thu Nov 3 16:09:25 2016 -0700
    Initialize tissues from cart. refs #17369
• src/hg/inc/hAnno.h
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/inc/hui.h
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
• src/hg/inc/pgSnp.h
  • lines changed 3, context: html, text, full: html, text
    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/inc/variant.h
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/inc/web.h
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    cbbb309fcbc6b5a8709f42c8ace1280f1a2c3cd3 Tue Oct 4 14:08:18 2016 -0700
    Support JWest page design w/o banner. Per JK suggestion reviewing GTEx track settings page with body map. refs #17639
• src/hg/js/hgGtexTrackSettings.js
  • lines changed 22, context: html, text, full: html, text
    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • lines changed 135, context: html, text, full: html, text
    ea41056f39eb940ef5ce1ad4e83512e2550bb647 Sat Oct 8 16:43:44 2016 -0700
    First steps to animage tissue selection panel that includes bodymap and table. Hover and click over tissue names and set all/clear all mostly working. Also some corrections to svg (missing colon sub-tissues, oddity in aorta id naming). refs 17369
  • lines changed 35, context: html, text, full: html, text
    a0901833881cdac3b2d194b91ccbfa484bac3df0 Sat Oct 8 17:12:14 2016 -0700
    Animate arteryAorta example mouseover ( leader line and white outline on hover ) . refs #17369
  • lines changed 58, context: html, text, full: html, text
    03728506f98789fc4375911a2e3726f1c61d297d Sat Oct 8 22:44:12 2016 -0700
    Add hover and click handling to bodyMap. Rough cut code for usability review. refs #17369
  • lines changed 85, context: html, text, full: html, text
    e04944e2ed12d0ad5a722755bb9a7fd0f2a3ba2d Thu Oct 20 17:02:39 2016 -0700
    Click handling on individual tissues and set all/clear all now works with DRAFT 04. refs #17369
  • lines changed 24, context: html, text, full: html, text
    4830cdd0baa82503411b2c3e2828cd65b6704c73 Thu Oct 20 17:53:30 2016 -0700
    Mouseover to highlight tissues on DRAFT 04 bodyMap largely working. Some tissues aren't popping up properly and tissue table not yet connected up fully. refs #17369
  • lines changed 11, context: html, text, full: html, text
    ae9a65f97412a6522e2e3ff4c5884895375ca5f2 Fri Oct 21 11:14:00 2016 -0700
    Fixes to click handling. refs #17369
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    ced6299cd30cba4ed8cde8b4765bbf08147613f9 Fri Oct 21 11:24:22 2016 -0700
    Mouseover tissue table now highlights organs in bodymap. refs #17369
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    b05548d6d1608de50964509c1185497bf4192b97 Mon Oct 24 14:56:06 2016 -0700
    Add hover event handler to tissue shapes. refs #17369
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    8a64798246e9ce75f8ce7c350096ef2f0c6532f6 Tue Oct 25 16:57:02 2016 -0700
    Improve mouseover viz. Draw tissue and highlight last so they pop to top. refs #17369
  • lines changed 54, context: html, text, full: html, text
    b1b6338b01cffb734c6e1694f7120855d024c0fa Wed Oct 26 15:37:55 2016 -0700
    Display tweaks; 1. Leader lines visible always, highlighted on mouseover (JK request). Border highlights on tissue table color patches on mouseover. refs #17369
  • lines changed 15, context: html, text, full: html, text
    578933212e6c900f4cda77f4d9cd1e7d01b9ace1 Thu Nov 3 16:09:25 2016 -0700
    Initialize tissues from cart. refs #17369
  • lines changed 20, context: html, text, full: html, text
    9a3d804d4836f8508ed10a5372e3cc50c4c5ff64 Thu Nov 3 20:50:16 2016 -0700
    Finish connection to hgTracks; create form and submit button, and get tissues into cart. refs #17369
  • lines changed 28, context: html, text, full: html, text
    4275e302d217370b4eb756d45842f03e1ada9ae1 Tue Nov 8 11:50:38 2016 -0800
    Changes to colorPatch in tissue table to better distinguish selected tissues: switch to white patch with tissue color border. Also fix to problem with select/deselect of tissues from SVG. refs #17369
  • lines changed 54, context: html, text, full: html, text
    f3e281ea29cd25805890d53e0cdba63e4ab55f3c Tue Nov 8 16:29:58 2016 -0800
    First round code cleanup. refs #17369
  • lines changed 304, context: html, text, full: html, text
    ad2c455833e131ab3fcfb22889803e88f6cadb96 Wed Nov 9 17:03:34 2016 -0800
    Major JS code cleanup and refactor. Also fixed some event handling. refs #17369
  • lines changed 6, context: html, text, full: html, text
    94ae7e1c166c598a2e7ea7659eff36efd332fbfe Wed Nov 9 17:09:23 2016 -0800
    Prune long lines. refs #17369
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    c83b730a18186bcddc4fe008a48317ac577d9bde Sat Nov 12 20:17:41 2016 -0800
    Fix twitchy highlights. refs #17369
• src/hg/js/hgTracks.js
  • lines changed 11, context: html, text, full: html, text
    9e064b7c08551b56508ae9f7e0b0573d7be7101b Tue Nov 8 11:03:09 2016 -0800
    adding keyboard shortcuts for zoom to x bp, no redmine. This message was approved by cmalee and mspeir
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    7a900c00cc6f3f7bc046dac0f6c8432394c8a43d Tue Nov 8 16:08:24 2016 -0800
    fix to zoom shortcuts for multi-exon mode, refs #18367
• src/hg/js/makefile
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    280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700
    First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
• src/hg/lib/annoFormatVep.c
  • lines changed 26, context: html, text, full: html, text
    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/annoGratorGpVar.c
  • lines changed 12, context: html, text, full: html, text
    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/cart.c
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    578933212e6c900f4cda77f4d9cd1e7d01b9ace1 Thu Nov 3 16:09:25 2016 -0700
    Initialize tissues from cart. refs #17369
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    7bc26524a7cd5a31d65b7a092f8ae0d835710efc Mon Nov 7 16:30:52 2016 -0800
    Fixes #18300. Added a missing popAbortHandler in cart.c. Trying to deal with early warnings in hgTables. In our current code, early warnings do not actually work -- instead they usually just produce a duplicate page header. But early aborts do work. So we have decided to convert the hgTables resource output exceeded warnings to errAbort.
• src/hg/lib/customTrack.c
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/gpFx.c
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    07db8c7cc0e21b21c49d9d37502e12101e54b22d Fri Nov 11 20:10:36 2016 +0000
    Don't errAbort if an exon edge is not an exon-intron junction but instead an exon-exon junction -- i.e. an alignment gap for a deletion in the reference. The ideal way to annotate an insertion where the reference has a deletion is an open question.
• src/hg/lib/gtexUi.c
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
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    78d777539cda826871e6b60e9287536f9f5879f1 Sat Nov 12 20:05:15 2016 -0800
    Tweak layout of track controls. refs #17369
• src/hg/lib/hAnno.c
  • lines changed 37, context: html, text, full: html, text
    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    7f51a5729d96af40876b1639eccfa57eaa96c72b Thu Nov 10 13:55:58 2016 -0800
    Turning codon numbers on by default for GenePred tracks, refs #15459
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    2088631197bdc3d5cd878dc3fe923aacde1f6b08 Thu Nov 10 14:31:49 2016 -0800
    fix problem introduced by XSS changes
• src/hg/lib/jWestBanner.html
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
• src/hg/lib/jWestHeader.html
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
• src/hg/lib/makefile
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    6ee08e1c05fbac92e545429f446d75b441c6c370 Thu Nov 3 12:55:15 2016 -0700
    Fixing dependency so web.o is rebuilt when jWestBanner.h is rebuilt.
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
• src/hg/lib/pgSnp.c
  • lines changed 22, context: html, text, full: html, text
    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/trackHub.c
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    9a685f7b0fde1b55268aadea67906197c9bacb19 Tue Nov 8 10:51:16 2016 -0800
    allowing hub+genomes+trackDb all in the hub.txt file for track hubs. I am just me, but BrianR and Hiram have approved this message. No redmine.
• src/hg/lib/variant.c
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/hg/lib/web.c
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    cbbb309fcbc6b5a8709f42c8ace1280f1a2c3cd3 Tue Oct 4 14:08:18 2016 -0700
    Support JWest page design w/o banner. Per JK suggestion reviewing GTEx track settings page with body map. refs #17639
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    5ab325050856f28fa3ed1a297afb5a22d49a51c7 Thu Oct 27 18:06:08 2016 -0700
    Fix extension to JWest-style shell. refs #17369
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    1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800
    Cleanup C code. refs #17369
• src/hg/makeDb/crisprTrack/convOffs.py
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
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    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/hg/makeDb/doc/gtex/V4.txt
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    ed22a783cddcbbf9ff41d2d939ee48ba5e5bd36f Mon Nov 7 10:04:38 2016 -0800
    Fix coord problem in experimental track. Thanks Angie for catching this. (But track is old (pilot) V4 so I will retire it in favor of a V6 version).
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
    cactus trackDb with chrom alias refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/rnaSeqData/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt
  • lines changed 287, context: html, text, full: html, text
    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
    adding rnaSeqData trackDb.txt files refs #13553
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    5ce805db07f699824d3050069a999128f52e1ea8 Tue Nov 8 14:39:02 2016 -0800
    updates from Ian for trackDb settings refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.cactus.trackDb.txt
  • lines changed 165, context: html, text, full: html, text
    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
    cactus trackDb with chrom alias refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/rnaSeqData/GCA_001624215.1_A_J_v1.trackDb.txt
  • lines changed 287, context: html, text, full: html, text
    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
    adding rnaSeqData trackDb.txt files refs #13553
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    5ce805db07f699824d3050069a999128f52e1ea8 Tue Nov 8 14:39:02 2016 -0800
    updates from Ian for trackDb settings refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.cactus.trackDb.txt
  • lines changed 165, context: html, text, full: html, text
    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
    cactus trackDb with chrom alias refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/rnaSeqData/GCA_001624295.1_AKR_J_v1.trackDb.txt
  • lines changed 77, context: html, text, full: html, text
    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
    adding rnaSeqData trackDb.txt files refs #13553
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    5ce805db07f699824d3050069a999128f52e1ea8 Tue Nov 8 14:39:02 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/rnaSeqData/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.cactus.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/rnaSeqData/GCA_001624475.1_CBA_J_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.cactus.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/rnaSeqData/GCA_001624505.1_DBA_2J_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.cactus.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/rnaSeqData/GCA_001624535.1_FVB_NJ_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.cactus.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/rnaSeqData/GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/rnaSeqData/GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.cactus.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/rnaSeqData/GCA_001624775.1_PWK_PhJ_v1.trackDb.txt
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• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/rnaSeqData/GCA_001624835.1_WSB_EiJ_v1.trackDb.txt
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/rnaSeqData/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/rnaSeqData/GCA_001632525.1_BALB_cJ_v1.trackDb.txt
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/rnaSeqData/GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/rnaSeqData/GCA_001632575.1_C3H_HeJ_v1.trackDb.txt
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.cactus.trackDb.txt
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    626f0e5be4bae57507e0a042b32bfd9e2cab64de Thu Nov 10 15:31:56 2016 -0800
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    11aa0192c56aff4a890c19e4b07b9494c2f64385 Mon Nov 7 13:22:29 2016 -0800
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    5ce805db07f699824d3050069a999128f52e1ea8 Tue Nov 8 14:39:02 2016 -0800
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• src/hg/makeDb/doc/mouseStrains/makefile
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    bf031e720df8cec4440ba118db350750c859e999 Tue Nov 8 14:41:46 2016 -0800
    install rules for rnaSeq data html and trackDb refs #13553
• src/hg/makeDb/doc/mouseStrains/rnaSeqStar.html
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    e7fddbd6a39275149867089aff1b927c709b1f5a Tue Nov 8 13:29:06 2016 -0800
    updated mouse strain START RNA-Seq track description
• src/hg/makeDb/trackDb/human/hg38/description.html
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    0a4bfd88ebde300a13a69c840a63ba1fb76508ac Thu Nov 10 11:26:02 2016 -0800
    Updating outdated link to genbank ftp site readme
• src/hg/makeDb/trackDb/human/trackDb.ra
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    726285f0411018a0a132b0ad85256cd05ea79740 Fri Nov 11 01:56:15 2016 -0800
    tweaking the clinvar track name a bit
• src/hg/makeDb/trackDb/mouse/mm10/mouseStrains.cactus.trackDb.ra
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    6e5118b8c0e6c06679404505a69f50d95cd72edd Thu Nov 10 16:12:43 2016 -0800
    adding mouse strains hal file refs #13553
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    15dd16e90158f2281b51f8b2874e56841c6cb44d Mon Nov 7 14:36:41 2016 -0800
    adding mouse SNPs from mouse strain comparison project refs #18305
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    6e5118b8c0e6c06679404505a69f50d95cd72edd Thu Nov 10 16:12:43 2016 -0800
    adding mouse strains hal file refs #13553
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra
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    df71d249dd0fcaaaf4d03c32f3265182cbc23584 Tue Nov 8 11:34:02 2016 -0800
    Hiding previous version of GENCODE Genes, VM9, on mm10, refs #18295
• src/hg/makeDb/trackDb/tagTypes.tab
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    e5892ec7dcef2c52f00f4983a23c23352d154d43 Thu Nov 10 15:40:47 2016 -0800
    adding halSnake to tagTypes refs #13553
• src/hg/makefile
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    d84f0465b2a1fb8b2ac9cd20f5202a5c0c8ce637 Mon Nov 7 09:59:19 2016 -0800
    Adding GTEx body map track settings CGI. refs #17369
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    190ba8082f1e7f99ab7ee3038b1b2eefb5791357 Thu Nov 10 17:26:32 2016 -0800
    Resolving merge conflicts
• src/hg/mouseStuff/chainCleaner/chainCleaner.c
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    b35995a8ba449a50f4a16131fe2e32edb27a3166 Thu Nov 10 10:48:06 2016 -0800
    update from Michael Hiller refs #17286
• src/hg/utils/automation/makefile
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
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    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
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    37608a22d891c5febb6c0dad94ef859258aea5b8 Mon Nov 7 16:24:09 2016 -0800
    add geneType and transcriptType to gtfToGenePred info output file
• src/hg/utils/gtfToGenePred/tests/expected/basic.info
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• src/hg/utils/gtfToGenePred/tests/expected/ensembl.info
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• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.info
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• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.info
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• src/hg/utils/gtfToGenePred/tests/expected/ignoreGroupWithoutExons.info
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• src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info
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• src/hg/utils/gtfToGenePred/tests/expected/srcPre.info
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• src/hg/utils/gtfToGenePred/tests/makefile
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    add geneType and transcriptType to gtfToGenePred info output file
• src/hg/utils/otto/clinvar/clinVarToBed
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    c388d3b08b827858adaf88bfbf47de558a2c2794 Fri Nov 11 00:46:06 2016 -0800
    fixing the clinvar parser again, info is spread over four files and fields have changed their meanings. no redmine yet.
• src/hg/utils/otto/clinvar/clinvar.as
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    c388d3b08b827858adaf88bfbf47de558a2c2794 Fri Nov 11 00:46:06 2016 -0800
    fixing the clinvar parser again, info is spread over four files and fields have changed their meanings. no redmine yet.
• src/hg/utils/vai.pl
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    b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700
    Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
• src/inc/common.mk
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    a3616feb00b8f200afb7379d2f8e5fa3107eebd1 Fri Nov 11 20:05:02 2016 +0000
    Add -lz after htslib -- without it, couldn't link on GBiB.
• src/inc/gff.h
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    37608a22d891c5febb6c0dad94ef859258aea5b8 Mon Nov 7 16:24:09 2016 -0800
    add geneType and transcriptType to gtfToGenePred info output file
• src/lib/gff.c
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    37608a22d891c5febb6c0dad94ef859258aea5b8 Mon Nov 7 16:24:09 2016 -0800
    add geneType and transcriptType to gtfToGenePred info output file
• src/lib/servcl.c
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    fe974de5e9ce0a6656ae862a851ff70967954a29 Fri Nov 11 18:42:01 2016 +0000
    Added env var JKTRASH so that when running on command line, trashDir can be something other than current directory.
• src/lib/udc.c
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
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    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
• src/product/installer/browserSetup.sh
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    c6961a123a07b21da18ad03045e4733b8f3496ac Tue Nov 8 14:42:07 2016 -0800
    adding goOnline to -f gbic mode, email from chmalee, no redmine
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    351524f39932ad70de5a3a5920a71e425531cfb6 Tue Nov 8 14:45:02 2016 -0800
    Reverting last (messed up) commit "adding goOnline to -f gbic mode, email from chmalee, no redmine" This reverts commit c6961a123a07b21da18ad03045e4733b8f3496ac.
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    de3b2529bc5088bc5904668fe8df77fe094c7b4c Tue Nov 8 14:53:08 2016 -0800
    fixing bug in gbic that forgot to go online with -f, email from chmalee
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    ce085e02ed3fe243f81020097ae3223bf5e3eff4 Wed Nov 9 15:53:07 2016 -0800
    adding addTools to gbic as suggested during genecats
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    444bb812892554802f588fdd08c9eeed31c67aea Wed Nov 9 17:05:26 2016 -0800
    fixing gbic docs a little more
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    f8e4ee48594ecaf00822d5f6cf05d9b49edd4923 Wed Nov 9 17:41:47 2016 -0800
    making sure we have wget in gbic
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    24559b24bec659aef90535e3d59022e4845b4b8e Wed Nov 9 19:25:15 2016 -0800
    making sure we have rsync in gbic
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    a171a8645402cca29ff90a17978ea12c74ad5f5f Wed Nov 9 21:19:32 2016 -0800
    skipping ENCODE PDF files in gbic
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    83705d755e68321c3d5f9d64f748f10010e4ea37 Wed Nov 9 21:34:13 2016 -0800
    fixing rsync command in gbic again
• src/utils/qa/weeklybld/buildEnv.csh
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    4e76008324cf928870ad31ff25872a28f5874e3b Mon Nov 14 10:11:18 2016 -0800
    v342 preview1 refs #18302

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• files changed: 248