All File Changes

v454_preview to v454_preview2 (2023-09-04 to 2023-09-11) v454

• java/src/edu/ucsc/genome/qa/cgiCheck/HGGeneCheck.java
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    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/HGNearCheck.java
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/PBGeneCheck.java
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java
  • lines changed 2, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/canFam1.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/ci1.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/full.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/hg17.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/hour.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/quick.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/cgiCheck/quickAll.props
  • lines changed 1, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/lib/HgTracks.java
  • lines changed 9, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• java/src/edu/ucsc/genome/qa/lib/TestTarget.java
  • lines changed 4, context: html, text, full: html, text
    b8ad41cb632c1fc82b73f9b2727e62147bc9f69d Thu Sep 7 00:15:13 2023 -0700
    Make java utils configurable between http and https, and https is the default. We are turning on redirect to https everywhere.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 4, context: html, text, full: html, text
    660233523b8443077366694e359818536b563abe Sun Sep 10 23:51:09 2023 -0700
    handle use of optional signal defintion
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    42359030b483e8b6b4ec32c743b0fff0b52b3e17 Wed Sep 6 08:20:00 2023 -0700
    improving error message when no regions are output in tb, refs #32061
• src/hg/hgTables/galaxy.c
  • lines changed 1, context: html, text, full: html, text
    ddc67048dafab9f09e2027816534beda83bedd72 Mon Sep 4 14:22:16 2023 -0700
    Fixing the outlink for galaxy, refs #20876
• src/hg/hgTables/gffOut.c
  • lines changed 1, context: html, text, full: html, text
    42359030b483e8b6b4ec32c743b0fff0b52b3e17 Wed Sep 6 08:20:00 2023 -0700
    improving error message when no regions are output in tb, refs #32061
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    42359030b483e8b6b4ec32c743b0fff0b52b3e17 Wed Sep 6 08:20:00 2023 -0700
    improving error message when no regions are output in tb, refs #32061
• src/hg/hgTables/seqOut.c
  • lines changed 5, context: html, text, full: html, text
    42359030b483e8b6b4ec32c743b0fff0b52b3e17 Wed Sep 6 08:20:00 2023 -0700
    improving error message when no regions are output in tb, refs #32061
• src/hg/hgc/bigBedClick.c
  • lines changed 2, context: html, text, full: html, text
    2a1c7786e6c5a0d56d3499efe713f722bb78abfb Mon Sep 4 12:18:02 2023 -0700
    fixing word break bug on bigBed extra tables, refs #29652
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    2a1c7786e6c5a0d56d3499efe713f722bb78abfb Mon Sep 4 12:18:02 2023 -0700
    fixing word break bug on bigBed extra tables, refs #29652
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    3936d80c4ab6899bbc757593729f1f3333d04ac7 Wed Sep 6 14:29:11 2023 +0200
    fixing browser grant number format, no redmine
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 46, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
  • lines changed 10, context: html, text, full: html, text
    f9b9f5835f0254f949b4b863b9dc906ff69fbd92 Fri Sep 8 13:30:18 2023 -0700
    Updating news announcement for GENCODE KnownGene V44 and VM33, refs #30840 #30841
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    3936d80c4ab6899bbc757593729f1f3333d04ac7 Wed Sep 6 14:29:11 2023 +0200
    fixing browser grant number format, no redmine
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
  • lines changed 2, context: html, text, full: html, text
    f9b9f5835f0254f949b4b863b9dc906ff69fbd92 Fri Sep 8 13:30:18 2023 -0700
    Updating news announcement for GENCODE KnownGene V44 and VM33, refs #30840 #30841
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    2a1c7786e6c5a0d56d3499efe713f722bb78abfb Mon Sep 4 12:18:02 2023 -0700
    fixing word break bug on bigBed extra tables, refs #29652
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    888d7be65ae0c3ec404176e55bc91fdea0e4b6a6 Fri Sep 8 14:00:26 2023 -0700
    Disable multi-wig download in download track in window pop up, refs #21342
• src/hg/js/utils.js
  • lines changed 27, context: html, text, full: html, text
    7c8985c0326a29d6bf3a58ceece3b8b23f06a713 Wed Sep 6 15:03:20 2023 -0700
    Make mouseovers show up when moving from item to item, refs #31365
  • lines changed 20, context: html, text, full: html, text
    6859799d7f0ff85994452c04c2aa568d74e35476 Fri Sep 8 14:02:48 2023 -0700
    Fix mouseovers not going away when moving away from them, refs #31365
  • lines changed 1, context: html, text, full: html, text
    43084309326c29e121a731690b288d53e67f273f Fri Sep 8 14:50:50 2023 -0700
    make mouseovers disappear on scrolling the document, refs #31365
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 119, context: html, text, full: html, text
    b8d07c062e6359ada0c6c24bdd1de490a59cddb1 Sat Sep 9 22:58:50 2023 -0700
    adding 119 for an update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    65f0fe2934e07ef62c5a6ed81010502cc64e509a Sat Sep 9 22:58:22 2023 -0700
    adding 9 for an update refs #29545
• src/hg/makeDb/doc/evaSnp5.txt
  • lines changed 600, context: html, text, full: html, text
    7e690f333eb9b803b3a6fcceed6a404f3fdf2fb7 Thu Sep 7 12:23:00 2023 -0700
    Staging new EvaSnp5 data QA Ready, refs #32095
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    82b5a0a38afcb12d66d77a9614ffddc3a0ba5726 Sat Sep 9 22:57:59 2023 -0700
    adding 14 for an update refs #29545
• src/hg/makeDb/doc/hs1/hprc.txt
  • lines changed 109, context: html, text, full: html, text
    7e9b6458995674dda83a8161788aa7b325875b9f Wed Sep 6 10:58:17 2023 -0700
    adding the multiple alignment to the hs1 browser refs #31561
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 14, context: html, text, full: html, text
    cb8a05fe7553710ba59e92af53662f2e524c232e Sun Sep 10 10:30:25 2023 -0700
    RefSeq update brings in a number of obsolete assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    cb8a05fe7553710ba59e92af53662f2e524c232e Sun Sep 10 10:30:25 2023 -0700
    RefSeq update brings in a number of obsolete assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    ebe26380aabb4931540c61996aa48e0d2554598a Sat Sep 9 21:35:49 2023 -0700
    adding 4 for an update refs #29545
• src/hg/makeDb/doc/mito/genes.txt
  • lines changed 179, context: html, text, full: html, text
    919608dc52ac2e23dcf184d2fcfb7b6f93103a52 Mon Sep 4 14:18:26 2023 -0700
    collecting the genes from various browsers no redmine
• src/hg/makeDb/doc/mito/snpView.txt
  • lines changed 158, context: html, text, full: html, text
    8a687b59577f35717a86b46b3a9f4e4ffc843ff5 Mon Sep 4 14:13:21 2023 -0700
    SNP view construction script for 104-way no redmine
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    4d3aec676416d678696b099fe4ba73137313415a Sat Sep 9 21:31:38 2023 -0700
    adding 4 for an update refs #29545
• src/hg/makeDb/trackDb/evaSnp5.html
  • lines changed 213, context: html, text, full: html, text
    7e690f333eb9b803b3a6fcceed6a404f3fdf2fb7 Thu Sep 7 12:23:00 2023 -0700
    Staging new EvaSnp5 data QA Ready, refs #32095
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
  • lines changed 106, context: html, text, full: html, text
    cceb66c59fe9cdc9b97ea9218efbc1db474ad07b Fri Sep 8 05:06:43 2023 -0700
    creating an alpha version of the clinvar track. This is the only way to play with changes to the clinvar track without risking a leak of the changes to the RR via the otto push and without pausing the otto push, no redmine yet
  • lines changed 1, context: html, text, full: html, text
    2a1a263c3c172bdf671affee41e2aa71b00534b4 Fri Sep 8 06:12:43 2023 -0700
    clinvar has added a new mol consequence type, no redmine
• src/hg/makeDb/trackDb/human/clinvar.ra
  • lines changed 105, context: html, text, full: html, text
    527a3531a7db419bad01537556693e9424e0ee04 Fri Sep 8 05:00:23 2023 -0700
    removing the trackDb prefix for clinvar tracks, no redmine
  • lines changed 1, context: html, text, full: html, text
    2a1a263c3c172bdf671affee41e2aa71b00534b4 Fri Sep 8 06:12:43 2023 -0700
    clinvar has added a new mol consequence type, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    f59a0760e5064af60766ae929d73d7c9626a5bcf Wed Sep 6 01:36:24 2023 -0700
    tiny change to gnomad docs, refs #31989
  • lines changed 2, context: html, text, full: html, text
    1568d08d5e4dcf92808af8928bd1d9d80aef45d6 Wed Sep 6 04:41:52 2023 -0700
    another tiny change to gnomad docs, refs #31989
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
  • lines changed 2, context: html, text, full: html, text
    c32de191ec21cf1f6e5750aa16c218ddc9cef9e2 Fri Sep 8 10:29:42 2023 -0700
    Clarifying the transcript ranking text on knownGene, refs #31834
• src/hg/makeDb/trackDb/human/hg38/knownGene.v44.alpha.ra
  • lines changed 44, context: html, text, full: html, text
    27e4f572c19f22f0975732c98eb5f02fe819ed87 Fri Sep 8 10:47:00 2023 -0700
    Removing kownGene alpha ra files, refs #30840 #30841
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
  • lines changed 1, context: html, text, full: html, text
    c84fcbdfd56805ce3240b4604c8ed3c8dd984a9e Thu Sep 7 10:11:33 2023 -0700
    Fixing up the URL label to be clearer, using the language that COSMIC uses themselves, refs #29625
  • lines changed 1, context: html, text, full: html, text
    65356a77a4d87cecf7df11712827e57cd1c10358 Fri Sep 8 10:53:16 2023 -0700
    Final clean up after recent knownGene release, no RM.
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 105, context: html, text, full: html, text
    527a3531a7db419bad01537556693e9424e0ee04 Fri Sep 8 05:00:23 2023 -0700
    removing the trackDb prefix for clinvar tracks, no redmine
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    acf32680ffc6c29c7bda0588e65a6af46d3d389c Thu Sep 7 17:13:40 2023 -0700
    Swapping links to https. Some of these were broken and after talking to LOVD, it was due to how they redirected http to https. No RM.
  • lines changed 1, context: html, text, full: html, text
    527a3531a7db419bad01537556693e9424e0ee04 Fri Sep 8 05:00:23 2023 -0700
    removing the trackDb prefix for clinvar tracks, no redmine
  • lines changed 2, context: html, text, full: html, text
    cceb66c59fe9cdc9b97ea9218efbc1db474ad07b Fri Sep 8 05:06:43 2023 -0700
    creating an alpha version of the clinvar track. This is the only way to play with changes to the clinvar track without risking a leak of the changes to the RR via the otto push and without pausing the otto push, no redmine yet
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 39, context: html, text, full: html, text
    27e4f572c19f22f0975732c98eb5f02fe819ed87 Fri Sep 8 10:47:00 2023 -0700
    Removing kownGene alpha ra files, refs #30840 #30841
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    1c249a4b1bdb700c68999bff5724a1cdfa75ac02 Wed Sep 6 17:25:50 2023 -0700
    Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    7e690f333eb9b803b3a6fcceed6a404f3fdf2fb7 Thu Sep 7 12:23:00 2023 -0700
    Staging new EvaSnp5 data QA Ready, refs #32095
• src/hg/utils/otto/malacards/update.sh
  • lines changed 20, context: html, text, full: html, text
    1ac6479e16d76dbfce8121b3aa493c3d9122a39a Tue Sep 5 06:37:48 2023 -0700
    adding otto script for malacards to git repo and adding the missing cd command, refs #26446
• src/inc/common.mk
  • lines changed 6, context: html, text, full: html, text
    85ea334cfc714b9ab269bcada5d43bf61ca44800 Sun Sep 10 21:12:26 2023 -0700
    Allow addition of LDFLAGS from the environment and remove no-op setting of CFLAGS
• src/lib/bbiWrite.c
  • lines changed 1, context: html, text, full: html, text
    0f82da7969da1610cbaa96808797f4458c2d13a6 Tue Sep 5 07:27:44 2023 -0700
    switching to LC_ALL in usage help, refs #20910
• src/optimalLeaf/makefile
  • lines changed 7, context: html, text, full: html, text
    63a55125598d99f88184730980751df9edf75fe0 Sun Sep 10 23:38:32 2023 -0700
    used of non-standard make variables for C++ causes difficulty compiling in some environments
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 2, context: html, text, full: html, text
    0f82da7969da1610cbaa96808797f4458c2d13a6 Tue Sep 5 07:27:44 2023 -0700
    switching to LC_ALL in usage help, refs #20910
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    0f82da7969da1610cbaa96808797f4458c2d13a6 Tue Sep 5 07:27:44 2023 -0700
    switching to LC_ALL in usage help, refs #20910
• src/utils/bedToBigBed/tests/expected/notSorted.err
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    44e6d5f1750cb51c6de03dd15e3f29c0d746ba79 Thu Sep 7 15:57:06 2023 -0700
    fixing up bedToBigBed expected output since the error message got reworded slightly.
• src/utils/qa/weeklybld/buildEnv.csh
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    8edee9f43f774a8d0bad355cc5b1a84341c25241 Mon Sep 11 10:45:39 2023 -0700
    v454 preview2
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
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    21d7c635c49a794bf9c3b807d527e5c5339210f0 Thu Sep 7 00:27:02 2023 -0700
    Tweak the scripsts that run robots written in C that should use https, since htmlPage code can use https but does not support redirects at this time. We are turning on redirect to https everywhere.
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    21d7c635c49a794bf9c3b807d527e5c5339210f0 Thu Sep 7 00:27:02 2023 -0700
    Tweak the scripsts that run robots written in C that should use https, since htmlPage code can use https but does not support redirects at this time. We are turning on redirect to https everywhere.

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• files changed: 75