All File Changes

v434_preview to v434_preview2 (2022-07-05 to 2022-07-11) v434

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    12a97f875efa825f7e316f79bec9f820de635970 Wed Jul 6 11:53:35 2022 -0700
    adding file missing from previous commit, ,refs #29583
• src/hg/hgTracks/bamTrack.c
  • lines changed 8, context: html, text, full: html, text
    7e6bfce5ff65b67d6e75b239c8b7fb3270f475fb Wed Jun 29 19:11:10 2022 -0700
    Making baseColorDrawItem(), baseColorOverdrawDiff(), and baseColorOverdrawQInsert() functions to from mrnaSeq parameter to qSeq/qOffset parameter pair. Currently qOffset is always zero, but have plans to use it so that not necessarily all of query sequence needs to be loaded. qSeq may be a whole chromosome for a chain.
  • lines changed 1, context: html, text, full: html, text
    76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
    Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 5, context: html, text, full: html, text
    d4e14ca0a20861998ad7c807a6b2473ade5c3c4f Wed Jul 6 06:31:12 2022 -0700
    add label hints for doWiggle and maxWindowCoverage tracks, refs #29715
• src/hg/hgTracks/cds.c
  • lines changed 137, context: html, text, full: html, text
    e1abdbe4945561b19dad7d4139982f511e4b2b5d Wed Jun 29 19:12:39 2022 -0700
    Expanding coloring based on query sequence to include chain tracks.
  • lines changed 32, context: html, text, full: html, text
    76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
    Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
  • lines changed 24, context: html, text, full: html, text
    91c4d60a5bcbf19016e3eb0fd4fdcccb2588a5b4 Thu Jun 30 19:03:04 2022 -0700
    Fixing BAM base level coloring recently introduced bug. Making the purple incompletely aligned ends be a little more visible and include the size of missing begin or end if zooomed in enough.
  • lines changed 34, context: html, text, full: html, text
    03270520d98b7251dc50b75c1a2815f8f5de63ec Fri Jul 1 18:37:18 2022 -0700
    Making ends with unmatched query just 2 pixels again. Need to fix some stuff before capping with anything more fancy.
  • lines changed 151, context: html, text, full: html, text
    3d2299a0b9690e88341c660965d913ad105970f2 Sun Jul 3 15:03:16 2022 -0700
    Improving caching behavior. Allowing it to cache less than a complete sequence. Handling reverse strand better.
  • lines changed 6, context: html, text, full: html, text
    ae53d1dc78b4079bb3427597efe465aa7bfe6ddc Mon Jul 4 17:34:00 2022 -0700
    Changing debugging output.
  • lines changed 1, context: html, text, full: html, text
    1da73beaaf2e06a18feeb0b15f5f3786a66fb60b Fri Jul 8 14:07:23 2022 -0700
    Making little purple and green ticks at end of RNA alignments smaller like they were before.
• src/hg/hgTracks/cds.h
  • lines changed 5, context: html, text, full: html, text
    7e6bfce5ff65b67d6e75b239c8b7fb3270f475fb Wed Jun 29 19:11:10 2022 -0700
    Making baseColorDrawItem(), baseColorOverdrawDiff(), and baseColorOverdrawQInsert() functions to from mrnaSeq parameter to qSeq/qOffset parameter pair. Currently qOffset is always zero, but have plans to use it so that not necessarily all of query sequence needs to be loaded. qSeq may be a whole chromosome for a chain.
  • lines changed 1, context: html, text, full: html, text
    76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
    Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
  • lines changed 2, context: html, text, full: html, text
    ae53d1dc78b4079bb3427597efe465aa7bfe6ddc Mon Jul 4 17:34:00 2022 -0700
    Changing debugging output.
• src/hg/hgTracks/chainTrack.c
  • lines changed 9, context: html, text, full: html, text
    e1abdbe4945561b19dad7d4139982f511e4b2b5d Wed Jun 29 19:12:39 2022 -0700
    Expanding coloring based on query sequence to include chain tracks.
  • lines changed 1, context: html, text, full: html, text
    76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
    Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    ae53d1dc78b4079bb3427597efe465aa7bfe6ddc Mon Jul 4 17:34:00 2022 -0700
    Changing debugging output.
  • lines changed 12, context: html, text, full: html, text
    d4e14ca0a20861998ad7c807a6b2473ade5c3c4f Wed Jul 6 06:31:12 2022 -0700
    add label hints for doWiggle and maxWindowCoverage tracks, refs #29715
  • lines changed 2, context: html, text, full: html, text
    10a07357508dcfdfcec414d5129388449eb0a083 Fri Jul 8 14:08:02 2022 -0700
    Removing debugging info to stderr on query cache.
• src/hg/hgTracks/hgTracks.h
  • lines changed 7, context: html, text, full: html, text
    e1abdbe4945561b19dad7d4139982f511e4b2b5d Wed Jun 29 19:12:39 2022 -0700
    Expanding coloring based on query sequence to include chain tracks.
  • lines changed 1, context: html, text, full: html, text
    c3713514c6475447ac5e1350c07c6610662fb916 Thu Jun 30 11:27:55 2022 -0700
    Adding qSize structure to linkedFeatures, the better to make psls out of it for base-by-base view of chains.
  • lines changed 9, context: html, text, full: html, text
    d4e14ca0a20861998ad7c807a6b2473ade5c3c4f Wed Jul 6 06:31:12 2022 -0700
    add label hints for doWiggle and maxWindowCoverage tracks, refs #29715
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    7e6bfce5ff65b67d6e75b239c8b7fb3270f475fb Wed Jun 29 19:11:10 2022 -0700
    Making baseColorDrawItem(), baseColorOverdrawDiff(), and baseColorOverdrawQInsert() functions to from mrnaSeq parameter to qSeq/qOffset parameter pair. Currently qOffset is always zero, but have plans to use it so that not necessarily all of query sequence needs to be loaded. qSeq may be a whole chromosome for a chain.
  • lines changed 5, context: html, text, full: html, text
    76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
    Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
  • lines changed 16, context: html, text, full: html, text
    d4e14ca0a20861998ad7c807a6b2473ade5c3c4f Wed Jul 6 06:31:12 2022 -0700
    add label hints for doWiggle and maxWindowCoverage tracks, refs #29715
• src/hg/hgc/hgc.c
  • lines changed 152, context: html, text, full: html, text
    a1cfd4eb6e2f1e0eb0e8756fd02ebcb602c77687 Tue Jun 28 13:08:30 2022 -0700
    Making base-by-base alignment display work for bigChains and bigPsls.
  • lines changed 62, context: html, text, full: html, text
    957e6639419c3faf3ca76d891903ea3023681555 Tue Jun 28 18:02:27 2022 -0700
    Making 'View details of parts of alignment within browser window.' link on bigPsl and psl work better when query sequence is big.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 22, context: html, text, full: html, text
    78979d05311d0c6ea80313ef4b0861fce9d5ddc5 Wed Jul 6 11:57:51 2022 -0700
    Code review changes refs #29706
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    cedffcafd9704d81d79381318468b85e900f2653 Thu Jun 30 15:51:07 2022 -0700
    Documenting new otherTwoBitUrl tag and addition to baseColorUseSequence tag. Also fixing little typo in bigDataUrl2 tag.
  • lines changed 17, context: html, text, full: html, text
    cf0805c7d57bf59f29969d3b17ba7a17c57cb81e Tue Jul 5 12:59:33 2022 -0700
    Adding coloring options and otherTwoBitUrl to chains and psls.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 3, context: html, text, full: html, text
    cedffcafd9704d81d79381318468b85e900f2653 Thu Jun 30 15:51:07 2022 -0700
    Documenting new otherTwoBitUrl tag and addition to baseColorUseSequence tag. Also fixing little typo in bigDataUrl2 tag.
  • lines changed 32, context: html, text, full: html, text
    cf0805c7d57bf59f29969d3b17ba7a17c57cb81e Tue Jul 5 12:59:33 2022 -0700
    Adding coloring options and otherTwoBitUrl to chains and psls.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 14, context: html, text, full: html, text
    cedffcafd9704d81d79381318468b85e900f2653 Thu Jun 30 15:51:07 2022 -0700
    Documenting new otherTwoBitUrl tag and addition to baseColorUseSequence tag. Also fixing little typo in bigDataUrl2 tag.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    fdc1a8d358ba5077b8503c5a399ed940e0b5f2f4 Fri Jul 8 11:24:16 2022 -0700
    Updating the grant number on pubs page refs #28595
  • lines changed 1, context: html, text, full: html, text
    67c6ad9c41851ea14e88b5d0db49595cef1f2815 Fri Jul 8 11:54:50 2022 -0700
    Adding full grant number refs #28595
  • lines changed 2, context: html, text, full: html, text
    71be930e95dc52c19f697b0366e3a95a3e158707 Mon Jul 11 08:02:57 2022 -0700
    Adding grant number to heading after email with Max, no RM
• src/hg/htdocs/training/upcoming.html
  • lines changed 27, context: html, text, full: html, text
    bb3edb67265e4ef26dcf90a81e300ac287f7939d Wed Jul 6 14:26:06 2022 -0700
    removed completed vienna and netherlands workshops
• src/hg/js/hgHubConnect.js
  • lines changed 19, context: html, text, full: html, text
    29098c97a3550b6caa4eb9e84e51b2dcaf1f7137 Fri Jul 8 01:54:43 2022 -0700
    fixing copy button bug that must have been there forever, thanks to Chris who found it. refs #29713
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    e3b577eca3df08b19af7168ac86223be72b91546 Wed Jun 29 19:05:57 2022 -0700
    Adding 2bit option to baseColorUseSequence tag.
  • lines changed 3, context: html, text, full: html, text
    4f7e594f8fdbf052a0d00a6c981c55f49d054782 Thu Jun 30 11:20:59 2022 -0700
    Enabling qInsert and incomplete-matching-to-query for chains and bigChains.
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 27, context: html, text, full: html, text
    326745a4a6e13e07a168cae439e93e7faa2401d2 Tue Jul 5 16:10:38 2022 -0700
    adding 27 for an update refs #29545
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 33, context: html, text, full: html, text
    2d2c836edaff720e31ac3fab4433e15f744b7245 Wed Jul 6 12:46:13 2022 -0700
    improve the description vs. the organism strings in the hub.txt refs #29545
  • lines changed 6, context: html, text, full: html, text
    1290eaf14faaf78d5ba17002f6e218a861f995a4 Wed Jul 6 14:06:28 2022 -0700
    the description is used in the pull down menu on gateway page should be common name then use organism for extra assembly info refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d9ed87e2aaef228e0db6ee588aac864ce1023cd1 Thu Jul 7 11:19:01 2022 -0700
    adding one for GenArk update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    3724599e33363bbf5e1807d5180ef0d5bafcfd6e Fri Jul 8 10:30:04 2022 -0700
    adding 7 for a GenArk update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 47, context: html, text, full: html, text
    491eccff49c233439e347c3dfa12f220bc09ad4f Wed Jul 6 16:17:52 2022 -0700
    recent updates have moved many assemblies to legacy status refs #29545
  • lines changed 6, context: html, text, full: html, text
    a903f12655c0a249e565738da40da8380883f831 Fri Jul 8 12:06:22 2022 -0700
    GenArk updates moved assemblies to legacy refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    3b6ebe76f680c5b2c7bf7eaa99e99b7ee63f41b3 Wed Jul 6 15:43:20 2022 -0700
    adding three for update refs #29545
  • lines changed 33, context: html, text, full: html, text
    7d575ebda40d60d503e170bcbd65c41ce9761cf0 Fri Jul 8 16:31:05 2022 -0700
    catch up GenArk with VGP assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    0b9f31851f3e27dd8440bedb84d0a65280439e51 Thu Jul 7 15:11:36 2022 -0700
    adding five for GenArk update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    adf76850d9c32b6dcfe0c78b4a218c9c96c08331 Wed Jul 6 10:50:52 2022 -0700
    adding two updates refs #29545
  • lines changed 3, context: html, text, full: html, text
    96e0638386a941c3890e3ef66db4fb2860c38b28 Fri Jul 8 14:48:56 2022 -0700
    catching up this GenArk list with the VGP assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    e6ab9f0288b5e46ed6f476b1f274015ad6e30c7e Thu Jul 7 14:10:27 2022 -0700
    adding three for an update refs #29545
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 2, context: html, text, full: html, text
    d0f769fd1aadc0641c34e742791c2ad9e27f5f7b Wed Jul 6 10:02:33 2022 -0700
    Fixing up the track desc in response by author, refs #23883
  • lines changed 3, context: html, text, full: html, text
    be16de4acd8ff396b9b2a58f5632275ccf3131e5 Wed Jul 6 12:12:52 2022 -0700
    Adding a link to the raw data at author's request, refs #23883
• src/hg/makeDb/trackDb/human/hmc.ra
  • lines changed 1, context: html, text, full: html, text
    a12c0a0d61a7f0ccc90da461fb8efa4c8e6f4b5a Tue Jul 5 16:10:07 2022 -0700
    Updating pennantIcon for the hmc track, refs #29153
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9895865c5765b9d8a3f07ac87f00ec227ea94730 Tue Jul 5 15:52:14 2022 -0700
    Removing release tag, refs #29153
  • lines changed 2, context: html, text, full: html, text
    3a1f19f3ba95f6d26ca2210fd52fab880af7d172 Fri Jul 8 02:01:11 2022 -0700
    fixing lrg search regex, refs #29720
  • lines changed 2, context: html, text, full: html, text
    ffcde059a691b371bdb9685398922da1e8f14af1 Fri Jul 8 05:23:02 2022 -0700
    tiny trackDb change for dbsnp, email with Chris
  • lines changed 1, context: html, text, full: html, text
    3efadb79e9d0cec978fad5ab911a90a288762c7a Fri Jul 8 17:38:55 2022 -0700
    Changing back the termRegex line for searchTable lrg, refs #29720
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 4, context: html, text, full: html, text
    83670939fee1a5751c5c0b7fa58b2d2343ddb6c6 Mon Jul 4 17:35:08 2022 -0700
    Adding chain and bigChain to some of the base-by-base display tags.
• src/inc/cacheTwoBit.h
  • lines changed 27, context: html, text, full: html, text
    7580a364f0819e5ab6244b2b1ff685980b93c188 Fri Jul 1 18:25:00 2022 -0700
    First cut at cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.
  • lines changed 11, context: html, text, full: html, text
    f8458ca93f0c0abe5456789dd7a9618d63e55e5b Sun Jul 3 15:01:40 2022 -0700
    Fixing bug on reverse strand and improving cache behavior. Making it so you can ask for a cached sequence without aborting if it doesn't exist.
  • lines changed 1, context: html, text, full: html, text
    efc87af4e5921d966a5bbc9ce8832b7f374f4599 Mon Jul 4 17:31:44 2022 -0700
    Added file parameter to cacheTwoBitRangesPrintStats.
  • lines changed 3, context: html, text, full: html, text
    ea5551fd4f1ea0c73e95fb5ee1f5ecd557509854 Fri Jul 8 14:06:33 2022 -0700
    Improving comments and diagnostic output.
• src/inc/common.mk
  • lines changed 8, context: html, text, full: html, text
    d49adb89518278594c8e7539134002658d8115df Thu Jul 7 11:49:40 2022 -0700
    update for brew version on mac OSX changes name of mariadb file locations no redmine
• src/inc/twoBit.h
  • lines changed 3, context: html, text, full: html, text
    be07e4273228ea43ed8f24dc076af4a633e7916f Sun Jul 3 14:58:45 2022 -0700
    Adding twoBitHasSeq function to query if a sequence exists in file.
• src/lib/cacheTwoBit.c
  • lines changed 175, context: html, text, full: html, text
    7580a364f0819e5ab6244b2b1ff685980b93c188 Fri Jul 1 18:25:00 2022 -0700
    First cut at cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.
  • lines changed 55, context: html, text, full: html, text
    f8458ca93f0c0abe5456789dd7a9618d63e55e5b Sun Jul 3 15:01:40 2022 -0700
    Fixing bug on reverse strand and improving cache behavior. Making it so you can ask for a cached sequence without aborting if it doesn't exist.
  • lines changed 7, context: html, text, full: html, text
    efc87af4e5921d966a5bbc9ce8832b7f374f4599 Mon Jul 4 17:31:44 2022 -0700
    Added file parameter to cacheTwoBitRangesPrintStats.
  • lines changed 7, context: html, text, full: html, text
    ea5551fd4f1ea0c73e95fb5ee1f5ecd557509854 Fri Jul 8 14:06:33 2022 -0700
    Improving comments and diagnostic output.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    7580a364f0819e5ab6244b2b1ff685980b93c188 Fri Jul 1 18:25:00 2022 -0700
    First cut at cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.
• src/lib/twoBit.c
  • lines changed 15, context: html, text, full: html, text
    be07e4273228ea43ed8f24dc076af4a633e7916f Sun Jul 3 14:58:45 2022 -0700
    Adding twoBitHasSeq function to query if a sequence exists in file.
• src/oneShot/testTwoBitRangeCache/testTwoBitRangeCache.c
  • lines changed 230, context: html, text, full: html, text
    a27a778580784849da8b9026ef2e34a5c67a7367 Fri Jul 1 16:50:30 2022 -0700
    Seems to work. I'll fix some of the names, maybe polish it some more, before moving it out of oneShot.
  • lines changed 167, context: html, text, full: html, text
    7580a364f0819e5ab6244b2b1ff685980b93c188 Fri Jul 1 18:25:00 2022 -0700
    First cut at cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.
• src/utils/qa/checkHTTPS
  • lines changed 1, context: html, text, full: html, text
    969f1306461a0420ad872004e5b36aefe0edb8ef Tue Jul 5 16:53:38 2022 -0700
    Adding servername to make sure domains running on same machine are properly caught, this fixed cells.edu not being read as genome.ucsc.edu. Refs email 'Site Certificates expiring in < 30 days'
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    b03770df8ed5de885a01f232b9499464e1fc8118 Mon Jul 11 10:05:05 2022 -0700
    v434 preview2, refs #29716

• lines changed: 1767
• files changed: 77