All File Changes

v443_preview2 to v443_base (2023-01-23 to 2023-01-30) v443

• src/hg/cgilib/hgSeq.c
  • lines changed 112, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/hgGene.h
  • lines changed 8, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/hgGeneData/section.ra
  • lines changed 5, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/primers.c
  • lines changed 49, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgGene/sequence.c
  • lines changed 12, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 39, context: html, text, full: html, text
    2a9d39b83afd2a71f4a0d57042b4a6fcee81a556 Thu Jan 26 14:54:41 2023 -0800
    Added two RSV clade systems (Goya et al. and Ramaekers et al.) and different sources (nextclade vs. tree vs. direct assignments) as coloring options in Nextstrain JSON output for RSV.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 51, context: html, text, full: html, text
    2a9d39b83afd2a71f4a0d57042b4a6fcee81a556 Thu Jan 26 14:54:41 2023 -0800
    Added two RSV clade systems (Goya et al. and Ramaekers et al.) and different sources (nextclade vs. tree vs. direct assignments) as coloring options in Nextstrain JSON output for RSV.
• src/hg/hgTables/hgTables.c
  • lines changed 6, context: html, text, full: html, text
    bf2f400dcf7342c1f31ca8d946b80ac90bbde89a Fri Jan 27 14:52:07 2023 -0800
    improving error message in table browser, no redmine, email with Lou, Brian, Anna
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 7, context: html, text, full: html, text
    00f964165ca3cef379e600e38bdb8d6f959723d9 Mon Jan 23 12:03:26 2023 -0800
    first cut at a demo of squishyPack mode.
• src/hg/hgTracks/chainSnakeTrack.c
  • lines changed 1726, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
  • lines changed 1, context: html, text, full: html, text
    6ac978dbd10fb9d0e8fbbe95c2f19acbcc52539c Tue Jan 24 17:09:31 2023 -0800
    drop printf
  • lines changed 18, context: html, text, full: html, text
    2571f42146cbc4c8d9e869a07ca8312d75330cd0 Thu Jan 26 07:15:22 2023 -0800
    fix compiler error is USE_HAL==0
• src/hg/hgTracks/halSnakeTrack.c
  • lines changed 1943, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/hgTracks/hgTracks.c
  • lines changed 51, context: html, text, full: html, text
    00f964165ca3cef379e600e38bdb8d6f959723d9 Mon Jan 23 12:03:26 2023 -0800
    first cut at a demo of squishyPack mode.
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    00f964165ca3cef379e600e38bdb8d6f959723d9 Mon Jan 23 12:03:26 2023 -0800
    first cut at a demo of squishyPack mode.
• src/hg/hgTracks/makefile
  • lines changed 3, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    00f964165ca3cef379e600e38bdb8d6f959723d9 Mon Jan 23 12:03:26 2023 -0800
    first cut at a demo of squishyPack mode.
  • lines changed 2, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/hgTracks/snake.h
  • lines changed 5, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1945, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/inc/hCommon.h
  • lines changed 6, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    2c16cc726ba2e25098de6f3e16bd88ead5a192f0 Mon Jan 30 10:14:32 2023 -0800
    New version number v443
• src/hg/lib/hCommon.c
  • lines changed 48, context: html, text, full: html, text
    387377eb3982c570bc06728b9e0380c3d1c006ec Wed Jan 25 05:30:25 2023 -0800
    adding linkout to primer3 RT-QPCR primer designer from hgGene, refs #30545
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    c5394c90bfe4cea43b6d7312bc692bdf5a9ec37a Thu Jan 26 14:43:01 2023 -0800
    adding GCF_019356215.1_ASM1935621v1 bacteria Acinetobacter_baumannii per user request refs #29545
  • lines changed 4, context: html, text, full: html, text
    3ed7bd005ff5f12c14b88ad974a38c211ede9988 Thu Jan 26 14:49:11 2023 -0800
    catch up some completed assemblies no redmine
• src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0_assembly_report.txt
  • lines changed 0, context: html, text, full: html, text
    c1880f06222d5757a2d9e1b1ba8f72aa355a672e Thu Jan 26 05:38:33 2023 -0800
    fixing a few MS DOS line endings to get rid of the git warnings in the daily build log, no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    baf89b481bf131014ea4d07d7fbc279428b379b6 Thu Jan 26 14:58:39 2023 -0800
    catching up to some that are already done no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    baf89b481bf131014ea4d07d7fbc279428b379b6 Thu Jan 26 14:58:39 2023 -0800
    catching up to some that are already done no redmine
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 3, context: html, text, full: html, text
    0c4258fc4b7fc9c00d52336fbdcdf7a652d386d7 Tue Jan 24 00:17:37 2023 -0800
    Fixing broken make alpha in trackDb buildTrix.
  • lines changed 3, context: html, text, full: html, text
    fa45027b9591cf32f179047690069902ca70e4b4 Tue Jan 24 09:39:43 2023 -0800
    Revert "Fixing broken make alpha in trackDb buildTrix." This reverts commit 0c4258fc4b7fc9c00d52336fbdcdf7a652d386d7.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    ac84effe1aaae8238148c6f73fc5d165f0eb0107 Mon Jan 23 12:34:01 2023 -0800
    Improving and standardizing the name of the GENCODE tracks, refs #30470
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    392b0fd9286c4bb217df61bd62b8dfa00ad75a10 Mon Jan 23 12:33:18 2023 -0800
    Improving the gnomAD filters based on MLQ, refs #30485
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    276eadb10feb50d4ce1d270bb593da91ca4ddb8d Thu Jan 26 10:27:41 2023 -0800
    Removing configuration boxes for tracks without config options, refs #30040
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 18, context: html, text, full: html, text
    c7e7fc2a9d822f7f83f2ccdd5d68764395809dd2 Tue Jan 24 00:23:02 2023 -0800
    fix row order for assembly stats. refs #29964
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
  • lines changed 1, context: html, text, full: html, text
    273ac35f4aad638497c98381c479458eef5bb281 Tue Jan 24 15:39:49 2023 -0800
    Changing priority on this track which was less than 0, causing it to appear in TB before even knownGene. No RM.
• src/hg/makeDb/trackDb/human/hg38/recombRate.ra
  • lines changed 1, context: html, text, full: html, text
    5371d68730bdad591a703287291fe49ece21abfb Mon Jan 23 14:54:16 2023 -0800
    Changing the deCODE Avg bigDataUrl to display the recombAvg.bw data, refs #30044
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    ac84effe1aaae8238148c6f73fc5d165f0eb0107 Mon Jan 23 12:34:01 2023 -0800
    Improving and standardizing the name of the GENCODE tracks, refs #30470
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 36, context: html, text, full: html, text
    747d414a3053db1454d223d0db7e74a4765e7c98 Tue Jan 24 17:00:18 2023 -0800
    re-introducing chainSnakes into the browser
  • lines changed 9, context: html, text, full: html, text
    b0fdd73c789126c2de7366c08fd823b63ab37a3a Thu Jan 26 13:35:40 2023 -0800
    fix up tagTypes problems
  • lines changed 24, context: html, text, full: html, text
    92ff35b50cf26c8c3c760fcdbf91295a3b7f45bc Sun Jan 29 16:40:08 2023 -0800
    some new snake chain experiments
• src/hg/makeDb/trackDb/human/hmc.ra
  • lines changed 1, context: html, text, full: html, text
    c60efe37dc4131ba3fb49206815dda0627509f68 Tue Jan 24 15:35:46 2023 -0800
    Changing default viz for HMC track based on user/max feedback, refs #29925
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    ac84effe1aaae8238148c6f73fc5d165f0eb0107 Mon Jan 23 12:34:01 2023 -0800
    Improving and standardizing the name of the GENCODE tracks, refs #30470
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    ac84effe1aaae8238148c6f73fc5d165f0eb0107 Mon Jan 23 12:34:01 2023 -0800
    Improving and standardizing the name of the GENCODE tracks, refs #30470
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    b0fdd73c789126c2de7366c08fd823b63ab37a3a Thu Jan 26 13:35:40 2023 -0800
    fix up tagTypes problems
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    03bb5dc5f6ceb04baff4f9d8f4004f090d16dbd5 Thu Jan 26 15:19:15 2023 -0800
    Adding pennantIcons for hg38 patch 14 release, refs #29964
• src/hg/makeDb/trackDb/virus/wuhCor1/ConservedAAs.html
  • lines changed 0, context: html, text, full: html, text
    c1880f06222d5757a2d9e1b1ba8f72aa355a672e Thu Jan 26 05:38:33 2023 -0800
    fixing a few MS DOS line endings to get rid of the git warnings in the daily build log, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/SNVconservation.html
  • lines changed 0, context: html, text, full: html, text
    c1880f06222d5757a2d9e1b1ba8f72aa355a672e Thu Jan 26 05:38:33 2023 -0800
    fixing a few MS DOS line endings to get rid of the git warnings in the daily build log, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/SynConsCodons.html
  • lines changed 0, context: html, text, full: html, text
    c1880f06222d5757a2d9e1b1ba8f72aa355a672e Thu Jan 26 05:38:33 2023 -0800
    fixing a few MS DOS line endings to get rid of the git warnings in the daily build log, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/potPathoIndel.html
  • lines changed 0, context: html, text, full: html, text
    c1880f06222d5757a2d9e1b1ba8f72aa355a672e Thu Jan 26 05:38:33 2023 -0800
    fixing a few MS DOS line endings to get rid of the git warnings in the daily build log, no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 4, context: html, text, full: html, text
    ad9d2ac60828bebace74450afabb7557410a7fbc Mon Jan 23 12:07:24 2023 -0800
    adding rs prefix to dbSnp ids in clinvar otto job, no redmine, email from Bob
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 16, context: html, text, full: html, text
    ed7e20316990e2e6e52e0baf73087222eb571b67 Fri Jan 20 12:58:02 2023 -0800
    Mask reversion G26530A in BA.1.1 because it made a mess of the branch leading to BA.1.1.1.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 12, context: html, text, full: html, text
    0a5af94686b36c7cc7389a447cd699c4ec421e48 Fri Jan 20 12:58:39 2023 -0800
    Correction to BA.2.18 path after re-checking designated sequences. New label BA.5.2_quad_22599T to prevent misassignment as CE.1 after reversion. New label BQ.1_17039 to prevent misassignment as BQ.1.1 after reversion. Added false A26530G to XD path due to new branch-specific masking in BA.1.1. New lineages.
• src/inc/srcVersion.h
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    2c16cc726ba2e25098de6f3e16bd88ead5a192f0 Mon Jan 30 10:14:32 2023 -0800
    New version number v443
• src/lib/https.c
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    3946be330702e6b5138a8fcc1e9fc9a4b8d82658 Wed Jan 25 15:50:27 2023 -0800
    Added domains from RR euro asia logs to the https whitelist. I will observe again in 3 weeks after another release cycle verify we actually have caught them all as expected.
• src/utils/qa/weeklybld/buildEnv.csh
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    717250d34f94de8ed87cce5964a0443caa0b4d0d Mon Jan 30 10:12:41 2023 -0800
    v443 final build, refs #30497

• lines changed: 6247
• files changed: 58