All File Changes

v332_preview to v332_preview2 (2016-04-18 to 2016-05-25) v332

• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    c173c4bc7a378d2354e1547714cd3c8a168dc0e8 Sat Apr 23 01:11:57 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    75ccede9d0662fca731e8c9fc9b3e52222c048cd Wed Apr 20 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
  • lines changed 1, context: html, text, full: html, text
    d7c0e51d69967f69cf1f9e3582f8d19c78623975 Thu Apr 21 01:11:37 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    c173c4bc7a378d2354e1547714cd3c8a168dc0e8 Sat Apr 23 01:11:57 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwCheckDataset/cdwCheckDataset.c
  • lines changed 123, context: html, text, full: html, text
    919b34c597b0c501cea07a18de4a74428d5f5e8d Mon Apr 18 12:40:45 2016 -0700
    First draft of this program, it seems to be working well and this may be its final form, refs #17187
    
• src/hg/cirm/cdw/cdwCheckDataset/makefile
  • lines changed 4, context: html, text, full: html, text
    919b34c597b0c501cea07a18de4a74428d5f5e8d Mon Apr 18 12:40:45 2016 -0700
    First draft of this program, it seems to be working well and this may be its final form, refs #17187
    
• src/hg/genePredToFakePsl/genePredToFakePsl.c
  • lines changed 6, context: html, text, full: html, text
    4e0e5a68eca6f220fc5553949ccfa8b8742bce7c Mon Apr 18 16:05:27 2016 -0700
    added note in about case that is not correctly handle
    
• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
  • lines changed 1, context: html, text, full: html, text
    fdef579bae3c23fe4057b74062858bcd60a79209 Mon Apr 18 14:42:07 2016 -0700
    removed accidently checked in garbage
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 32, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 4, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    3dbe3acc6ce41b7cd460b75ef149d7f9b886ba19 Thu Apr 21 13:56:03 2016 -0700
    adding a help menu entry in hgTracks for the shortcuts, refs #17212
    
  • lines changed 1, context: html, text, full: html, text
    592bcd96827ff8a911094d25ff8012f5bf00726e Thu Apr 21 16:25:04 2016 -0700
    fixing typo in last commit
    
  • lines changed 8, context: html, text, full: html, text
    c6cbddabb1c64bda5e814db3057299a3da4158bf Fri Apr 22 10:06:49 2016 -0700
    adding shortcut indicators in light gray to menubar, like in SAA/CUA applications. refs #17212
    
• src/hg/hgTracks/menu.c
  • lines changed 21, context: html, text, full: html, text
    1ee35161c11e26203026dbb8ab352f306b8603ed Fri Apr 22 10:42:36 2016 -0700
    adding file forgotten in previous commit
    
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    0c8315e78d684221b53def0d7396d105dd45d560 Mon Apr 18 16:11:34 2016 -0700
    back out a change I made to put allow the presence or abscence of a
    version number that was including id's that were prefixed by the id we
    were looking for.
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    cc9b876308790ce53bf47d3d5728e3e0613e0843 Mon Apr 18 10:11:28 2016 -0700
    rheMac8 credits, refs# 16744
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    42c48916eb62156f324514a45e4e436b7ec31883 Tue Apr 19 09:54:27 2016 -0700
    Fixing typos from code review on customTrackText.html refs #17200
    
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 5, context: html, text, full: html, text
    80d28f527b8d84e950c6dc7e1ace5daee28a5571 Tue Apr 19 10:41:22 2016 -0700
    Adding detail about new next exon behavior, refs #17064
    
  • lines changed 7, context: html, text, full: html, text
    bd14efda89da04f05a7dc407448f42c3ae05066b Thu Apr 21 11:34:02 2016 -0700
    Fixing up next/prev exon documentation based on feedback, refs #17064
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 4, context: html, text, full: html, text
    974a4b3e74c52f17e655d1eeded7a5a742c07b76 Wed Apr 20 13:15:40 2016 -0700
    Fixings session gallery text from code review refs #17200
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 53, context: html, text, full: html, text
    d25710f7ea0429712c49d6fc37586a25cdac67f1 Wed Apr 20 16:06:07 2016 -0700
    Made a quick editing pass on the GTEx announcement, then migrated text to news archive page.
    
  • lines changed 2, context: html, text, full: html, text
    4003ca71c92462fbcc997ae1e9bddd0b55ff5e05 Wed Apr 20 17:07:10 2016 -0700
    Fixing links to gtex session, refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    b6b3e1471bee74d909af4f8e638f338557d2058d Fri Apr 22 07:44:36 2016 -0700
    Re-adding announcement about Lens Patents track, refs #14486
    
• src/hg/htdocs/images/gtexAnnounceExample.png
  • lines changed 0, context: html, text, full: html, text
    dc8e5f43f137fd11ff0f00cb92ae20c31e1a7812 Mon Apr 18 14:40:36 2016 -0700
    Updating image for gtex announcement, refs #15645
    
• src/hg/htdocs/images/session.hg19.OMIM.png
  • lines changed 0, context: html, text, full: html, text
    81274b2f916d225efebe16b7b57a6d7e6a49d973 Mon Apr 18 10:47:53 2016 -0700
    Replacing image for sessions gallery, refs #1263
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 14, context: html, text, full: html, text
    6e2af1cb46cacb092d2e927c0af3bb5193b43d2f Fri Apr 22 10:47:32 2016 -0700
    updating global nav bar, refs #17212
    
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    d0e054ad7c3474a8aee0497ae4506a4f2649577c Mon Apr 18 14:23:00 2016 -0700
    Tweaks to intro paragraph of GTEx announcement.
    
  • lines changed 3, context: html, text, full: html, text
    dc8e5f43f137fd11ff0f00cb92ae20c31e1a7812 Mon Apr 18 14:40:36 2016 -0700
    Updating image for gtex announcement, refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    e906b59669be81b854db661c5bb9c4209f4c4bbe Mon Apr 18 15:16:20 2016 -0700
    Restore commenting out for staging purposes.
    
  • lines changed 13, context: html, text, full: html, text
    4340f42241e6c5840fb5327e5190efe1b62ba639 Mon Apr 18 15:37:45 2016 -0700
    Editing gtex announcement, refs #15645
    
  • lines changed 20, context: html, text, full: html, text
    81e2b4c294447d686f055b2d794be7f0da11bbc9 Mon Apr 18 16:28:25 2016 -0700
    More wordcrafting on GTEx announcement. Ready for Donna...
    
  • lines changed 191, context: html, text, full: html, text
    d25710f7ea0429712c49d6fc37586a25cdac67f1 Wed Apr 20 16:06:07 2016 -0700
    Made a quick editing pass on the GTEx announcement, then migrated text to news archive page.
    
  • lines changed 2, context: html, text, full: html, text
    4003ca71c92462fbcc997ae1e9bddd0b55ff5e05 Wed Apr 20 17:07:10 2016 -0700
    Fixing links to gtex session, refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    b6b3e1471bee74d909af4f8e638f338557d2058d Fri Apr 22 07:44:36 2016 -0700
    Re-adding announcement about Lens Patents track, refs #14486
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 11, context: html, text, full: html, text
    c6cbddabb1c64bda5e814db3057299a3da4158bf Fri Apr 22 10:06:49 2016 -0700
    adding shortcut indicators in light gray to menubar, like in SAA/CUA applications. refs #17212
    
• src/hg/htdocs/training/index.html
  • lines changed 2, context: html, text, full: html, text
    03edb57409a79fe375f9398c818a31c621391f72 Sun Apr 24 12:43:11 2016 -0700
    added link to session gallery. Refs #1263
    
• src/hg/js/dbDbTaxonomy.hgwdev.js
  • lines changed 1087, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/dbDbTaxonomy.js
  • lines changed 1089, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/dbDbTaxonomy.rr.js
  • lines changed 530, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/hgGateway.js
  • lines changed 60, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/hgTracks.js
  • lines changed 11, context: html, text, full: html, text
    3dbe3acc6ce41b7cd460b75ef149d7f9b886ba19 Thu Apr 21 13:56:03 2016 -0700
    adding a help menu entry in hgTracks for the shortcuts, refs #17212
    
  • lines changed 28, context: html, text, full: html, text
    c6cbddabb1c64bda5e814db3057299a3da4158bf Fri Apr 22 10:06:49 2016 -0700
    adding shortcut indicators in light gray to menubar, like in SAA/CUA applications. refs #17212
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/lib/cartJson.c
  • lines changed 13, context: html, text, full: html, text
    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/hg/lib/genePred.c
  • lines changed 5, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/lib/jksql.c
  • lines changed 8, context: html, text, full: html, text
    17e81564934600bd6c06c966d4ade17f4e49d689 Mon Apr 18 14:28:20 2016 -0700
    get sqlTableExists to work is table names of the form db.table when
    tableList caching is being used
    
• src/hg/makeDb/doc/cavPor3.txt
  • lines changed 117, context: html, text, full: html, text
    7795690e07537e24b0185f057eb0689b115d2758 Wed Apr 20 17:08:56 2016 -0700
    running up lastz to cavPor3 refs #17180
    
• src/hg/makeDb/doc/dbDbTaxonomy.txt
  • lines changed 60, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/makeDb/doc/galGal5/initialBuild.txt
  • lines changed 12, context: html, text, full: html, text
    68d942ec48230e65199d05365d0460f4e04e9d30 Tue Apr 19 12:14:21 2016 -0700
    genbank done refs #17168
    
• src/hg/makeDb/doc/rouAeg1/initialBuild.txt
  • lines changed 169, context: html, text, full: html, text
    9e78c0fbc6baecfa38909aa954a543b1a8320268 Tue Apr 19 13:29:09 2016 -0700
    running up genbank refs #17178
    
  • lines changed 54, context: html, text, full: html, text
    e3bca14287ae3766cb17c4652a62b23428058c02 Wed Apr 20 12:30:34 2016 -0700
    ready for downloads and pushQ refs #17167
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    d50eb372dca5000f8852ac00c70566b920e93016 Tue Apr 19 12:13:26 2016 -0700
    Added galGal5 - chicken refs #17168
    
  • lines changed 1, context: html, text, full: html, text
    b439662394ec4ed3c49f38135f74be414b33b775 Wed Apr 20 11:07:33 2016 -0700
    Added rouAeg1 Egyptian rousette fruit bat - Rousettus aegyptiacus - refs #17167
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    54bf1752bf9f9a4774973a81c2bad5d37be9e6b3 Tue Apr 19 13:26:46 2016 -0700
    Added rouAeg Egyptian rousette (fruit bat) - Rousettus aegyptiacus; refs #17167
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    d50eb372dca5000f8852ac00c70566b920e93016 Tue Apr 19 12:13:26 2016 -0700
    Added galGal5 - chicken refs #17168
    
  • lines changed 1, context: html, text, full: html, text
    b439662394ec4ed3c49f38135f74be414b33b775 Wed Apr 20 11:07:33 2016 -0700
    Added rouAeg1 Egyptian rousette fruit bat - Rousettus aegyptiacus - refs #17167
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    54bf1752bf9f9a4774973a81c2bad5d37be9e6b3 Tue Apr 19 13:26:46 2016 -0700
    Added rouAeg Egyptian rousette (fruit bat) - Rousettus aegyptiacus; refs #17167
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 3, context: html, text, full: html, text
    a7f4d921b739cf892c225997a3d85cea3db25f18 Thu Apr 21 16:20:24 2016 -0700
    fixed bug were polyA table wasn't being loaded
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 85, context: html, text, full: html, text
    785136193faa141057fdbe9bf48b372c69139e2a Wed Apr 20 11:59:46 2016 -0700
    added joiner rules for gencode VM9
    
  • lines changed 31, context: html, text, full: html, text
    4466fa974b7e21735f2f4829a9b9b6efc4ab6658 Wed Apr 20 12:22:22 2016 -0700
    adding rouAeg1 definitions refs #17167
    
  • lines changed 8, context: html, text, full: html, text
    0226229307e78ebea5fd7b5185950a0f9d2f42a3 Wed Apr 20 13:00:36 2016 -0700
    adding galGal5 refs #17168
    
  • lines changed 36, context: html, text, full: html, text
    f742e87de2e9f4b49308d34c367213bf26649475 Thu Apr 21 13:54:16 2016 -0700
    change genabank metadata database to hgFixed from gbMeta in all.joiner
    
• src/hg/makeDb/trackDb/bonobo/panPan2/description.html
  • lines changed 64, context: html, text, full: html, text
    dd384a94d98dbb23c89b8644dba1d518544132e2 Tue Apr 19 10:38:30 2016 -0700
    adding panPan2 to the build refs #17167
    
• src/hg/makeDb/trackDb/bonobo/panPan2/gap.html
  • lines changed 34, context: html, text, full: html, text
    dd384a94d98dbb23c89b8644dba1d518544132e2 Tue Apr 19 10:38:30 2016 -0700
    adding panPan2 to the build refs #17167
    
• src/hg/makeDb/trackDb/bonobo/panPan2/gold.html
  • lines changed 34, context: html, text, full: html, text
    dd384a94d98dbb23c89b8644dba1d518544132e2 Tue Apr 19 10:38:30 2016 -0700
    adding panPan2 to the build refs #17167
    
• src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    dd384a94d98dbb23c89b8644dba1d518544132e2 Tue Apr 19 10:38:30 2016 -0700
    adding panPan2 to the build refs #17167
    
• src/hg/makeDb/trackDb/human/encodeAffyEncode25bpProbes.html
  • lines changed 1, context: html, text, full: html, text
    3c28303ef80cf1c460d246986a74c947639994b3 Tue Apr 19 16:26:12 2016 -0700
    Fixing bad url for hg16 ENCODE pages, no RM
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 10, context: html, text, full: html, text
    5c8cdfe422d2ba2b58c9bf96267520eb8f0a3136 Tue Apr 19 08:48:27 2016 -0700
    Remove difference graph info, add squish info. refs #15645
    
• src/hg/makeDb/trackDb/human/hg16/encodeAffyRnaSignal.html
  • lines changed 1, context: html, text, full: html, text
    3c28303ef80cf1c460d246986a74c947639994b3 Tue Apr 19 16:26:12 2016 -0700
    Fixing bad url for hg16 ENCODE pages, no RM
    
• src/hg/makeDb/trackDb/human/hg16/encodeAffyRnaTransfrags.html
  • lines changed 1, context: html, text, full: html, text
    3c28303ef80cf1c460d246986a74c947639994b3 Tue Apr 19 16:26:12 2016 -0700
    Fixing bad url for hg16 ENCODE pages, no RM
    
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
  • lines changed 5, context: html, text, full: html, text
    32709f2448c61845a61667820cd3291ec15a2729 Wed Apr 20 08:33:13 2016 -0700
    Minor changes to reference links, refs #16765
    
• src/hg/makeDb/trackDb/makefile
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    dd384a94d98dbb23c89b8644dba1d518544132e2 Tue Apr 19 10:38:30 2016 -0700
    adding panPan2 to the build refs #17167
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    171fd897a6882c4b8b1f91f4627db6db0d2a0e46 Fri Apr 22 13:17:07 2016 -0700
    Turning Gencode VM7 off by default and fixing wrong publication link on gencode super track page, refs #17007
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.ra
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    171fd897a6882c4b8b1f91f4627db6db0d2a0e46 Fri Apr 22 13:17:07 2016 -0700
    Turning Gencode VM7 off by default and fixing wrong publication link on gencode super track page, refs #17007
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.html
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    bd64a004742578ab7710f8598b2ac989e7c8dbf7 Wed Apr 20 11:54:50 2016 -0700
    Fixing links on Gencode VM9, refs #17007
    
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    769d3db243983771e01224d94a0a1c396bf94abe Thu Apr 21 16:08:57 2016 -0700
    Fixing outdated publication link, refs #17007
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra
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    48254c04280712ad02cb3184108955fa3736d5fd Tue Apr 19 12:09:19 2016 -0700
    fixed incorrect label in mouse GENCODE
    
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    a82f0470f75c56f6f5992b2741f6ebc4d1eba030 Wed Apr 20 12:12:10 2016 -0700
    Turning pseudogenes off by default on VM9 to match default VM7, refs #17007
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
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    8e323ec95b8eee0af2f2e128a25f779d1ac103a5 Mon Apr 18 13:20:03 2016 -0700
    Fixing table lines and refs, rheMac8, redmine #16744
    
• src/hg/mrnaToGene/mrnaToGene.c
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    747563375ea7f3caaaeb7a6d0092706078b0bde9 Mon Apr 18 16:57:33 2016 -0700
    simplified the code a bit
    
• src/hg/mrnaToGene/tests/README
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    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/expected/allCds.gp
  • lines changed 21, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/expected/base.gp
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/expected/frame.gp
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/expected/noCds.gp
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/input/base.cds
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/input/base.psl
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/mrnaToGene/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
    Deal with case were CDS specifications that were create by other
    software that didn't correctly set the completeness flags create frames
    incorrectly on end-truncated sequences. This code can't possible do the
    right thing all the time if completeness isn't correctly flag, however
    this makes it more likely to do the right thing when software start from
    the beginning of the first coding defining CDS without actually setting
    completeness flags.
    
• src/hg/near/hgMapToGene/hgMapToGene.c
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    bb6e19c532f47fca7d991f5a5c0f025e27ed3fa9 Mon Apr 18 22:10:17 2016 -0700
    Added override option for trackDb setting Otherwise an hg.conf with multiple trackDb tables causes a seg fault, refs #15315
    
• src/hg/utils/makefile
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
• src/hg/utils/transMapPslToGenePred/makefile
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
• src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp
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    422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
    added gap filling options
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp
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    422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
    added gap filling options
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp
  • lines changed 33, context: html, text, full: html, text
    422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
    added gap filling options
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/hg/utils/transMapPslToGenePred/tests/makefile
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
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    422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
    added gap filling options
    
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
    add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
    
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    ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
    fixed issues with reverse strand and frame
    
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    422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
    added gap filling options
    
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    a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
    fixed bug with negative strand gene with CDS truncation
    
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    04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
    fixed bug with frame with merging block on negative strand
    
• src/inc/jsonWrite.h
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    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/lib/asParse.c
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    1e6566439ca544eb838a2247ade0dd2d08c6b762 Wed Apr 20 09:54:01 2016 -0700
    Adding special case to asTypeNameFromSqlType: sometimes a field is declared as string in .as but then in .sql it's changed to date (e.g. gbCdnaInfo.moddate), so treat sql type date as string.
    
• src/lib/jsonWrite.c
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    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/product/ex.hg.conf
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    30056ddd2a71593a731606f5c6bb81b17965b717 Wed Apr 20 09:35:59 2016 -0700
    Adding documentation of new setting hgGateway.dbDbTaxonomy to src/product/ex.hg.conf, should have been part of 915f56e3f. refs #15277
    
• src/utils/git-reports/git-reports.c
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    422a29eda108dd8b0091804ab76329292d679df0 Thu Apr 21 00:58:40 2016 -0700
    Making js/css show/hide details link option for the commit and files views. Allows users to see or hide the details about the commit id and date. This is very handy to have if you are just working off of a list of git sha hashIds.
    
• src/utils/git-reports/makefile
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    422a29eda108dd8b0091804ab76329292d679df0 Thu Apr 21 00:58:40 2016 -0700
    Making js/css show/hide details link option for the commit and files views. Allows users to see or hide the details about the commit id and date. This is very handy to have if you are just working off of a list of git sha hashIds.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    dbe3762bb5c2e82e236d8b2af0aa4d930d0b94cc Mon Apr 25 09:56:47 2016 -0700
    v332 preview2 refs #17202
    

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