All File Changes

v371_base to v372_preview (2018-09-10 to 2018-09-17) v372

• confs/preview.hg.conf
  • lines changed 244, context: html, text, full: html, text
    e67ec0cb0d5b957b842f3ef74f056bbec5e34f3a Sun Sep 16 01:15:23 2018 -0700
    Installing updated hg.conf files from UCSC servers
• java/javaenv
  • lines changed 1, context: html, text, full: html, text
    e0897697614162d19d975f6f3f16a1c729da1a08 Tue Sep 11 14:44:06 2018 -0700
    take jtidy out of special UCSC installed things
• src/hg/hgMirror/hgMirror
  • lines changed 1, context: html, text, full: html, text
    b8f0d399dd01cf78ff184e5fa79731aa1b8cbd7d Thu Sep 13 12:16:57 2018 -0700
    Fixing problemw with setTimeout usage and CSP protections. Now that hgMirror uses CSP, this fix is needed too.
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    5dcf4017bd19b7c13cdb1bc730b10cf25628fbb6 Thu Sep 13 09:06:02 2018 -0700
    Removing link to openhelix from table browser text, refs #21947
• src/hg/hgTracks/barChartTrack.c
  • lines changed 106, context: html, text, full: html, text
    6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba Tue Sep 11 06:29:55 2018 -0700
    updating phegenToBed, refs #21052
  • lines changed 106, context: html, text, full: html, text
    56e310552abf565c1bce2c7a58705e951e3bbf8f Tue Sep 11 06:43:48 2018 -0700
    I don't know what happened here. I committed the completely wrong file, sorry. Reverting it now. Revert "updating phegenToBed, refs #21052" This reverts commit 6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba.
  • lines changed 7, context: html, text, full: html, text
    7c539b520039bad054dbc791f73101fdb69317fb Tue Sep 11 11:58:02 2018 -0700
    Add error check for trackDb/data file mismatch. refs #22058
• src/hg/hgTracks/extTools.c
  • lines changed 2, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    85ce72b6bf9b8aba1d6f010c3e3f32f13cb2af62 Tue Sep 11 06:33:42 2018 -0700
    tiny printf change to hgTracks, for future css changes, no redmine
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba Tue Sep 11 06:29:55 2018 -0700
    updating phegenToBed, refs #21052
  • lines changed 6, context: html, text, full: html, text
    56e310552abf565c1bce2c7a58705e951e3bbf8f Tue Sep 11 06:43:48 2018 -0700
    I don't know what happened here. I committed the completely wrong file, sorry. Reverting it now. Revert "updating phegenToBed, refs #21052" This reverts commit 6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba.
• src/hg/hgTracks/interactTrack.c
  • lines changed 15, context: html, text, full: html, text
    06be007e1b8b1724b61efcf0535089db5abb10da Wed Aug 29 15:00:46 2018 -0700
    Refactor in preparation for flipped display. refs #21917
  • lines changed 156, context: html, text, full: html, text
    4a6eac658a9442df276cfeedde11a0bc299af4ae Wed Aug 29 15:43:08 2018 -0700
    Refactor in preparation for flipped display. refs #21917
  • lines changed 18, context: html, text, full: html, text
    ec63f97739cc4b22e80a26a9db52e80416879d39 Wed Aug 29 15:48:37 2018 -0700
    Refactor in preparation for flipped display. refs #21917
  • lines changed 88, context: html, text, full: html, text
    227226fa2553637314e05bec16a320063220aecc Wed Aug 29 17:41:30 2018 -0700
    First cut flipped display. Doesn't yet flip ellipses, and mapbox on curves sometimes misplaced. refs #21917
  • lines changed 4, context: html, text, full: html, text
    628c91b14577ebbe372dd3eddec9f089bb1c832a Fri Aug 31 10:46:00 2018 -0700
    Remove debug code. refs #21917
  • lines changed 4, context: html, text, full: html, text
    3fb824368b08731386237ed46a4627e137cd4e47 Tue Sep 11 13:06:29 2018 -0700
    Fix grab boxes on flipped curves, refs #21917
  • lines changed 8, context: html, text, full: html, text
    1adad10dff1c663fc38f51ad8f8ac2f3eec38de8 Tue Sep 11 13:19:26 2018 -0700
    Implement flipped ellipses. refs #21917
  • lines changed 6, context: html, text, full: html, text
    e7fea0a31b28f2e17c44b19af2128a177e45e785 Tue Sep 11 13:49:29 2018 -0700
    Fix compiler warnings (and superfluous vars).
  • lines changed 2, context: html, text, full: html, text
    01a0d6cbc7ba5a3847625f158dd9fad8005ac2e3 Wed Sep 12 10:22:52 2018 -0700
    Remove unnecessary tweak for flipped curve grab point. refs #21917
  • lines changed 1, context: html, text, full: html, text
    bbf22aaa85d4bd1eca708b8f7886ee868c3ceef9 Wed Sep 12 10:23:36 2018 -0700
    Remove unnecessary tweak for flipped curve grab point. refs #21917
• src/hg/hgc/bigBedClick.c
  • lines changed 7, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/hgc/hgc.c
  • lines changed 60, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/hgc/hgc.h
  • lines changed 6, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/hgc/interactClick.c
  • lines changed 7, context: html, text, full: html, text
    06be007e1b8b1724b61efcf0535089db5abb10da Wed Aug 29 15:00:46 2018 -0700
    Refactor in preparation for flipped display. refs #21917
  • lines changed 73, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/hgc/lrgClick.c
  • lines changed 3, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 4, context: html, text, full: html, text
    3a0198acd1f859a603f5aad90188bee2d82efe0c Mon Sep 10 17:06:46 2018 -0700
    Removing additional OpenHelix links. Ref#21947
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 2, context: html, text, full: html, text
    3a0198acd1f859a603f5aad90188bee2d82efe0c Mon Sep 10 17:06:46 2018 -0700
    Removing additional OpenHelix links. Ref#21947
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
  • lines changed 3, context: html, text, full: html, text
    3a0198acd1f859a603f5aad90188bee2d82efe0c Mon Sep 10 17:06:46 2018 -0700
    Removing additional OpenHelix links. Ref#21947
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 3, context: html, text, full: html, text
    3a0198acd1f859a603f5aad90188bee2d82efe0c Mon Sep 10 17:06:46 2018 -0700
    Removing additional OpenHelix links. Ref#21947
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    eaeaf20b2411e80d5e99f6fcae1a4c4767b0ee79 Mon Sep 10 16:29:30 2018 -0700
    Removing OpenHelix links as they are down. Ref#21947
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 3, context: html, text, full: html, text
    3a0198acd1f859a603f5aad90188bee2d82efe0c Mon Sep 10 17:06:46 2018 -0700
    Removing additional OpenHelix links. Ref#21947
• src/hg/inc/barChartUi.h
  • lines changed 14, context: html, text, full: html, text
    6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba Tue Sep 11 06:29:55 2018 -0700
    updating phegenToBed, refs #21052
  • lines changed 14, context: html, text, full: html, text
    56e310552abf565c1bce2c7a58705e951e3bbf8f Tue Sep 11 06:43:48 2018 -0700
    I don't know what happened here. I committed the completely wrong file, sorry. Reverting it now. Revert "updating phegenToBed, refs #21052" This reverts commit 6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba.
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/inc/hvGfx.h
  • lines changed 2, context: html, text, full: html, text
    e7ff0f9913e737366d8155e4ba28c94ea460ea99 Tue Sep 11 18:32:35 2018 -0700
    Disable dashes on ellipse drawer (it hangs). refs #22068
• src/hg/inc/interactUi.h
  • lines changed 3, context: html, text, full: html, text
    06be007e1b8b1724b61efcf0535089db5abb10da Wed Aug 29 15:00:46 2018 -0700
    Refactor in preparation for flipped display. refs #21917
• src/hg/lib/hui.c
  • lines changed 23, context: html, text, full: html, text
    e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a Wed Sep 12 17:19:14 2018 -0700
    IMplement fieldName> expansion in trackDb url setting. refs #22078
• src/hg/lib/mathWig.c
  • lines changed 12, context: html, text, full: html, text
    76541502f60ad17d6f23dec970af30a07e9ebc84 Fri Sep 14 15:59:34 2018 -0700
    oops, forgot to close bigWig files after reading. #22088
• src/hg/makeDb/doc/dm6.txt
  • lines changed 70, context: html, text, full: html, text
    fceaa02c18486335f4a0f693313a0012ea153d1a Wed Sep 12 15:26:36 2018 -0700
    lastz/chain/net to droSim2 per user request refs #22074
• src/hg/makeDb/doc/hg38/snpedia.txt
  • lines changed 9, context: html, text, full: html, text
    0a011ac3d88de3406cde96c03f9f6f42e9e863e4 Tue Sep 11 06:32:29 2018 -0700
    must have forgotten to commit the final files for the snpedia track, refs #19811
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    fe963552c863e70b30e81b87037847f025afab0e Sun Sep 16 19:39:58 2018 -0700
    Gencode knownGene release stuff
• src/hg/makeDb/scripts/snpedia/bed4Note.as
  • lines changed 9, context: html, text, full: html, text
    0a011ac3d88de3406cde96c03f9f6f42e9e863e4 Tue Sep 11 06:32:29 2018 -0700
    must have forgotten to commit the final files for the snpedia track, refs #19811
• src/hg/makeDb/scripts/snpedia/getPos.py
  • lines changed 3, context: html, text, full: html, text
    0a011ac3d88de3406cde96c03f9f6f42e9e863e4 Tue Sep 11 06:32:29 2018 -0700
    must have forgotten to commit the final files for the snpedia track, refs #19811
• src/hg/makeDb/scripts/snpedia/makeAll.py
  • lines changed 24, context: html, text, full: html, text
    0a011ac3d88de3406cde96c03f9f6f42e9e863e4 Tue Sep 11 06:32:29 2018 -0700
    must have forgotten to commit the final files for the snpedia track, refs #19811
• src/hg/makeDb/trackDb/human/hg19/trackDb.geneHancer.ra
  • lines changed 125, context: html, text, full: html, text
    c6f7cbfa188c729f89f04ebbb1449a82c065758c Wed Sep 12 17:23:22 2018 -0700
    Add GeneHancer track. refs #22048
  • lines changed 4, context: html, text, full: html, text
    d1aa38610dabfa7080a48da3c9522a5804cb8d7e Fri Sep 14 13:23:01 2018 -0700
    Tweak defaults on and release
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    c6f7cbfa188c729f89f04ebbb1449a82c065758c Wed Sep 12 17:23:22 2018 -0700
    Add GeneHancer track. refs #22048
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 13, context: html, text, full: html, text
    fe963552c863e70b30e81b87037847f025afab0e Sun Sep 16 19:39:58 2018 -0700
    Gencode knownGene release stuff
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    c6f7cbfa188c729f89f04ebbb1449a82c065758c Wed Sep 12 17:23:22 2018 -0700
    Add GeneHancer track. refs #22048
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
  • lines changed 2, context: html, text, full: html, text
    5644f9bd5a0e4d3764c9f69c5a658c6ff2eb2021 Tue Sep 11 06:35:08 2018 -0700
    add all +- buttons to uniprot track, refs #20174
• src/utils/phegenToBed
  • lines changed 19, context: html, text, full: html, text
    6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba Tue Sep 11 06:29:55 2018 -0700
    updating phegenToBed, refs #21052
  • lines changed 19, context: html, text, full: html, text
    56e310552abf565c1bce2c7a58705e951e3bbf8f Tue Sep 11 06:43:48 2018 -0700
    I don't know what happened here. I committed the completely wrong file, sorry. Reverting it now. Revert "updating phegenToBed, refs #21052" This reverts commit 6985ec2b43b98f50d26ff7b3f72cefce3f6d5eba.
  • lines changed 19, context: html, text, full: html, text
    c23a3877f7282272a39ca38bbca6fc8544d2e8ac Tue Sep 11 06:47:32 2018 -0700
    updating phegenToBed, refs #21052
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ce83b095322091124bcfaed97be7d9ad4f16ecc8 Mon Sep 17 10:36:10 2018 -0700
    v372 preview1, refs #21989

• lines changed: 1363
• files changed: 56