All File Changes

v428_preview2 to v428_base (2022-03-07 to 2022-03-14) v428

• confs/hgwbeta.hg.conf
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    50892b483b07af21b878c22af539f4f4b4bedb35 Sun Mar 13 01:12:02 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/garTable.pl
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    8ab2c89057f9168c8aebc3fe7f21bc0ab0d3d2d9 Tue Mar 8 10:51:00 2022 -0800
    change hideAll to be showAll refs #28930
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    65cc3900649623b8366ab05d9b285e528f8f2959 Tue Mar 8 11:58:53 2022 -0800
    now using a new initial column for the view/request function and correctly counting hasIucn columns refs #28930
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    e25b1163ff40d3eacbd7115f0074353a841f9b18 Mon Mar 7 12:58:51 2022 -0800
    hub developer mode was already on by default but was not controlled via hg.conf. Leave it on by default but allow it to be turned off via hg.conf, and clarify that in the documentation, refs #28831
• src/hg/hgTracks/barChartTrack.c
  • lines changed 2, context: html, text, full: html, text
    63abfc194497bf296afda0797dd8d6c47b6d69f2 Fri Mar 11 10:22:32 2022 -0800
    Changes from code review. Advance the x coordinate of the next bar in a barChart by the barWidth of the previous bar, which may be from our dynamic calculation or a user defined min width, refs #29060
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    3d7ab89bf0b35a1e0cdff1a8dadba713e5495981 Fri Mar 11 11:40:37 2022 -0800
    Fix x coordinate of mapbox I forgot to fix with previous change, refs #29060
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    f49326a813b4eed9190dc40d164b6184b3401323 Mon Mar 7 11:25:55 2022 -0800
    turn on mouseOverEnabled on by default can still be turned off refs #21980
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 5, context: html, text, full: html, text
    3d6c26a28372e86f6477032ec6210a4583dc55b1 Wed Mar 9 12:56:13 2022 -0800
    Adding requested commas in code review refs #29059
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    7a2f77d1e52358d1d1af0e4cbd54a45ef5140ace Tue Mar 8 07:34:55 2022 -0800
    explaining that extra fields are not counted for bed > 8 constraint, refs #29069, email from Galaxy Project
  • lines changed 9, context: html, text, full: html, text
    10d9befbf922acaa30830943c613c1370f568892 Tue Mar 8 16:15:30 2022 -0800
    Adding a reminder up high in filters about the added . or + required, e.g., type bigBed 9 + refs #29069
• src/hg/htdocs/images/platinumTree.jpg
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    8d5b24a3132e3509854137683310074b0979a284 Wed Mar 9 16:16:41 2022 -0800
    Adding image to platinum track per email conversation with b0b and Lou
• src/hg/htdocs/style/gar.css
  • lines changed 20, context: html, text, full: html, text
    e90dbdb30604a8ea020036a3623ce74a1062b95e Tue Mar 8 10:16:23 2022 -0800
    better position for the borderOne rules refs #28930
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    95d31eaa8f97abfc5df963cf32265b9365366dba Tue Mar 8 10:46:34 2022 -0800
    better shadow around the pull-down menu boxes refs #28930
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    65cc3900649623b8366ab05d9b285e528f8f2959 Tue Mar 8 11:58:53 2022 -0800
    now using a new initial column for the view/request function and correctly counting hasIucn columns refs #28930
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    e63eaf218669b968f124b81ca45ea0c287943f75 Fri Mar 11 16:26:26 2022 -0800
    use bpt index if available for 2bit assembly hubs
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    343590bdfc6fd45427d54b922944781eff4a1c22 Mon Mar 14 10:11:30 2022 -0700
    New version number v428
• src/hg/js/gar.js
  • lines changed 38, context: html, text, full: html, text
    6aba66d1a3b3e28e00e2f3d89491a4927e92bd30 Tue Mar 8 10:17:54 2022 -0800
    reset hideAll to be showAll refs #28930
  • lines changed 6, context: html, text, full: html, text
    65cc3900649623b8366ab05d9b285e528f8f2959 Tue Mar 8 11:58:53 2022 -0800
    now using a new initial column for the view/request function and correctly counting hasIucn columns refs #28930
• src/hg/lib/chromAlias.c
  • lines changed 81, context: html, text, full: html, text
    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/hg/lib/evaSnp.as
  • lines changed 9, context: html, text, full: html, text
    c80188a28d8286a54322364ea43a40aa13739f4b Wed Mar 9 07:44:50 2022 -0800
    modified file to standardize btw new canFam and mm39 to include VAI fields, per collab w Lou
• src/hg/lib/trackHub.c
  • lines changed 14, context: html, text, full: html, text
    e63eaf218669b968f124b81ca45ea0c287943f75 Fri Mar 11 16:26:26 2022 -0800
    use bpt index if available for 2bit assembly hubs
• src/hg/makeDb/doc/hg19.txt
  • lines changed 23, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
  • lines changed 6, context: html, text, full: html, text
    1049c9c012c170c8ae3f2d7ebcbfa5019356b551 Fri Mar 11 12:20:43 2022 -0800
    Adding SNP/CNV array track refs #23591
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 26, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
  • lines changed 17, context: html, text, full: html, text
    1049c9c012c170c8ae3f2d7ebcbfa5019356b551 Fri Mar 11 12:20:43 2022 -0800
    Adding SNP/CNV array track refs #23591
• src/hg/makeDb/doc/mm39/ncbiRefSeqSelect.txt
  • lines changed 22, context: html, text, full: html, text
    72d86ba1b9dc598edbdc2e43e66e6333460dadd8 Mon Mar 7 13:14:18 2022 -0800
    Adding ncbiRefSeqSelect tracks for mm10 / mm39. Refs #28130
• src/hg/makeDb/doc/wuhCor1/resistPred.doc
  • lines changed 3, context: html, text, full: html, text
    ecb8f7c3b5c982cfe747aba300b88692fe2fbd58 Mon Mar 7 16:23:36 2022 -0800
    Adding doc for removing dups from file refs #29035
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    b020ca265daf4249483970fb402f58bbad20e6d0 Mon Mar 7 17:43:30 2022 -0800
    removed two liter settings that are actually the defaults per lou. refs
• src/hg/makeDb/trackDb/human/hg19/panelApp.html
  • lines changed 95, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 39, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
• src/hg/makeDb/trackDb/human/hg38/panelApp.html
  • lines changed 103, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
• src/hg/makeDb/trackDb/human/hg38/snpCnvArrays.html
  • lines changed 51, context: html, text, full: html, text
    1049c9c012c170c8ae3f2d7ebcbfa5019356b551 Fri Mar 11 12:20:43 2022 -0800
    Adding SNP/CNV array track refs #23591
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 56, context: html, text, full: html, text
    cff386c4731971ed35c2a379135a6387d8bf0c9f Thu Mar 10 16:33:41 2022 -0800
    Panel App track engineering refs #25568
  • lines changed 32, context: html, text, full: html, text
    1049c9c012c170c8ae3f2d7ebcbfa5019356b551 Fri Mar 11 12:20:43 2022 -0800
    Adding SNP/CNV array track refs #23591
• src/hg/makeDb/trackDb/human/jarvis.ra
  • lines changed 13, context: html, text, full: html, text
    779e638014cc0d2acc1be3edcad748bdb8ec2124 Thu Mar 10 02:29:37 2022 -0800
    adding alpha version of jarvis track, no redmine yet.
• src/hg/makeDb/trackDb/human/platinumGenomes.html
  • lines changed 56, context: html, text, full: html, text
    b783f9e658057de6ade55b8d8b8932c9e6d606c8 Fri Mar 11 14:13:58 2022 -0800
    At b0b's request revising the Platinum Genomes Track Description page, no RM
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    e75ee7807a3856fa9fa49446575701e9c648a3c9 Fri Mar 11 14:36:47 2022 -0800
    Few extra changes to platinum genomes page.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    779e638014cc0d2acc1be3edcad748bdb8ec2124 Thu Mar 10 02:29:37 2022 -0800
    adding alpha version of jarvis track, no redmine yet.
• src/hg/makeDb/trackDb/mouse/mm10/refSeqComposite.html
  • lines changed 284, context: html, text, full: html, text
    2fb396be379cedbeff51d7265994517ddb42f597 Tue Mar 8 07:35:48 2022 -0800
    Restructuring the trackDb stanzas due to trackDb error, the ncbiRefSeqSelect track needs to be stated at the organism level since that is where the include statement is found. Refs #28130
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    2fb396be379cedbeff51d7265994517ddb42f597 Tue Mar 8 07:35:48 2022 -0800
    Restructuring the trackDb stanzas due to trackDb error, the ncbiRefSeqSelect track needs to be stated at the organism level since that is where the include statement is found. Refs #28130
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
  • lines changed 284, context: html, text, full: html, text
    2fb396be379cedbeff51d7265994517ddb42f597 Tue Mar 8 07:35:48 2022 -0800
    Restructuring the trackDb stanzas due to trackDb error, the ncbiRefSeqSelect track needs to be stated at the organism level since that is where the include statement is found. Refs #28130
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    2fb396be379cedbeff51d7265994517ddb42f597 Tue Mar 8 07:35:48 2022 -0800
    Restructuring the trackDb stanzas due to trackDb error, the ncbiRefSeqSelect track needs to be stated at the organism level since that is where the include statement is found. Refs #28130
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    02cc2a77ce84c8a208f92bb4e6cb41bdeac01f04 Wed Mar 9 09:13:09 2022 -0800
    Commenting out the evaSnp track which slipped out early with ncbiRefseqSelect. Refs #24787
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    72d86ba1b9dc598edbdc2e43e66e6333460dadd8 Mon Mar 7 13:14:18 2022 -0800
    Adding ncbiRefSeqSelect tracks for mm10 / mm39. Refs #28130
  • lines changed 12, context: html, text, full: html, text
    2fb396be379cedbeff51d7265994517ddb42f597 Tue Mar 8 07:35:48 2022 -0800
    Restructuring the trackDb stanzas due to trackDb error, the ncbiRefSeqSelect track needs to be stated at the organism level since that is where the include statement is found. Refs #28130
• src/hg/makeDb/trackDb/virus/wuhCor1/galaxyEna.ra
  • lines changed 120, context: html, text, full: html, text
    d5e7a3945f3558a83c11eeaf5cc04e4766b59c76 Tue Mar 8 06:04:14 2022 -0800
    adding first version of galaxy ENA track made by Wolfgang Meier, Galaxy Project, refs #29069
  • lines changed 62, context: html, text, full: html, text
    a7d5a782de93ff40c6a101977e089c1d0d8deff3 Wed Mar 9 06:38:37 2022 -0800
    fixing galayEna wuhCor1 tdb, refs #29069
  • lines changed 4, context: html, text, full: html, text
    cfc6ef8d77e49b717edca940caab8b4efd4c190f Fri Mar 11 02:22:58 2022 -0800
    release tag cleanup for wuhCor1, refs #29069
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d5e7a3945f3558a83c11eeaf5cc04e4766b59c76 Tue Mar 8 06:04:14 2022 -0800
    adding first version of galaxy ENA track made by Wolfgang Meier, Galaxy Project, refs #29069
  • lines changed 1, context: html, text, full: html, text
    cfc6ef8d77e49b717edca940caab8b4efd4c190f Fri Mar 11 02:22:58 2022 -0800
    release tag cleanup for wuhCor1, refs #29069
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    df04c1f66cdd6895471998c6d9c70b1a413f7d4e Sat Mar 12 20:33:25 2022 -0800
    Use new --include-nt option when generating taxonium protobufs. Also watch out for EPI_ISL as part of GenBank name.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    baa98a4c7bb930fd0bf6365f92436eb900ade8e3 Sat Mar 12 20:31:52 2022 -0800
    Prevent duplicate lines in ncbi_dataset.plusBioSample.tsv.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 76, context: html, text, full: html, text
    914fa0581c7c17a37b1d598c92a4e42e427d1bcb Sun Feb 27 12:02:01 2022 -0800
    Adding more IDs from pango-designation issues.
  • lines changed 171, context: html, text, full: html, text
    0b90c5052025ceeea65ca83ee8440c681206d170 Tue Mar 1 09:53:52 2022 -0800
    Added more IDs from pango-designation
  • lines changed 27, context: html, text, full: html, text
    9d334a5f23ebdd944e0a2591f484c06ce0229537 Thu Mar 3 09:56:42 2022 -0800
    More updates from pango-designation issues
  • lines changed 66, context: html, text, full: html, text
    fc65b0a377a7cda3f03078dd255d5c8d6933a5b4 Thu Mar 3 18:33:07 2022 -0800
    More updates from pango-designation
  • lines changed 751, context: html, text, full: html, text
    f488be28f1793410327aa93ac1ba01982b37f260 Sat Mar 12 20:34:27 2022 -0800
    Adding lots of updates from pango-designation; also COG-UK names because not all are in GenBank downloads yet.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 44, context: html, text, full: html, text
    3bdcfd94b4905ad578c1ae99c9bb47fbb937893c Sat Mar 12 20:35:04 2022 -0800
    Mask out deleted sites in BA.1 and BA.2
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 21, context: html, text, full: html, text
    847e5bdd773beb9f499db99b1f03ff57c95ca586 Mon Feb 28 15:38:51 2022 -0800
    Added BA.1.16, BA.1.16.1, BA.1.17, BA.1.17.1, BA.1.1.[1-16] and BC.1 -- pango-designation v1.2.130
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    d07abd6a8dabab3342586f2be472c4ae4a8ad32f Sat Mar 12 20:38:50 2022 -0800
    Added AY.36.1, BA.2.1-3, removed BC.1 -- pango-designation v1.2.131
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    df04c1f66cdd6895471998c6d9c70b1a413f7d4e Sat Mar 12 20:33:25 2022 -0800
    Use new --include-nt option when generating taxonium protobufs. Also watch out for EPI_ISL as part of GenBank name.
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    0192d4b02dfdb61e29f71ab65340876d95d7af7a Sat Mar 12 23:32:19 2022 -0800
    have pslToBigPsl check for FASTA sequence length not matching PSL instead of having browser generate an error
• src/hg/utils/pslToBigPsl/tests/input/MamRep605b.fa
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    0192d4b02dfdb61e29f71ab65340876d95d7af7a Sat Mar 12 23:32:19 2022 -0800
    have pslToBigPsl check for FASTA sequence length not matching PSL instead of having browser generate an error
• src/hg/utils/pslToBigPsl/tests/input/MamRep605b.psl
  • lines changed 1, context: html, text, full: html, text
    0192d4b02dfdb61e29f71ab65340876d95d7af7a Sat Mar 12 23:32:19 2022 -0800
    have pslToBigPsl check for FASTA sequence length not matching PSL instead of having browser generate an error
• src/hg/utils/pslToBigPsl/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    0192d4b02dfdb61e29f71ab65340876d95d7af7a Sat Mar 12 23:32:19 2022 -0800
    have pslToBigPsl check for FASTA sequence length not matching PSL instead of having browser generate an error
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    f39d46885edb7bfab12a10158d13895a5010d2ff Sun Mar 13 11:21:26 2022 -0700
    fixed shell check for command that should have failed
• src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
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    c6eed4550b6684cc7cde7779b9084a72573b5d83 Fri Mar 11 19:54:00 2022 -0800
    added ability to read ascii version of bigRmskAlign files
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    57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700
    added ability to override incorrect sizes often found in RepeatMaster alignments
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    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
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    d99300bbd4e6250c0a72144745b3383a973adb14 Sun Mar 13 12:32:04 2022 -0700
    drop querys not in repSizes file rather than generate an error
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    015db67f25bdbaffebb795b6e952c405f15e1e23 Sun Mar 13 14:10:06 2022 -0700
    premature commit of -repSizes, this really made things worse; back out
• src/hg/utils/rmskAlignToPsl/tests/expected/hg38BigRmskTest.psl
  • lines changed 759, context: html, text, full: html, text
    c6eed4550b6684cc7cde7779b9084a72573b5d83 Fri Mar 11 19:54:00 2022 -0800
    added ability to read ascii version of bigRmskAlign files
  • lines changed 759, context: html, text, full: html, text
    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
• src/hg/utils/rmskAlignToPsl/tests/expected/hg38Test.psl
  • lines changed 60, context: html, text, full: html, text
    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
• src/hg/utils/rmskAlignToPsl/tests/expected/mm39ProbTest.psl
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    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
• src/hg/utils/rmskAlignToPsl/tests/expected/mm39Test.psl
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    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
• src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.out
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    d99300bbd4e6250c0a72144745b3383a973adb14 Sun Mar 13 12:32:04 2022 -0700
    drop querys not in repSizes file rather than generate an error
• src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.psl
  • lines changed 5, context: html, text, full: html, text
    57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700
    added ability to override incorrect sizes often found in RepeatMaster alignments
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    661558a587c48930ceb19f3baa526c78d236f8d8 Sun Mar 13 10:49:48 2022 -0700
    fixed expected output
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    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
• src/hg/utils/rmskAlignToPsl/tests/input/hg38.dfam_3.3.bigRmskIn
  • lines changed 997, context: html, text, full: html, text
    56cfd7a79faa415392733aab06c016139e59a350 Sun Mar 13 09:47:25 2022 -0700
    test cases was actually Dfam 3.3
• src/hg/utils/rmskAlignToPsl/tests/input/hg38.dfam_3.5.bigRmskIn
  • lines changed 997, context: html, text, full: html, text
    c6eed4550b6684cc7cde7779b9084a72573b5d83 Fri Mar 11 19:54:00 2022 -0800
    added ability to read ascii version of bigRmskAlign files
  • lines changed 997, context: html, text, full: html, text
    56cfd7a79faa415392733aab06c016139e59a350 Sun Mar 13 09:47:25 2022 -0700
    test cases was actually Dfam 3.3
• src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.bigRmskIn
  • lines changed 6, context: html, text, full: html, text
    57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700
    added ability to override incorrect sizes often found in RepeatMaster alignments
  • lines changed 3, context: html, text, full: html, text
    d99300bbd4e6250c0a72144745b3383a973adb14 Sun Mar 13 12:32:04 2022 -0700
    drop querys not in repSizes file rather than generate an error
  • lines changed 9, context: html, text, full: html, text
    015db67f25bdbaffebb795b6e952c405f15e1e23 Sun Mar 13 14:10:06 2022 -0700
    premature commit of -repSizes, this really made things worse; back out
• src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.sizes
  • lines changed 1, context: html, text, full: html, text
    57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700
    added ability to override incorrect sizes often found in RepeatMaster alignments
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    015db67f25bdbaffebb795b6e952c405f15e1e23 Sun Mar 13 14:10:06 2022 -0700
    premature commit of -repSizes, this really made things worse; back out
• src/hg/utils/rmskAlignToPsl/tests/makefile
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    c6eed4550b6684cc7cde7779b9084a72573b5d83 Fri Mar 11 19:54:00 2022 -0800
    added ability to read ascii version of bigRmskAlign files
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    56cfd7a79faa415392733aab06c016139e59a350 Sun Mar 13 09:47:25 2022 -0700
    test cases was actually Dfam 3.3
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    57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700
    added ability to override incorrect sizes often found in RepeatMaster alignments
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    661558a587c48930ceb19f3baa526c78d236f8d8 Sun Mar 13 10:49:48 2022 -0700
    fixed expected output
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    e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700
    fixed repeat counts
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    d99300bbd4e6250c0a72144745b3383a973adb14 Sun Mar 13 12:32:04 2022 -0700
    drop querys not in repSizes file rather than generate an error
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    015db67f25bdbaffebb795b6e952c405f15e1e23 Sun Mar 13 14:10:06 2022 -0700
    premature commit of -repSizes, this really made things worse; back out
• src/inc/bbiAlias.h
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/inc/bbiFile.h
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/inc/srcVersion.h
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    343590bdfc6fd45427d54b922944781eff4a1c22 Mon Mar 14 10:11:30 2022 -0700
    New version number v428
• src/index/bptForTwoBit/bptForTwoBit.c
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    e63eaf218669b968f124b81ca45ea0c287943f75 Fri Mar 11 16:26:26 2022 -0800
    use bpt index if available for 2bit assembly hubs
• src/lib/bbiAlias.c
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/lib/bbiWrite.c
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/lib/makefile
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/lib/twoBit.c
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    e63eaf218669b968f124b81ca45ea0c287943f75 Fri Mar 11 16:26:26 2022 -0800
    use bpt index if available for 2bit assembly hubs
• src/product/ex.hg.conf
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    0c201aeee868c8449908abfd67a6d24812a1ea08 Mon Mar 7 11:29:36 2022 -0800
    turn on mouseOverEnabled on by default can still be turned off refs #21980
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    df63c136ad9014616fdd43bcd5d67ca4014d0086 Mon Mar 7 12:05:13 2022 -0800
    Adding undoc'd settings now being made defaults. Refs #28831
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    194e0e1f7f8f80e3a9e5b5c5a4f42d24241d4f50 Mon Mar 7 12:06:50 2022 -0800
    Adding undoc'd settings now being made defaults. Refs #28831
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    e25b1163ff40d3eacbd7115f0074353a841f9b18 Mon Mar 7 12:58:51 2022 -0800
    hub developer mode was already on by default but was not controlled via hg.conf. Leave it on by default but allow it to be turned off via hg.conf, and clarify that in the documentation, refs #28831
• src/utils/bedToBigBed/bedToBigBed.c
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    7df99795b147931dfea8220ed5ab305d11fde6b4 Thu Mar 10 15:41:46 2022 -0800
    move some chromAlias stuff around so bedToBigBed can use a chromAlias bigBed as a chromAlias file.
• src/utils/qa/weeklybld/buildEnv.csh
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    22de971aa69a04002de5c4292acd7a91606fe560 Mon Mar 14 10:10:04 2022 -0700
    v428 final build, refs #29014

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• files changed: 109