All File Changes

v375_preview2 to v375_base (2018-12-03 to 2018-12-10) v375

• .gitignore
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    7fb9856107ffbc3bed974e893a58f299b138cbac Mon Dec 10 09:02:00 2018 -0800
    Ignore gcov-generated .gcno files.
• confs/hgwdev.hg.conf
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    a38832f67dc1290fc7020d68efd5fd2f83411a2c Sun Dec 9 01:11:24 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBeacon/hgBeacon
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    93aa0d638500f9dc142eed45be1c9687a9d75369 Tue Dec 4 03:10:41 2018 -0800
    removing my stupid and useless hgBeacon debug message that somehow even made it into the build, as per email from Jairo
• src/hg/hgSession/hgSession.c
  • lines changed 17, context: html, text, full: html, text
    24ca4059b153e028d788b163bc80e55d50e1bfdf Fri Dec 7 07:54:25 2018 -0800
    hgSession prints out the link text to a session instead of hiding the link behind <a> tags, refs #8520
• src/hg/htdocs/goldenPath/credits.html
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    2eab44f3b11781ac4b913b4adb3f71eccc478df7 Tue Dec 4 09:26:06 2018 -0800
    Adding , after Ann Zweig in ponAbe2 credits, refs #22567
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    5249b99c48ff2f24154e8f9263bd5468628752ac Mon Dec 3 12:20:05 2018 -0800
    Slightly modifying 'Asia-based mirror' wording.
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 1, context: html, text, full: html, text
    a2e1671b582be8e0a27187d62494c797dfe9100a Tue Dec 4 08:50:56 2018 -0800
    Adding missing commas from code review feedback
• src/hg/htdocs/goldenPath/newsarch.html
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    bbe9fb2db5939b21d54cfab8a8e315c708f66486 Tue Dec 4 16:20:21 2018 -0800
    Announcing the release of snp151 tracks for hg38 and hg19, refs #21010
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    8fcb9fa05b7fc7c61c5a0c33f6fc3935a56e5b35 Tue Dec 4 19:25:34 2018 -0800
    added comment about x-axis of graph
• src/hg/htdocs/images/SNPs151Announce.jpg
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    868d6f886ea9d65240942a494439a298fd78dcef Tue Dec 4 15:49:06 2018 -0800
    Adding Bob's graph for the snp151 announcement, refs #21010
• src/hg/htdocs/images/phylo/dm6_124way.png
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    1e8c1d53861da257cdac7eba7029c5dfc6fc8019 Fri Dec 7 15:29:28 2018 -0800
    organized by kmer counting and then phylip neighbor joining tree construction refs #22550
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    bbe9fb2db5939b21d54cfab8a8e315c708f66486 Tue Dec 4 16:20:21 2018 -0800
    Announcing the release of snp151 tracks for hg38 and hg19, refs #21010
• src/hg/htdocs/training/index.html
  • lines changed 73, context: html, text, full: html, text
    d9ab1e2c893414894c709313a526075e51902917 Fri Dec 7 18:33:17 2018 -0800
    dropping completed brazil and city of hope workshops. moving ucsf and UOregon to the active list. adding links to future large meetings so people might find us early enough to register
• src/hg/inc/versionInfo.h
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    0a8766dc9b50da2cca3ee86fdb02c95bb7e9893e Mon Dec 10 10:03:02 2018 -0800
    New version number v375
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    57eae5f7b2e6b074ec603bbe3d1c3bf6b409e81a Tue Dec 4 15:10:58 2018 -0800
    turn off scoreFilters for bigBeds unless explicitly asked for
• src/hg/lib/variantProjector.c
  • lines changed 168, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/makeDb/doc/galGal6/multiz77way.txt
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    e26231e4b8727422759359b75297e48b285306a3 Wed Dec 5 08:41:33 2018 -0800
    through the 4d estimation refs #18874
• src/hg/makeDb/doc/mm10.txt
  • lines changed 79, context: html, text, full: html, text
    790efe7b423a4e2cf4cd0f605983c3252467077f Mon Dec 3 10:51:49 2018 -0800
    eliminate duplicated section for cotJap2 lastz chainNet refs #22330
• src/hg/makeDb/genbank/etc/gbMetadataTables.txt
  • lines changed 24, context: html, text, full: html, text
    760ecc83576c7ceed0c52b1e37422b1e263907cc Fri Dec 7 08:56:47 2018 -0800
    tweak list of metadata tables
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    22b335d8692298ebae89e458406ff286250b3003 Fri Dec 7 08:59:54 2018 -0800
    Updating HTTP to HTTPS for macEug2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    071a0fcf2008f9778b16d645e1501d8ad5d48eb4 Tue Dec 4 07:57:19 2018 -0800
    adding tdb for mastermind track, refs #21895
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    b621a83713fda3947ae569fd8db69bfcc68fdd1b Tue Dec 4 08:25:09 2018 -0800
    add some numeric filters to mastermind
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 6, context: html, text, full: html, text
    2299316e43cab5b7623dce7c86ae4619ccbf4a23 Fri Nov 30 10:54:12 2018 -0800
    Moving the closing </li> tag to the proper place. Undoing some link updates pointed out during Code Review, CR #22517
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld10.html
  • lines changed 17, context: html, text, full: html, text
    dfd6b5c8ed45c026515b6828c5cccf9a61295b8e Tue Dec 4 11:31:26 2018 -0800
    Adding the missing knownGeneOld10.html page for the Old UCSC Genes track on hg38, refs #21644
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
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    87be2041d5afe60239287bc1e0558ced9c0caafb Thu Dec 6 10:20:37 2018 -0800
    Adding the pennantIcon to the new SNP 151 tracks, refs #21010
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    da753ef04d9b5df6a4e4b45469d1cd832ed77515 Mon Dec 3 10:46:00 2018 -0800
    Removing state pennantIcon frm UCSC Genes mm10
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.4way.ra
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    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM13.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.ra
  • lines changed 1, context: html, text, full: html, text
    a8b5206098cabe0a1ed3e822aa7c9be565f02319 Wed Dec 5 09:51:12 2018 -0800
    Changing visibility settings on Dev so default tracks match RR on mm10/mm9/hg38/hg19 ref#20458
• src/hg/makeDb/trackDb/tagTypes.tab
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    332207fe1483a73616d1ab83d7e38552540b31ea Tue Dec 4 08:20:14 2018 -0800
    make tdbQuery tolerate the special Filter variables that have field names prepended.
• src/hg/oneShot/pslExpandIndelGaps/makefile
  • lines changed 3, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/pslExpandIndelGaps.c
  • lines changed 122, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsNM.psl
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    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsNM.stderr
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    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsXM.psl
  • lines changed 1, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsXM.stderr
  • lines changed 1, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/input/galGal6.NM_001030566.1.psl
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    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/input/galGal6.XM_025152810.1.psl
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    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/makefile
  • lines changed 23, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
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    e284f65f676b94960f0233e6deacd0cdfdfc38ed Mon Dec 3 11:08:48 2018 -0800
    correct target/query 2Bit and Sizes argument comments refs #22562
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
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    d22f2f9bbd1ebebfc1a5d084f4d91700875349dd Wed Dec 5 12:04:31 2018 -0800
    Changing errAbort to warning for unnecessary alignment gaps (reported to Terence Murphy at NCBI) for chicken transcript NM_001030566.1. It's not really a problem for reporting differences, but variantProjector will need a little work in order to handle it.
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 19, context: html, text, full: html, text
    332207fe1483a73616d1ab83d7e38552540b31ea Tue Dec 4 08:20:14 2018 -0800
    make tdbQuery tolerate the special Filter variables that have field names prepended.
• src/inc/psl.h
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    1791b48abfff1cb403041e39962c4021d3680664 Fri Dec 7 17:03:41 2018 -0800
    Making pslRecalcBounds public for use elsewhere.
• src/inc/srcVersion.h
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    0a8766dc9b50da2cca3ee86fdb02c95bb7e9893e Mon Dec 10 10:03:02 2018 -0800
    New version number v375
• src/lib/psl.c
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    1791b48abfff1cb403041e39962c4021d3680664 Fri Dec 7 17:03:41 2018 -0800
    Making pslRecalcBounds public for use elsewhere.
• src/utils/qa/checkTrackUiLinks.csh
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    daf86f8075efae8886a3d88dc0ab6b763dd6cb1c Wed Dec 5 16:08:35 2018 -0800
    Changing hgGateway to hgBlat to allow htmlcheck getVars to return hgsid, in the past in 2007 when this script was working it would return values, but hgGateway changed, so update allows hgsid to be assigned in this code, discovered by Hiram and Conner in reviewing error logs.
• src/utils/qa/weeklybld/buildEnv.csh
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    a4b9d8643407b8bebb0cfb06e446903a729ce75d Mon Dec 10 10:02:17 2018 -0800
    v375 final build, refs #22531

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• files changed: 51