All File Changes

v441_preview to v441_preview2 (2022-11-28 to 2022-12-05) v441

• confs/asia.hg.conf
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    2d030505b8ec9d0882bbb4279f4910d868fd2d92 Sun Dec 4 01:11:25 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    2d030505b8ec9d0882bbb4279f4910d868fd2d92 Sun Dec 4 01:11:25 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    2d030505b8ec9d0882bbb4279f4910d868fd2d92 Sun Dec 4 01:11:25 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    2d030505b8ec9d0882bbb4279f4910d868fd2d92 Sun Dec 4 01:11:25 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPhyloPlace/phyloPlace.c
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    827de614bca5613228664b8944048f61c61f336a Fri Dec 2 09:44:45 2022 -0800
    Use @yceh's new --existing_samples option to usher-sampled-server as a faster alternative to running matUtils.
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    d4e0a5e68076aafa81d0852705fca8fe90fa19ac Fri Dec 2 15:23:04 2022 -0800
    Avoid regex when looking for isolate component of each name in tree; just look for slashes and distance between them. When user uploads names, this saves ~40s.
• src/hg/hgPhyloPlace/phyloPlace.h
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    827de614bca5613228664b8944048f61c61f336a Fri Dec 2 09:44:45 2022 -0800
    Use @yceh's new --existing_samples option to usher-sampled-server as a faster alternative to running matUtils.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 67, context: html, text, full: html, text
    827de614bca5613228664b8944048f61c61f336a Fri Dec 2 09:44:45 2022 -0800
    Use @yceh's new --existing_samples option to usher-sampled-server as a faster alternative to running matUtils.
• src/hg/hgTracks/hicTrack.c
  • lines changed 33, context: html, text, full: html, text
    e7f02d37914178e82c5f2b481cf6f294c6687d39 Mon Nov 28 16:35:16 2022 -0800
    Allow users to invert Hi-C plots, refs #30330, #30343
• src/hg/hgc/gencodeClick.c
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    77dba36e6886565e458923533d0dd4d173641fb4 Thu Dec 1 12:21:46 2022 -0800
    display GENCODE transcript rank in hgc when it is available
• src/hg/hgc/hgcData/barChartBoxplot.R
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    251299d12265bc22ef7c540884208974d36271de Thu Dec 1 11:22:04 2022 -0800
    Allow hash char in boxplot category names for barChar tracks, refs #30347
• src/hg/inc/hicUi.h
  • lines changed 6, context: html, text, full: html, text
    e7f02d37914178e82c5f2b481cf6f294c6687d39 Mon Nov 28 16:35:16 2022 -0800
    Allow users to invert Hi-C plots, refs #30330, #30343
• src/hg/lib/hicUi.c
  • lines changed 13, context: html, text, full: html, text
    e7f02d37914178e82c5f2b481cf6f294c6687d39 Mon Nov 28 16:35:16 2022 -0800
    Allow users to invert Hi-C plots, refs #30330, #30343
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 34, context: html, text, full: html, text
    5ffc12008daeacde7cddf891ab0f608087950b79 Mon Nov 28 09:56:16 2022 -0800
    catching up 34 assemblies for VGP refs #29545
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    1edfbfe359de39c06db7b6146b12d50d7593ee3d Wed Nov 30 21:30:38 2022 -0800
    adding GCA_003660325.2_Oct15_3.7Mb_N50_Jamaican_Lion_Assembly per user request refs #30332
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
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    8a48909099f3b349c33c99244d63530d2a9832e6 Mon Nov 28 14:45:30 2022 -0800
    relaxing the limits for fish legacy an VGP assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    5239d4ca823ce6c2fa94e00e99fc14236ef51e17 Mon Nov 28 10:21:36 2022 -0800
    catching up 4 VGP assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    771f125492518517ad0f81a3c9629a9272b508dc Mon Nov 28 11:15:22 2022 -0800
    adding 16 for VGP catch up refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    e2a2093ed6b550b4272c12ac462fb36989bd287a Mon Nov 28 11:57:08 2022 -0800
    adding 9 catch up for VGP refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    1edfbfe359de39c06db7b6146b12d50d7593ee3d Wed Nov 30 21:30:38 2022 -0800
    adding GCA_003660325.2_Oct15_3.7Mb_N50_Jamaican_Lion_Assembly per user request refs #30332
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    fddeb26a1ca96fb3d447d016a7cd1d4b8258d919 Mon Nov 28 11:34:24 2022 -0800
    catch up 2 assemblies for VGP project refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    a4384852d4d0aaa1a301a28e29f47a734479d14c Mon Nov 28 11:58:01 2022 -0800
    adding 3 catch up for VGP refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
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    4312c884bef3a7db6c2fb009aa8f0fa6c657f911 Mon Nov 28 13:10:34 2022 -0800
    catch up about 34 assemblies for VGP refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    4312c884bef3a7db6c2fb009aa8f0fa6c657f911 Mon Nov 28 13:10:34 2022 -0800
    catch up about 34 assemblies for VGP refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 32, context: html, text, full: html, text
    4312c884bef3a7db6c2fb009aa8f0fa6c657f911 Mon Nov 28 13:10:34 2022 -0800
    catch up about 34 assemblies for VGP refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 35, context: html, text, full: html, text
    4312c884bef3a7db6c2fb009aa8f0fa6c657f911 Mon Nov 28 13:10:34 2022 -0800
    catch up about 34 assemblies for VGP refs #29545
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 7, context: html, text, full: html, text
    94f6c02614e12c0c96d63ff59f193e8231a203a9 Mon Nov 28 13:58:04 2022 -0800
    hgTrackDb should change the tdb->settingsHash when it does label substitution, refs #30324
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    ff5d21f573f467d2481aacb2b0bc42945828f41b Tue Nov 29 09:29:47 2022 -0800
    The substituted html field of trackDb does not belong in the settings hash, refs Jonathan email
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 8, context: html, text, full: html, text
    e5c8e16b5b39ac86e1aad15ee0216c5ddd708beb Wed Nov 30 12:36:47 2022 -0800
    buildTrix called by trackDb makefile can update trackDb snippet indexes
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 104, context: html, text, full: html, text
    d0913f7b67368f5da446aefdb66d0ce2b242921a Tue Nov 29 15:50:13 2022 -0800
    Releasing the nesting of dbSNP153 in dbSNP Archive to the RR, refs #30252
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d0913f7b67368f5da446aefdb66d0ce2b242921a Tue Nov 29 15:50:13 2022 -0800
    Releasing the nesting of dbSNP153 in dbSNP Archive to the RR, refs #30252
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 76, context: html, text, full: html, text
    d0913f7b67368f5da446aefdb66d0ce2b242921a Tue Nov 29 15:50:13 2022 -0800
    Releasing the nesting of dbSNP153 in dbSNP Archive to the RR, refs #30252
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d0913f7b67368f5da446aefdb66d0ce2b242921a Tue Nov 29 15:50:13 2022 -0800
    Releasing the nesting of dbSNP153 in dbSNP Archive to the RR, refs #30252
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d0913f7b67368f5da446aefdb66d0ce2b242921a Tue Nov 29 15:50:13 2022 -0800
    Releasing the nesting of dbSNP153 in dbSNP Archive to the RR, refs #30252
• src/hg/makeDb/trackDb/makeTrixLinks
  • lines changed 4, context: html, text, full: html, text
    e5c8e16b5b39ac86e1aad15ee0216c5ddd708beb Wed Nov 30 12:36:47 2022 -0800
    buildTrix called by trackDb makefile can update trackDb snippet indexes
• src/hg/utils/automation/chromAlias.pl
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    5ab456ddf76e0e021fe6a7f5fb821888edbf1c2f Mon Nov 28 13:27:24 2022 -0800
    more generic use of file names refs #30326
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 9, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
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    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.attrs
  • lines changed 96, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
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    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/mm10GencodeTest.attrs
  • lines changed 48, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
  • lines changed 48, context: html, text, full: html, text
    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/nameAttrNameTest.attrs
  • lines changed 12, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
  • lines changed 12, context: html, text, full: html, text
    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
  • lines changed 48, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
  • lines changed 48, context: html, text, full: html, text
    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs
  • lines changed 162, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
  • lines changed 162, context: html, text, full: html, text
    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/gff3ToGenePred/tests/expected/useNameTest.attrs
  • lines changed 12, context: html, text, full: html, text
    5c34b9229866a9c0033003e2c21509b8de55f87e Tue Nov 29 09:39:18 2022 -0800
    include some of the GFF3 positional value in the attributes output file
  • lines changed 12, context: html, text, full: html, text
    c96203c4fb3523f0339e83da69a708fab7706250 Tue Nov 29 09:44:08 2022 -0800
    opps, the previous commit left out the all-important name in gff3ToGenePred attributes
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    0598b71e08f7ce3db112b5a5fa4d5194a8435f5e Fri Dec 2 11:05:57 2022 -0800
    Add more info to taxonium file, dump out list of samples in public tree.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
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    0f91220571b0892ed4374511f992931de5d58fe8 Fri Dec 2 11:07:32 2022 -0800
    Update regex to match Omicrons/recombinants.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    66463568b2220779915874153b9347a33af97f09 Fri Dec 2 11:08:40 2022 -0800
    Increase maxAttempts, sometimes AWS is flaky but resolves.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    d80e5aa50badf8d4b1e0fbadfb5cd346b812d18e Fri Dec 2 11:09:52 2022 -0800
    Remove outdated options from datasets command; don't waste time sleeping after final failure.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 59, context: html, text, full: html, text
    89f7d08712d352128fc01e2688df63bb188fc56b Fri Dec 2 11:10:47 2022 -0800
    Adding recent samples
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    b777f63dced2a62cdf363cc456ded46d569ceb46 Fri Dec 2 11:11:11 2022 -0800
    Update nextclade output column indices
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    3ed65430d066888a23f7f97ebbc11eac3269586b Fri Dec 2 11:13:14 2022 -0800
    Mask more UTR noisy positions in BA.2 onward.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    1b0eba97a41a2b733ce4a3b1998fe3cd264b3e08 Fri Dec 2 11:24:24 2022 -0800
    Move 21L (BA.2) node back; add new clades 22E and 22F.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    e442dc70425e6e5ec1220b81de6da8f60ae32703 Fri Dec 2 11:15:52 2022 -0800
    New slew of lineages from v1.16 and beyond.
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
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    404482949921223c604b2361aeaa5d2e37b5d990 Fri Dec 2 11:17:57 2022 -0800
    Use multiple cores in pangolin for cluster run -- the number of jobs per machine is limited by RAM.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    e66bfc81c03088103c395a9a09bda494be3e1132 Fri Dec 2 11:23:44 2022 -0800
    Add more pruning before downsampling: sequences with two or more reversions relative to lineage root, and high mutation density branches. Add -P file to speed up reannotation on rerooted tree.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    6b7b5c359f41944103a1209a09b076cdade0044b Fri Dec 2 11:25:11 2022 -0800
    Add check for unannotated lineages.
• src/inc/common.mk
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    860f671b8332c9be7d88450c7f5ad7ac5c25dd21 Wed Nov 30 16:10:14 2022 -0800
    and yet another brew upgrade addition for the Mac OSX no redmine
• src/utils/bigGuessDb/bigGuessDb
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
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    40428f923657ec045d64b54de7bf444dc140dd33 Tue Nov 29 07:36:43 2022 -0800
    using only assemblies on the RR in bigGuessDb now, refs #30316
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    1bead704f880dcea50b2067c50261e6f3a0fab77 Tue Nov 29 07:40:39 2022 -0800
    sorting assemblies in bigGuessDb by orderKey, refs #30316
• src/utils/bigGuessDb/makefile
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
• src/utils/bigGuessDb/tests/guessAssembly.txt.gz
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
• src/utils/bigGuessDb/tests/in/hg19.bb
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
• src/utils/bigGuessDb/tests/in/mm10.bw
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
• src/utils/bigGuessDb/tests/makefile
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    6a6d7a78f1de5456925fc8f4f675795cbb61ee35 Tue Nov 29 03:16:02 2022 -0800
    adding tests for bigGuessDb, refs #30316
• src/utils/qa/weeklybld/buildEnv.csh
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    edefe59bb5d66e8787ed89b82a4472b7f9a8c576 Mon Dec 5 10:09:20 2022 -0800
    v441 preview2, refs #30323

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• files changed: 72