All File Changes

v450_preview2 to v450_base (2023-06-20 to 2023-06-26) v450

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1a730a0c2e91ed2d48a2030527649a096645dbaa Sun Jun 25 01:11:54 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1a730a0c2e91ed2d48a2030527649a096645dbaa Sun Jun 25 01:11:54 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1a730a0c2e91ed2d48a2030527649a096645dbaa Sun Jun 25 01:11:54 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    1a730a0c2e91ed2d48a2030527649a096645dbaa Sun Jun 25 01:11:54 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1a730a0c2e91ed2d48a2030527649a096645dbaa Sun Jun 25 01:11:54 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/geoIpToCountry/README
  • lines changed 12, context: html, text, full: html, text
    6ff8d018525b73c8836fa687bf16f45ccc1a11f1 Wed Jun 21 23:33:34 2023 -0700
    Adding a utility for using our existing geoIp infrastructure to lookup a 2-letter country code from an IP address (IPv4 or IPv6). Gives an error if the IP address is malformed, gives an error if hgcentral.geoIpCountry6 table does not exist, then uses it to lookup the country. If it is not found in our Maxmind table, then it returns "not found". Hopefully Hiram and others can use this.
• src/hg/geoIpToCountry/geoIpToCountry.c
  • lines changed 64, context: html, text, full: html, text
    6ff8d018525b73c8836fa687bf16f45ccc1a11f1 Wed Jun 21 23:33:34 2023 -0700
    Adding a utility for using our existing geoIp infrastructure to lookup a 2-letter country code from an IP address (IPv4 or IPv6). Gives an error if the IP address is malformed, gives an error if hgcentral.geoIpCountry6 table does not exist, then uses it to lookup the country. If it is not found in our Maxmind table, then it returns "not found". Hopefully Hiram and others can use this.
  • lines changed 81, context: html, text, full: html, text
    7176f0c1738d9a29208b1206d4427e4ee16ce7d0 Thu Jun 22 15:04:39 2023 -0700
    now working on a list and can print out full country names no redmine
  • lines changed 4, context: html, text, full: html, text
    2f95561ff616d8660c93bfeab326763ddbb0f7c2 Thu Jun 22 19:23:01 2023 -0700
    free up the result from the query no redmine
• src/hg/geoIpToCountry/ip.list
  • lines changed 18, context: html, text, full: html, text
    7176f0c1738d9a29208b1206d4427e4ee16ce7d0 Thu Jun 22 15:04:39 2023 -0700
    now working on a list and can print out full country names no redmine
• src/hg/geoIpToCountry/makefile
  • lines changed 21, context: html, text, full: html, text
    6ff8d018525b73c8836fa687bf16f45ccc1a11f1 Wed Jun 21 23:33:34 2023 -0700
    Adding a utility for using our existing geoIp infrastructure to lookup a 2-letter country code from an IP address (IPv4 or IPv6). Gives an error if the IP address is malformed, gives an error if hgcentral.geoIpCountry6 table does not exist, then uses it to lookup the country. If it is not found in our Maxmind table, then it returns "not found". Hopefully Hiram and others can use this.
  • lines changed 5, context: html, text, full: html, text
    65e1825f28d198d64399e07bcfde2ca00c9e944e Thu Jun 22 15:06:39 2023 -0700
    add compile target no redmine
• src/hg/geoIpToCountry/twoLetterCodes.tsv
  • lines changed 250, context: html, text, full: html, text
    7176f0c1738d9a29208b1206d4427e4ee16ce7d0 Thu Jun 22 15:04:39 2023 -0700
    now working on a list and can print out full country names no redmine
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    cdc3b001835dd48266edca0bd125ea25942247c3 Fri Jun 23 05:07:21 2023 -0700
    fixing ct trash icon when more than one ct is loaded. adding tooltip, moving icon to the left side. refs #31504
• src/hg/hgGeneGraph/README.txt
  • lines changed 5, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 150, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    06605872392e3b2265dd48b380179cb57e38640c Tue Jun 20 17:29:47 2023 -0700
    Add another missing call to htmlEncode, this time during the saving of session names, refs #31338
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    cdc3b001835dd48266edca0bd125ea25942247c3 Fri Jun 23 05:07:21 2023 -0700
    fixing ct trash icon when more than one ct is loaded. adding tooltip, moving icon to the left side. refs #31504
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 29, context: html, text, full: html, text
    1471dd6785665dbe477cbfd128fde779f40e046c Thu Jun 22 11:28:54 2023 -0700
    add specific message for users that fail the captcha test refs #31325
  • lines changed 1, context: html, text, full: html, text
    7886f37c844729b87414796971d4b02c29eee48b Fri Jun 23 18:23:30 2023 -0700
    change mailto prompt refs #31325
  • lines changed 1, context: html, text, full: html, text
    4fe6b615585c57c8c9fa7510d542bf9e7fc55c56 Sun Jun 25 23:39:22 2023 -0700
    default THRESHOLD -0.1 will allow anything in refs #31325
  • lines changed 1, context: html, text, full: html, text
    6edcaa6369e2e2c2baa1c0c84e99e2474e259fdf Sun Jun 25 23:59:25 2023 -0700
    correct email genome-www@soe not my test email refs #31325
  • lines changed 2, context: html, text, full: html, text
    2871f2dfd5d65014281d7cde31d0f8c7edf787b2 Mon Jun 26 10:23:28 2023 -0700
    correctly use mailTo function for genome-www@soe.ucsc.edu refs #31325
• src/hg/htdocs/goldenPath/help/cloud.html
  • lines changed 2, context: html, text, full: html, text
    1e5471fab322302a10e19adf907ff26e020535f0 Thu Jun 22 12:55:37 2023 +0200
    adding -bed option to bigBedToBed, also removing the -maxItems option as it never worked, is not used anywhere at least in our code repo and also fixing the documentation page and a typo in the usage docs and the documentation page. refs #31531
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    78bd22b50e73eb5f60e403c47bf0c4bbc35c66bf Thu Jun 22 02:11:47 2023 -0700
    increasing distance of alt/fix patch note warning, refs #31121
  • lines changed 1, context: html, text, full: html, text
    cdc3b001835dd48266edca0bd125ea25942247c3 Fri Jun 23 05:07:21 2023 -0700
    fixing ct trash icon when more than one ct is loaded. adding tooltip, moving icon to the left side. refs #31504
• src/hg/inc/bigChain.h
  • lines changed 74, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/inc/geoMirror.h
  • lines changed 4, context: html, text, full: html, text
    6ff8d018525b73c8836fa687bf16f45ccc1a11f1 Wed Jun 21 23:33:34 2023 -0700
    Adding a utility for using our existing geoIp infrastructure to lookup a 2-letter country code from an IP address (IPv4 or IPv6). Gives an error if the IP address is malformed, gives an error if hgcentral.geoIpCountry6 table does not exist, then uses it to lookup the country. If it is not found in our Maxmind table, then it returns "not found". Hopefully Hiram and others can use this.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    925d3cb6efcdd497a15d38b0fa3178495b2247c4 Mon Jun 26 12:08:03 2023 -0700
    New version number v450
• src/hg/js/hgTracks.js
  • lines changed 70, context: html, text, full: html, text
    aa3580cd95ee1400a9fa6ad63ce7db846059185a Fri Jun 23 10:13:52 2023 -0700
    Make notification box redraw highlights, refs #30670
• src/hg/lib/bigChain.c
  • lines changed 181, context: html, text, full: html, text
    72535938e4d91de0bd56e9a3fd77b76f47e0b2da Fri Jun 23 13:57:33 2023 -0700
    add bigChain parsing code to library
• src/hg/lib/bigChain.h
  • lines changed 74, context: html, text, full: html, text
    72535938e4d91de0bd56e9a3fd77b76f47e0b2da Fri Jun 23 13:57:33 2023 -0700
    add bigChain parsing code to library
  • lines changed 74, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/lib/chainBreaks.as
  • lines changed 14, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/lib/geoMirror.c
  • lines changed 66, context: html, text, full: html, text
    6ff8d018525b73c8836fa687bf16f45ccc1a11f1 Wed Jun 21 23:33:34 2023 -0700
    Adding a utility for using our existing geoIp infrastructure to lookup a 2-letter country code from an IP address (IPv4 or IPv6). Gives an error if the IP address is malformed, gives an error if hgcentral.geoIpCountry6 table does not exist, then uses it to lookup the country. If it is not found in our Maxmind table, then it returns "not found". Hopefully Hiram and others can use this.
• src/hg/lib/hubConnect.c
  • lines changed 10, context: html, text, full: html, text
    35f4a8a263bc827c1d57bb9a0fbdf13941d1a3f3 Thu Jun 22 13:19:36 2023 -0700
    Revert "First attempt at surfacing up hub errors when the requested hub database doesn't exist, refs #30832" This reverts commit 8f399a09d7b39a87eadc3cc0a89c33598ddc5d2a. Conflicts: src/hg/lib/trackHub.c
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    72535938e4d91de0bd56e9a3fd77b76f47e0b2da Fri Jun 23 13:57:33 2023 -0700
    add bigChain parsing code to library
• src/hg/lib/trackHub.c
  • lines changed 6, context: html, text, full: html, text
    35f4a8a263bc827c1d57bb9a0fbdf13941d1a3f3 Thu Jun 22 13:19:36 2023 -0700
    Revert "First attempt at surfacing up hub errors when the requested hub database doesn't exist, refs #30832" This reverts commit 8f399a09d7b39a87eadc3cc0a89c33598ddc5d2a. Conflicts: src/hg/lib/trackHub.c
• src/hg/makeDb/doc/hg38/hprcBreaks.txt
  • lines changed 24, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/makeDb/revel/revel.as
  • lines changed 5, context: html, text, full: html, text
    1a51df9e3e5ada3fef5b68622e0fb4d2b9cbffe8 Thu Jun 22 02:09:59 2023 -0700
    fixing up revel.as file, email from Angie, found by buildTableDescriptions cron job
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/pyLib/README.txt
  • lines changed 8, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/hgLib.py
  • lines changed 2, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/hgLib3.py
  • lines changed 1040, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/makefile
  • lines changed 15, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/LICENSE
  • lines changed 19, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/__init__.py
  • lines changed 185, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/_auth.py
  • lines changed 266, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/charset.py
  • lines changed 209, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/connections.py
  • lines changed 1367, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/CLIENT.py
  • lines changed 38, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/COMMAND.py
  • lines changed 32, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/CR.py
  • lines changed 68, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/ER.py
  • lines changed 474, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/FIELD_TYPE.py
  • lines changed 31, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/FLAG.py
  • lines changed 15, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/SERVER_STATUS.py
  • lines changed 10, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/constants/__init__.py
  • lines changed 0, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/converters.py
  • lines changed 364, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/cursors.py
  • lines changed 496, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/err.py
  • lines changed 143, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/optionfile.py
  • lines changed 18, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/protocol.py
  • lines changed 358, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/pyLib/pymysql/times.py
  • lines changed 20, context: html, text, full: html, text
    fded6ce46cb167faaae559ff93b050c2b7d18ff1 Mon Jun 26 08:59:00 2023 -0700
    Porting hgGeneGraph to python3. refs #31563
• src/hg/utils/bigChainBreaks/bigChainBreaks.c
  • lines changed 112, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/utils/bigChainBreaks/makefile
  • lines changed 3, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    13d3857bbc66cfaeac0b2b9b1f90340ad7fceff9 Mon Jun 26 05:58:25 2023 -0700
    first pass at a synteny breaks track
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 1, context: html, text, full: html, text
    8a1149c22482aaa4787bb02799a62f348c5dc2b2 Thu Jun 22 10:17:38 2023 -0700
    Send verbose usher_to_taxonium output to log
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 1, context: html, text, full: html, text
    ba4425b7d509f2d52bec87b22c3cd8a6802ef3db Thu Jun 22 10:17:25 2023 -0700
    Not making full nextalign.fa.xz at this point, just incrementals.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 17, context: html, text, full: html, text
    e2df9883de70a2ab2d08b96aaec1a62f916a426a Thu Jun 22 10:17:09 2023 -0700
    Update datasets command line options and biosample filename for latest version. pangoLEARN has been discontinued so use default usher mode in pangolin and skip scorpio for speed.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 15, context: html, text, full: html, text
    2f86bf00b7eff014176677a0bfb4fdaaf9ad842f Thu Jun 22 10:17:15 2023 -0700
    Added recombinant spotted by @aviczhl2 in sars-cov-2-variants/lineage-proposals#174
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 1, context: html, text, full: html, text
    9011b709f1fa87332b94a5920062582f5a725f68 Thu Jun 22 10:17:30 2023 -0700
    Watch out for empty name and date columns for COG-UKs in GenBank
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 135, context: html, text, full: html, text
    5d6035bbe436dacd64aeb482b8b45669f1cbdf49 Thu Jun 22 09:34:26 2023 -0700
    Many new lineages (and a few tweaks). pango-designation v1.21
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
  • lines changed 1, context: html, text, full: html, text
    5dd7dc49abd77ba2cbbebba8d818cdacf5d00af8 Thu Jun 22 10:17:00 2023 -0700
    pangoLEARN has been discontinued so use default usher mode in pangolin and skip scorpio for speed.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    925d3cb6efcdd497a15d38b0fa3178495b2247c4 Mon Jun 26 12:08:03 2023 -0700
    New version number v450
• src/utils/qa/hubCheckDraftEmails.py
  • lines changed 155, context: html, text, full: html, text
    68c9515cb37ea293c7eeb106c8761ed1daea644b Wed Jun 21 12:15:44 2023 -0700
    Adding cronjob scripts to run hubCheck for Public Hubs, refs #29319
• src/utils/qa/hubCheckPublicHubs.sh
  • lines changed 17, context: html, text, full: html, text
    68c9515cb37ea293c7eeb106c8761ed1daea644b Wed Jun 21 12:15:44 2023 -0700
    Adding cronjob scripts to run hubCheck for Public Hubs, refs #29319
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    79fb71ae04f82239f2a1bc82cfcf1202dd057c35 Mon Jun 26 11:29:33 2023 -0700
    v450 final build, refs #31506

• lines changed: 6928
• files changed: 78