All File Changes

v428_base to v429_preview (2022-03-14 to 2022-03-21) v429

• src/hg/cirm/cdw/cdwUpdateIx/cdwUpdateIx
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    0e59a61d79e9b70108a03d37270dc58cdad5d324 Thu Mar 17 14:08:53 2022 -0700
    oops this parameter is needed for cirm for full text indexing
• src/hg/hgPublicSessions/hgPublicSessions.c
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    3c336b221ead841fd5504ce0652874f5901e979c Thu Mar 10 20:12:17 2022 -0800
    Fixing a couple of injection vulnerabilities, refs #29086
• src/hg/hgSession/hgSession.c
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    c68067f0a368163016f57cf9f5230f838f7a83fd Thu Mar 10 19:52:36 2022 -0800
    Re-saving over a session shouldn't destroy the description, refs #22901
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    3c336b221ead841fd5504ce0652874f5901e979c Thu Mar 10 20:12:17 2022 -0800
    Fixing a couple of injection vulnerabilities, refs #29086
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    efffc477cc2f67d7668905675361447edff7bec8 Wed Mar 16 13:36:04 2022 -0700
    Initial commit of requiring a description when adding a session to the public listing. Also fixing a typo in an update statement. refs #21229
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
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    55e0b15e79ab362926642bbab4d7648ec307eae7 Tue Mar 15 08:10:06 2022 -0700
    Fixing reported 404 in static doc pages, updating links to stable PMC articles on protein database, no RM
• src/hg/htdocs/inc/recTrackSets.hg38.tab
  • lines changed 14, context: html, text, full: html, text
    6b70a2e653405b851fb05d3e39d08ab8a5f69ef8 Wed Mar 16 16:15:21 2022 -0700
    Adding rec track sets to hg38 refs #28209
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    6f28e1e56368bedeb6c850fb63c74910e7884abf Thu Mar 17 15:32:26 2022 -0700
    Fixing small spacing issue in tab file, refs #28209
• src/hg/lib/hui.c
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    6a5717fcf09d93534d76ff908c6a3e140ce4124f Fri Mar 18 09:33:53 2022 -0700
    enable density coverage mode option for PSL
• src/hg/lib/makefile
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    8654ed78664068f06114719493d5e3fff2550d33 Tue Mar 15 12:31:00 2022 -0700
    Fixups to get the genbank related code to compile after common.mk and hg/lib -> cgilib changes
• src/hg/lib/variantProjector.c
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    4942ea5baf9a2b0f232b08e69fa9969fe640b925 Mon Mar 14 16:57:17 2022 -0700
    Thanks Lou for a test case (mm39 rs3399875136, NM_146282.2) in which a frameshifting deletion causes a stop loss but the transcript has no 3'UTR sequence so we cannot find a new stop codon. Instead, truncated predicted sequence led to incorrect coords from trimRefAlt and then an end < start error from indelShift. Now, just set vpPep->cantPredict and skip the rest of the steps since we just don't have enough info.
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/build.txt
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    b0856ca59f90cd3965886704dd604e821b8bd1db Wed Mar 2 14:35:24 2022 -0800
    add rDNA models
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
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    6ffdb62e185cb4cdd3aaa078a84fc974652e7d1a Sun Mar 6 15:10:09 2022 -0800
    fixed formating of CHM13
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/doc/chm13v2.0_CytoBandMapping.readme.txt
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/doc/chm13v2.0_CytoBandMapping.tsv
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/catLiftOffGenes.html
  • lines changed 104, context: html, text, full: html, text
    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/proseq.html
  • lines changed 67, context: html, text, full: html, text
    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/rdnaModel.html
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    b0856ca59f90cd3965886704dd604e821b8bd1db Wed Mar 2 14:35:24 2022 -0800
    add rDNA models
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/rnaseq.html
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
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    6ffdb62e185cb4cdd3aaa078a84fc974652e7d1a Sun Mar 6 15:10:09 2022 -0800
    fixed formating of CHM13
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/sedefSegDups.html
  • lines changed 40, context: html, text, full: html, text
    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/makefile
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    b0856ca59f90cd3965886704dd604e821b8bd1db Wed Mar 2 14:35:24 2022 -0800
    add rDNA models
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
  • lines changed 4, context: html, text, full: html, text
    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/schema/sedefSegDups.as
  • lines changed 48, context: html, text, full: html, text
    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/catLiftOffGenes.trackDb.txt
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/cytoBandMapped.trackDb.txt
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/drnaModel.trackDb.txt
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    b0856ca59f90cd3965886704dd604e821b8bd1db Wed Mar 2 14:35:24 2022 -0800
    add rDNA models
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/proseq.trackDb.txt
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/rdnaModel.trackDb.txt
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/rnaseq.trackDb.txt
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    a9b73dddfd3592bf439efab408380eedb3938e5a Wed Mar 2 21:29:48 2022 -0800
    added RNA-Seq and rDNA arrays
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    0deb2b5b7d3651d35812b5f70d883168c6fad514 Mon Mar 14 10:23:49 2022 -0700
    added files for CAT/Liftoff genes. Ensure tracks are not concatenated
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/sedefSegDups.trackDb.txt
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    523f18621dab1d7994334cb25037f67b406c947a Fri Feb 25 13:11:48 2022 -0800
    addition CHM13 V2.0 assembly T2T supplyed tracks
• src/hg/makeDb/doc/asmHubs/groups.txt
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    ed15a7c2b2eccf01200abcc289429fe283bce148 Tue Mar 15 12:33:12 2022 -0700
    update group lables to more complete descriptions refs #28961
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    430076e29a82930d89c6290946436fd6781e18f2 Thu Mar 17 10:05:04 2022 -0700
    adding bpt indexes for 2bit files and correct copy of 2bit file and gfidx files and fixup group titles refs #28961
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    5ff5dda17f2044b59aebf9d7009b7e1fadbc171a Thu Mar 17 23:04:42 2022 -0700
    correctly write out the groups file refs #28961
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 8, context: html, text, full: html, text
    430076e29a82930d89c6290946436fd6781e18f2 Thu Mar 17 10:05:04 2022 -0700
    adding bpt indexes for 2bit files and correct copy of 2bit file and gfidx files and fixup group titles refs #28961
• src/hg/makeDb/doc/hg38/multiz100way.txt
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    690a38c3b39e4f52daab9dcfe00dd0952908d438 Wed Mar 16 17:10:46 2022 -0700
    adding knownGene protAA and protNuc fa.gz files per user request refs #29093
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    b0856ca59f90cd3965886704dd604e821b8bd1db Wed Mar 2 14:35:24 2022 -0800
    add rDNA models
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    72d170c4d17ecf0349bbe4aeab8cb75e026bb366 Mon Mar 14 19:38:41 2022 -0700
    Adding user requested asmbly refs #29090
• src/hg/makeDb/genbank/common.mk
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    8654ed78664068f06114719493d5e3fff2550d33 Tue Mar 15 12:31:00 2022 -0700
    Fixups to get the genbank related code to compile after common.mk and hg/lib -> cgilib changes
• src/hg/makeDb/genbank/src/inc/gbFileOps.h
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    8654ed78664068f06114719493d5e3fff2550d33 Tue Mar 15 12:31:00 2022 -0700
    Fixups to get the genbank related code to compile after common.mk and hg/lib -> cgilib changes
• src/hg/makeDb/genbank/src/inc/gbSql.h
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    8654ed78664068f06114719493d5e3fff2550d33 Tue Mar 15 12:31:00 2022 -0700
    Fixups to get the genbank related code to compile after common.mk and hg/lib -> cgilib changes
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.html
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    766e88001609c5b4cf4204ee8aa913d8ad0c789f Thu Mar 17 10:17:51 2022 -0700
    Edited description page for Merged Cells and Tabula Sapiens track. Removed cell ontology label from cell type name for Tabula Sapiens.
• src/hg/makeDb/trackDb/human/hg38/snpCnvArrays.html
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    e3d601464631aeaf43868bdc1924ae7495222a2f Wed Mar 16 11:31:45 2022 -0700
    Code review minor edits #29100
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.html
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    766e88001609c5b4cf4204ee8aa913d8ad0c789f Thu Mar 17 10:17:51 2022 -0700
    Edited description page for Merged Cells and Tabula Sapiens track. Removed cell ontology label from cell type name for Tabula Sapiens.
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    8131a47952792a48fa770fa3d2fed980f3d6473a Thu Mar 17 10:20:45 2022 -0700
    Removed sentence in Display Conventions section.
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    219c5c915a9de4413ab852203ef8b439b22aa764 Thu Mar 17 13:47:18 2022 -0700
    Re-added sentence into Display Conventions and added in Errata section per Jim's request.
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    b7714d1f954676e7527912788cb430aee9dc0405 Thu Mar 17 14:09:54 2022 -0700
    Capitalized Cell Classification.
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    24351d26ea3175f54e0972ccf562525c39a4ea00 Thu Mar 17 14:48:29 2022 -0700
    Added missing quote for link to Tabula Details track.
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    21c0d25b0b37f18e9e36d4826d629958f8a9abcb Fri Mar 18 14:00:36 2022 -0700
    Small edits to References section. refs #28692
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.ra
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    766e88001609c5b4cf4204ee8aa913d8ad0c789f Thu Mar 17 10:17:51 2022 -0700
    Edited description page for Merged Cells and Tabula Sapiens track. Removed cell ontology label from cell type name for Tabula Sapiens.
• src/hg/makeDb/trackDb/human/panelApp.html
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    e3d601464631aeaf43868bdc1924ae7495222a2f Wed Mar 16 11:31:45 2022 -0700
    Code review minor edits #29100
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    e9934975b34d714a60fefb524c24d8d42a617863 Wed Mar 16 11:35:35 2022 -0700
    Resolving merge refs #29100
• src/hg/makeDb/trackDb/human/trackDb.ra
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    b43fd111ea4b4c7afec79088d25dbbe7c3beaea4 Fri Mar 18 10:45:17 2022 -0700
    Adding a bigDataUrl to fix strange crash stalling rec track sets refs# 29210, 28209
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    2499a735e08eafd667b7e8b9b354d806a008f0c7 Fri Mar 18 11:14:16 2022 -0700
    Correcting path in bigDataUrl to fix strange crash stalling rec track sets refs# 29210, 28209
• src/hg/utils/automation/aliasTextToBed.pl
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    f68f5f242e08e5273b10f63d4fbc65f2528ee954 Fri Mar 18 15:22:54 2022 -0700
    initial version of conversion from chromAlias.txt to chromAlias.bb refs #29109
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    1318c99c7958fcfacf703bf6047b7ae25bd6efc9 Sun Mar 20 10:25:12 2022 -0700
    Make hgwdev URL to share daily directories with processed COG-UK files.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    9aa849960d756c2cc2c2a1f5bfe5916051f6f95c Sun Mar 20 10:25:56 2022 -0700
    De-duplicate NCBI fasta. Make hgwdev URL to share daily directories with processed INSDC/GenBank files.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    498826cbc4a360849640a2f9ee0f6987169c5c15 Mon Mar 14 16:58:05 2022 -0700
    Add a couple more IDs from pango-designation.
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    f30a323bbecc0ff1d3c9fd0bbe20be9ceabafbbb Sun Mar 20 10:18:00 2022 -0700
    Added a designated lineage column. Removed witdrawn issue 470 (duplicate) and some duplicate lines. Added a few updates.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    e0ceb707ee674eed7c05ace93e71d4e958a15537 Sun Mar 20 10:19:28 2022 -0700
    Filter out sequences with missing EPI_ISL_ID from new GISAID download format.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    feb0c6c24faed625f7e15874ade55a3f8968886c Sun Mar 20 10:20:35 2022 -0700
    Adding some BA.1 Spike/amplicon dropout positions that are problematic but so far don't affect proposed Delta/BA.1 recombinants.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    838794ab7f4eed40bd79e058846b83ac1fe7bce3 Wed Mar 16 17:48:55 2022 -0700
    Added recombinants XD, XE, XF -- pango-designation v1.2.133. Also a little correction to BA.1.3.
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    f2c38b414669a86d1dd00a73ff17cfd62b8f1a10 Thu Mar 17 15:39:25 2022 -0700
    Getting a bit ahead of pango-designation: adding back BC.1 even though it has been temporarily withdrawn while pipelines are tested, and some of the proposed recombinant lineages for ease of spotting/tracking in the tree.
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    81f98040bb5b097503e8096db9a664ecdbeedb51 Sun Mar 20 10:15:58 2022 -0700
    Oops, forgot to mask 241 in a couple of the propsed lineages - necessary for annotating a pango-masked protobuf. Also missed the last few mutations for proposed448, thx Cornelius Roemer for spotting.
• src/lib/obscure.c
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    8ca78d3a7a71282970c6cefd998a19504271d520 Tue Mar 15 18:23:41 2022 -0700
    In hashTwoColumnFile, first check if the input is tab-separated so we can tolerate spaces in the second column. If no tabs, then fall back to space-separated.
• src/lib/udc.c
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    b3b4bcf548ce981c06ecb3f54a125447ab32cfe1 Mon Mar 14 12:35:20 2022 -0700
    fix comment to specify max udc slurp is 256K not 64K
• src/utils/qa/weeklybld/buildEnv.csh
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    6d46d22787226f722cb17b8214a73769518c8e4d Mon Mar 21 10:15:13 2022 -0700
    v429 preview1, refs #29124

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• files changed: 79