All File Changes

v372_preview to v372_preview2 (2018-09-17 to 2018-09-24) v372

• confs/preview.hg.conf
  • lines changed 244, context: html, text, full: html, text
    5737d058128f1324f8f09e9f5e977de039f10f86 Sun Sep 23 01:11:07 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 1, context: html, text, full: html, text
    1e0d91e44a32dc8c37c9da7ed3fcefe5d27855a6 Tue Sep 18 15:59:54 2018 -0700
    Changing JCVI image URL. Making search box only appear on cirm.ucsc.edu. no redmine
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 1, context: html, text, full: html, text
    3678c73a4d4b97e647827dc1c163beb0112ee912 Tue Sep 18 16:05:04 2018 -0700
    Changing background of pubs page main title bar to match menu bar button color. no redmine.
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 11, context: html, text, full: html, text
    a720f3dc2fee90251f6f5dc21511003bd30b7b41 Wed Sep 19 12:09:32 2018 -0700
    Removing link to CIRM wiki. Added some icons to external and PDF links. refs #22108
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    1e0d91e44a32dc8c37c9da7ed3fcefe5d27855a6 Tue Sep 18 15:59:54 2018 -0700
    Changing JCVI image URL. Making search box only appear on cirm.ucsc.edu. no redmine
• src/hg/cirm/gateway/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    8997547ca50ffb024af71fb5b19fb110733fa04d Mon Sep 17 14:44:37 2018 -0700
    Old version of makefile would make a new htdocs/style dir and put the cirmStyle file in there. New one should not do this. no redmine
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 1, context: html, text, full: html, text
    571504b8602e77298d8b8d7cbdf5bddc348e6020 Fri Sep 21 15:53:28 2018 -0700
    hgSuggest, when invoked with no params, was getting a SEGV instead of printing a 'Status: 400' header and error message. There were two problems: a param was being used before the test for lack of params, and htmlVaBadRequestAbort was used only as an AbortHandler -- it needs to be a WarnHandler, otherwise the error message is printed out before the header. A couple other places also needed to install htmlVaBadRequestAbort as a WarnHandler not just AbortHandler.
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    571504b8602e77298d8b8d7cbdf5bddc348e6020 Fri Sep 21 15:53:28 2018 -0700
    hgSuggest, when invoked with no params, was getting a SEGV instead of printing a 'Status: 400' header and error message. There were two problems: a param was being used before the test for lack of params, and htmlVaBadRequestAbort was used only as an AbortHandler -- it needs to be a WarnHandler, otherwise the error message is printed out before the header. A couple other places also needed to install htmlVaBadRequestAbort as a WarnHandler not just AbortHandler.
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 8, context: html, text, full: html, text
    571504b8602e77298d8b8d7cbdf5bddc348e6020 Fri Sep 21 15:53:28 2018 -0700
    hgSuggest, when invoked with no params, was getting a SEGV instead of printing a 'Status: 400' header and error message. There were two problems: a param was being used before the test for lack of params, and htmlVaBadRequestAbort was used only as an AbortHandler -- it needs to be a WarnHandler, otherwise the error message is printed out before the header. A couple other places also needed to install htmlVaBadRequestAbort as a WarnHandler not just AbortHandler.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 10, context: html, text, full: html, text
    6d28c056697ec2989673dcbfaac0ae1e99e9f777 Wed Sep 19 01:02:09 2018 -0700
    Adding needed note about translated queries and coordinates to PSL in formats FAQ.
• src/hg/inc/interact.h
  • lines changed 7, context: html, text, full: html, text
    7f7b1d915bb9dd28229092ea4f2de80c3646a131 Tue Sep 18 17:17:38 2018 -0700
    Additional validation for interact coords, and a tool to correct them. refs #21917
  • lines changed 4, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/lib/cart.c
  • lines changed 12, context: html, text, full: html, text
    45a0d85fb6aa60d70be70d79af40efda21cdce1d Wed Sep 19 11:08:47 2018 -0700
    take out cart stuffing bot check #22109
• src/hg/lib/interact.c
  • lines changed 34, context: html, text, full: html, text
    7f7b1d915bb9dd28229092ea4f2de80c3646a131 Tue Sep 18 17:17:38 2018 -0700
    Additional validation for interact coords, and a tool to correct them. refs #21917
  • lines changed 66, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/doc/geneHancer.txt
  • lines changed 65, context: html, text, full: html, text
    394cbe47add4e0d5e3e462fa1e5aff25adf958f6 Tue Sep 18 13:49:22 2018 -0700
    Initial work on geneHancer track. refs #22048
  • lines changed 4, context: html, text, full: html, text
    c1bded498ecf62af6dc258037bc72927bef15a74 Tue Sep 18 17:18:40 2018 -0700
    Correcting coords on geneHancer interact files. refs #22048
  • lines changed 56, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh
  • lines changed 91, context: html, text, full: html, text
    6b16b5b4ba9cdc1567da994f19c82bf1077d9d76 Mon Sep 17 15:01:36 2018 -0700
    check in of UCSC genes make doc for Gencode V29 knownGene
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 61, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/trackDb/human/hg16/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    fd586c59531ad83106278620738cedb4cdb3a1c2 Wed Sep 19 16:15:58 2018 -0700
    Moving all tracks on by default to the correct order, refs #19187
• src/hg/makeDb/trackDb/human/hg19/trackDb.geneHancer.ra
  • lines changed 12, context: html, text, full: html, text
    4497acd7bfae1b7f6a966a32ff9095e6802d2dff Tue Sep 18 11:44:27 2018 -0700
    Corrections to color and view settings. refs #22048
  • lines changed 113, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 95, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    fd586c59531ad83106278620738cedb4cdb3a1c2 Wed Sep 19 16:15:58 2018 -0700
    Moving all tracks on by default to the correct order, refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    7ca8370e38b7baa1add15ac1a6eb676b12ec98fd Fri Sep 21 14:05:09 2018 -0700
    removing xenoClinvar from mouse and moving to mm10
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    fd586c59531ad83106278620738cedb4cdb3a1c2 Wed Sep 19 16:15:58 2018 -0700
    Moving all tracks on by default to the correct order, refs #19187
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    65f10eb5f448a386183b2c776441fc9772b15f78 Fri Sep 21 14:03:29 2018 -0700
    removing xenoClinvar from non-mouse assemblies
  • lines changed 11, context: html, text, full: html, text
    7ca8370e38b7baa1add15ac1a6eb676b12ec98fd Fri Sep 21 14:05:09 2018 -0700
    removing xenoClinvar from mouse and moving to mm10
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    65f10eb5f448a386183b2c776441fc9772b15f78 Fri Sep 21 14:03:29 2018 -0700
    removing xenoClinvar from non-mouse assemblies
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
  • lines changed 2, context: html, text, full: html, text
    ff4df538ba90235c28fbec6d459a7c1f6d72d039 Wed Sep 19 10:05:34 2018 -0700
    Updating redirected links for taeGut2, uiLinks cronjob.
• src/hg/mouseStuff/axtToMaf/axtToMaf.c
  • lines changed 1, context: html, text, full: html, text
    24d93a5d8c0db07faac21f58b4de6b01aaf227ef Wed Sep 19 17:13:02 2018 -0700
    srcName array too small reported by user. Doubling to 256.
• src/hg/utils/automation/doAugustus.pl
  • lines changed 5, context: html, text, full: html, text
    ae4ff075a93ab4137dacf3dcdfb8582a72a11d89 Wed Sep 19 10:48:20 2018 -0700
    Use latest version of augustus, recompiled for new hgwdev & cluster.
• src/hg/utils/automation/openStack/initParasol
  • lines changed 1, context: html, text, full: html, text
    6740b845785b2de13f9108958e1cb3fa3de3be8e Fri Sep 21 11:33:05 2018 -0700
    a bit more versatile identification of self IP address refs #18874
• src/hg/utils/automation/openStack/nodeReport.sh
  • lines changed 1, context: html, text, full: html, text
    6740b845785b2de13f9108958e1cb3fa3de3be8e Fri Sep 21 11:33:05 2018 -0700
    a bit more versatile identification of self IP address refs #18874
• src/hg/utils/interactFixRanges/interactFixRanges.c
  • lines changed 40, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/hg/utils/interactFixRanges/makefile
  • lines changed 3, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/inc/basicBed.h
  • lines changed 3, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/inc/htmshell.h
  • lines changed 4, context: html, text, full: html, text
    571504b8602e77298d8b8d7cbdf5bddc348e6020 Fri Sep 21 15:53:28 2018 -0700
    hgSuggest, when invoked with no params, was getting a SEGV instead of printing a 'Status: 400' header and error message. There were two problems: a param was being used before the test for lack of params, and htmlVaBadRequestAbort was used only as an AbortHandler -- it needs to be a WarnHandler, otherwise the error message is printed out before the header. A couple other places also needed to install htmlVaBadRequestAbort as a WarnHandler not just AbortHandler.
• src/inc/memgfx.h
  • lines changed 3, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/lib/basicBed.c
  • lines changed 10, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/lib/htmshell.c
  • lines changed 5, context: html, text, full: html, text
    571504b8602e77298d8b8d7cbdf5bddc348e6020 Fri Sep 21 15:53:28 2018 -0700
    hgSuggest, when invoked with no params, was getting a SEGV instead of printing a 'Status: 400' header and error message. There were two problems: a param was being used before the test for lack of params, and htmlVaBadRequestAbort was used only as an AbortHandler -- it needs to be a WarnHandler, otherwise the error message is printed out before the header. A couple other places also needed to install htmlVaBadRequestAbort as a WarnHandler not just AbortHandler.
• src/lib/memgfx.c
  • lines changed 8, context: html, text, full: html, text
    e5606b4f483bd08425af83b289ab4c3937b333da Thu Sep 20 13:11:03 2018 -0700
    Finishing touches on geneHancer track. Includes tool to fix incorrect ranges. refs #22048
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    f595be841599e92e00bd649c8a6647ab8c61b73c Wed Sep 19 10:30:31 2018 -0700
    allow descriptions to be made for trackDb and hgFindSpec no redmine
• src/utils/faSplit/faSplit.c
  • lines changed 1, context: html, text, full: html, text
    d505acbbb6c188c0529190efe1d6584e50c66d9c Wed Sep 19 16:58:11 2018 -0700
    bug reported by user on github that had a 32GB fasta file.
  • lines changed 1, context: html, text, full: html, text
    6c40490a20e23744370bd4f8e546e3cccb1683ee Wed Sep 19 17:02:57 2018 -0700
    little comment improvment
• src/utils/faSplit/t.c
  • lines changed 34, context: html, text, full: html, text
    e9242488b189378b8473f11299f1590b78ca280c Wed Sep 19 10:27:21 2018 -0700
    unwanted test file t.c -- it was never fleshed, and does no more than faCount in any case. Has not been used since 2003.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    77c847f18e2c9ae3eff990b22a677d95dfe6d3e3 Mon Sep 24 09:59:21 2018 -0700
    v372 preview2, refs #21989

• lines changed: 1077
• files changed: 49