All File Changes

v398_preview2 to v398_base (2020-05-04 to 2020-05-11) v398

• src/hg/hgTracks/hgTracks.c
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    dea81fb17cc857a898e9caebeadb93b64ded61c0 Tue May 5 12:53:39 2020 -0700
    get the Short Match track to recognize RNA.
• src/hg/hgTracks/imageV2.c
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    353870e81dfb3fbc45a83f3f808e1f7f31cad968 Thu May 7 09:52:19 2020 -0700
    Removing commeneted out code from an old experiment, refs #25498
• src/hg/hgc/rnaFoldClick.c
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    41bbd268df98df338d98b6b98c62ab595d85aff1 Mon May 4 14:19:12 2020 -0700
    don't print out conf field in rnaStruct tables if not present. Added link to PseudoViewer
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 34, context: html, text, full: html, text
    d5f33c3bbb34ad7fd6c08714156b9dfbf292d3bf Tue May 5 16:26:38 2020 -0700
    Adding a FAQ about the asmEquivalent table, refs #21074
• src/hg/htdocs/covid19.html
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    4fc9ab4f1eab9388746ed20ac55b8ecfd088bb82 Mon May 4 10:03:11 2020 -0700
    Updating the date of the COVID landing page, no Redmine.
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 4, context: html, text, full: html, text
    f46d6ed891db29b9aca07f4e088e5bd3c21ec58c Wed May 6 15:32:12 2020 -0700
    Adding a link to MLQ in short match track to someday be replaced by FAQ refs #25522
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 38, context: html, text, full: html, text
    986087931ac64c4f3ada375576fdaa6d92e7be83 Mon May 4 16:21:41 2020 -0700
    new announcement Problematic Regions track refs #24245
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    9c2dfa33b42a7ff3d3e21b70872d6fe3b7a62d0b Tue May 5 10:27:24 2020 -0700
    Undoing and recomitting Ana's announcement - she accidentally changed the formatting on newsarchive page, no RM
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    3626ef115a289cde99ec6d57688f5e054b9f639a Tue May 5 16:13:46 2020 -0700
    added _blank to all links refs #24245
• src/hg/htdocs/indexNews.html
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    986087931ac64c4f3ada375576fdaa6d92e7be83 Mon May 4 16:21:41 2020 -0700
    new announcement Problematic Regions track refs #24245
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    9c2dfa33b42a7ff3d3e21b70872d6fe3b7a62d0b Tue May 5 10:27:24 2020 -0700
    Undoing and recomitting Ana's announcement - she accidentally changed the formatting on newsarchive page, no RM
• src/hg/htdocs/style/images/ui-icons_00498f_256x240.png
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    24d0b50be1ae5a7e10da3936bb1132da62afdef3 Sun May 10 21:30:34 2020 -0700
    Switch to dark blue for info icon (distinguish from controls). Found this dark blue in another jquery theme (dot luv). refs #23365
• src/hg/htdocs/style/jquery-ui.css
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    7c47407414f3e8304a2c1ef094694f29e1d316a2 Sun May 10 21:18:42 2020 -0700
    Change info icon to blue. More visible. Request by Ana. refs #23365
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    a9ff8ca467d396a070053e61f6f462deb13396a8 Sun May 10 21:26:36 2020 -0700
    Increase size of info icon slightly. Request of Ana. refs #23365
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    24d0b50be1ae5a7e10da3936bb1132da62afdef3 Sun May 10 21:30:34 2020 -0700
    Switch to dark blue for info icon (distinguish from controls). Found this dark blue in another jquery theme (dot luv). refs #23365
• src/hg/inc/hui.h
  • lines changed 5, context: html, text, full: html, text
    d0818261483ef1cbd71e9fb2fc400aeaac0cd072 Mon May 11 08:58:27 2020 -0700
    Code cleanup for info icon. refs #23365
• src/hg/inc/rnaSecStr.h
  • lines changed 5, context: html, text, full: html, text
    41bbd268df98df338d98b6b98c62ab595d85aff1 Mon May 4 14:19:12 2020 -0700
    don't print out conf field in rnaStruct tables if not present. Added link to PseudoViewer
• src/hg/inc/versionInfo.h
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    d23d2136d43f72838418c5c296109d1fc289c340 Mon May 11 10:38:07 2020 -0700
    New version number v398
• src/hg/lib/hui.c
  • lines changed 17, context: html, text, full: html, text
    d1c83e6381e0dba3db4c89808a8833cb896d3bfc Thu May 7 12:25:13 2020 -0700
    Replace ? with jquery info icon. refs #23365
  • lines changed 4, context: html, text, full: html, text
    7c47407414f3e8304a2c1ef094694f29e1d316a2 Sun May 10 21:18:42 2020 -0700
    Change info icon to blue. More visible. Request by Ana. refs #23365
  • lines changed 24, context: html, text, full: html, text
    5eb21a72bda1cb7a5f9c293c972565caf24ffef7 Mon May 11 08:58:04 2020 -0700
    Code cleanup for info icon. refs #23365
• src/hg/lib/jksql.c
  • lines changed 16, context: html, text, full: html, text
    d77912f2c1142e295dacfffb3fa1d36ff45e95b5 Mon May 11 10:10:53 2020 -0700
    Fix sqlDescribe to still find table description if a table does not exist in the table cache, refs #25536
• src/hg/lib/rnaSecStr.c
  • lines changed 19, context: html, text, full: html, text
    41bbd268df98df338d98b6b98c62ab595d85aff1 Mon May 4 14:19:12 2020 -0700
    don't print out conf field in rnaStruct tables if not present. Added link to PseudoViewer
• src/hg/lib/rnaSecStrShort.as
  • lines changed 12, context: html, text, full: html, text
    55530c42a84a4f8f0cca02b2c27c722099592212 Wed May 6 14:23:26 2020 -0700
    add AS file for the short form of rnaStruct tables without conf field
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 7, context: html, text, full: html, text
    a3221ce060e8efe2e9ef46392625606896f64f96 Fri May 8 23:06:59 2020 -0700
    do not print links to other assembly hubs from VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 2, context: html, text, full: html, text
    a3221ce060e8efe2e9ef46392625606896f64f96 Fri May 8 23:06:59 2020 -0700
    do not print links to other assembly hubs from VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 3, context: html, text, full: html, text
    a3221ce060e8efe2e9ef46392625606896f64f96 Fri May 8 23:06:59 2020 -0700
    do not print links to other assembly hubs from VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 13, context: html, text, full: html, text
    a3221ce060e8efe2e9ef46392625606896f64f96 Fri May 8 23:06:59 2020 -0700
    do not print links to other assembly hubs from VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/vgp.asmId.commonName.tsv
  • lines changed 4, context: html, text, full: html, text
    c254573e477c6da281ca8d4f041770cd06d417b3 Mon May 4 15:11:59 2020 -0700
    two genbank assemblies have become refseq assemblies refs #23734
• src/hg/makeDb/doc/asmHubs/vgp.commonName.asmId.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    c254573e477c6da281ca8d4f041770cd06d417b3 Mon May 4 15:11:59 2020 -0700
    two genbank assemblies have become refseq assemblies refs #23734
• src/hg/makeDb/doc/hg19.txt
  • lines changed 83, context: html, text, full: html, text
    f872e1088fcd06308ca592418458d7787aca1bf1 Tue May 5 10:42:31 2020 -0700
    Load GTEx V8 gene expression for hg19. refs #25130
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 123, context: html, text, full: html, text
    dfa6639914399df4d023ebc3df4f4009238c645e Mon May 4 16:50:39 2020 -0700
    Fix chron order in make doc. refs #25130
• src/hg/makeDb/doc/wuhCor1/ncbiGene.txt
  • lines changed 5, context: html, text, full: html, text
    2d63320364a72e3a63a5dd1203accea0cea1f634 Mon May 4 12:00:56 2020 -0700
    build some an ix file for ncbiGene
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    e144b7538591e1f30557edebb315f0cb78622e33 Tue May 5 10:01:35 2020 -0700
    Adding one more name for wuhCor1 for genbank
• src/hg/makeDb/trackDb/human/dbVar_common.html
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    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
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    7164821eac1d076015e892bc6b3961f5760f382d Fri May 8 09:56:05 2020 -0700
    Adding NCBI Conflict SVs track as a companion to common svs, refs #25424
• src/hg/makeDb/trackDb/human/gtexGeneV8.html
  • lines changed 9, context: html, text, full: html, text
    1cec534c306475b701fb148763bc3edc021a0be5 Mon May 4 16:35:08 2020 -0700
    Fix formatting error in track description. refs #25130
• src/hg/makeDb/trackDb/human/hg19/problematic.html
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    7ae7b659684aac7aaceb6a06c3cedda7fa554c82 Mon May 4 10:29:33 2020 -0700
    Minor typo fix #24245
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    669c537dfa733feff69fdbf3dceba6d838da2772 Mon May 4 10:41:35 2020 -0700
    fixing typos #24245
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    6e379d7b8b4f2fef83c8fd027336a6616a214900 Mon May 4 15:44:16 2020 -0700
    change browser links from hg38 to hg19 refs #24245
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    8726cb283faace8ec8547669d8727beb6507d02b Wed May 6 15:15:48 2020 -0700
    added 'hide empty subtracks' sentence in the description refs #25494
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    da3168ed1a32e1510833aabb83fa392e0770fafc Thu May 7 19:17:32 2020 -0700
    corrected typo hyphens and first sentence refs #25494
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    669c537dfa733feff69fdbf3dceba6d838da2772 Mon May 4 10:41:35 2020 -0700
    fixing typos #24245
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    c9ac5ef159c88fa4ee95580dbce66938e7fe0466 Mon May 4 10:44:50 2020 -0700
    fixing typos #24245
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    e93b992b1a2d71acee155133188efb5152ec4ab9 Wed May 6 12:22:01 2020 -0700
    Adding a pennantIcon to problematic regions #24245
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    584a3abae52e84c03de4a5f895878a84f860893b Thu May 7 12:22:07 2020 -0700
    Changing hideEmpty to off by default #24245
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    b45b92884e6f47d8d0ceae9efb779b142d2fe210 Thu May 7 12:26:47 2020 -0700
    HideEmpty tracks should go out with the feature default off until later in feature rollout. refs #23365
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
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    7e47092189d71484b444f08b569c67b1a933c6d0 Tue May 5 14:24:43 2020 -0700
    Add Mouse cCRE track from ENCODE. refs #24668
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    7e47092189d71484b444f08b569c67b1a933c6d0 Tue May 5 14:24:43 2020 -0700
    Add Mouse cCRE track from ENCODE. refs #24668
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 75, context: html, text, full: html, text
    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
  • lines changed 42, context: html, text, full: html, text
    7164821eac1d076015e892bc6b3961f5760f382d Fri May 8 09:56:05 2020 -0700
    Adding NCBI Conflict SVs track as a companion to common svs, refs #25424
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 3, context: html, text, full: html, text
    7e47092189d71484b444f08b569c67b1a933c6d0 Tue May 5 14:24:43 2020 -0700
    Add Mouse cCRE track from ENCODE. refs #24668
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 1, context: html, text, full: html, text
    1cbb97baa2f15ef7edcad7cd0e83b68ffae3c6cf Tue May 5 15:14:45 2020 -0700
    Fixing typo in assembly accession, refs #25512
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
  • lines changed 1, context: html, text, full: html, text
    1cbb97baa2f15ef7edcad7cd0e83b68ffae3c6cf Tue May 5 15:14:45 2020 -0700
    Fixing typo in assembly accession, refs #25512
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    7e47092189d71484b444f08b569c67b1a933c6d0 Tue May 5 14:24:43 2020 -0700
    Add Mouse cCRE track from ENCODE. refs #24668
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    7e47092189d71484b444f08b569c67b1a933c6d0 Tue May 5 14:24:43 2020 -0700
    Add Mouse cCRE track from ENCODE. refs #24668
• src/hg/makeDb/trackDb/twinscan.html
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    6b5710a00b132c7643e6a7741dd0c3fc33412c83 Thu May 7 08:43:04 2020 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/makeDb/trackDb/virus/wuhCor1/artic.html
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    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html
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    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra
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    803d54e19a57e546e7cc9d46460b474916f0b80a Tue May 5 08:14:01 2020 -0700
    renaming epitopes tracks, as per david, refs #25461
• src/hg/makeDb/trackDb/virus/wuhCor1/kimTranscripts.html
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    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.ra
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    ad14d4075e71002254083b61457eb7a10d633cf6 Mon May 4 11:57:02 2020 -0700
    add some additional search text for NCBI Genes
• src/hg/makeDb/trackDb/virus/wuhCor1/rfam.html
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    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/rnaStructRangan.html
  • lines changed 1, context: html, text, full: html, text
    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/targets.html
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    d764706b245fcd34e7c668e93a8de672557d54aa Thu May 7 13:48:26 2020 -0700
    Fixing desc pages in response to CR refs #25496
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra
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    a6dd687f9d58da63c02a407d40d19b12ba38ec5c Fri May 8 16:53:27 2020 -0700
    small experiment with a 7-way refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    690d7d9685b59113c0de6e7cf970e4aab8d290bb Tue May 5 08:06:15 2020 -0700
    adding nextstrain clade variant frequency, refs #25481
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    dcfeaed04f4c47a794aa766b4fe336da5fdaf2bd Tue May 5 09:14:38 2020 -0700
    Make Nextstrain Variants visible by default. refs #25188
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    8b513721959e2c4cc9a6d7704519f268ef7cb680 Wed May 6 06:45:15 2020 -0700
    fixing a nextstrain release tag problem that was my fault and found by the nightly build
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    a6dd687f9d58da63c02a407d40d19b12ba38ec5c Fri May 8 16:53:27 2020 -0700
    small experiment with a 7-way refs #25090
• src/hg/makeDb/trackDb/worm/ce2/picTar.html
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    6b5710a00b132c7643e6a7741dd0c3fc33412c83 Thu May 7 08:43:04 2020 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/utils/otto/dbVar/checkDbVar.sh
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    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
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    7164821eac1d076015e892bc6b3961f5760f382d Fri May 8 09:56:05 2020 -0700
    Adding NCBI Conflict SVs track as a companion to common svs, refs #25424
• src/hg/utils/otto/dbVar/dbVarWrapper.sh
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    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
• src/hg/utils/otto/dbVar/makefile
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    bc5c961b757f1fff2266780c4e24a5ceac3642ef Thu May 7 15:17:26 2020 -0700
    Adding dbVar track hub common SVs as a native track, refs #25424
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    590d349ae81a1ea322bc821c93f68652cde2d208 Thu May 7 09:41:02 2020 -0700
    Make a safe directory for files linked from /gbdb, so gbdb links don't point to corrupted daily files when a rebuild gets an error. refs #25188
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    ff98aaa63b498de1a055e7b7c1d8caab74e59f81 Thu May 7 10:28:46 2020 -0700
    Added Max's alternate allele count bigWigs. refs #25481
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    837084f92db89608a8403d2fc27a780725c59cc7 Mon May 4 10:32:20 2020 -0700
    Use '$' instead of ';' as a separator in internal node labels because ';' is used to terminate Newick trees and gives phyloTree indigestion.
• src/inc/common.mk
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    6e49b6de0de742e4e8cb8057440a63ece6e7ec53 Sun May 10 12:27:57 2020 -0700
    updates to work with Mac OSX Catalina and brew install of mariadb and openssl no redmine
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    a2e177597fbd6c1a6dc7f8ea5f4f45ec9b8f08ac Sun May 10 13:23:19 2020 -0700
    better time to select libmariadbclient.a for Mac OSX Catalina no redmine
• src/inc/dnautil.h
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    dea81fb17cc857a898e9caebeadb93b64ded61c0 Tue May 5 12:53:39 2020 -0700
    get the Short Match track to recognize RNA.
• src/inc/srcVersion.h
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    d23d2136d43f72838418c5c296109d1fc289c340 Mon May 11 10:38:07 2020 -0700
    New version number v398
• src/lib/dnautil.c
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    dea81fb17cc857a898e9caebeadb93b64ded61c0 Tue May 5 12:53:39 2020 -0700
    get the Short Match track to recognize RNA.
• src/lib/pairHmm.c
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    5234cfcb4a8b7c971f749002bfa4c26ff6f05804 Tue May 5 11:33:58 2020 -0700
    fixup needLargeMem argument type to get this to work with SARS MERS alignment no redmine
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    dc6d6e4b842178bd00a20da9a03ddf6deeee9e94 Thu May 7 10:55:45 2020 -0700
    and fixup pointer arithmetic due to correct needLargeMem argument and hence much larger array sizes for difficult alignments no redmine
• src/utils/pslScore/pslScore.pl
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    725a8349dd0337b68ba8bedf10cf9fe1ab7492d3 Mon May 11 09:48:12 2020 -0700
    fix calculation for protein blat on negative strand refs #25538
• src/utils/pslScore/tests/NP_149062.psl
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    725a8349dd0337b68ba8bedf10cf9fe1ab7492d3 Mon May 11 09:48:12 2020 -0700
    fix calculation for protein blat on negative strand refs #25538
• src/utils/pslScore/tests/expect.NP_149062.tab
  • lines changed 9, context: html, text, full: html, text
    725a8349dd0337b68ba8bedf10cf9fe1ab7492d3 Mon May 11 09:48:12 2020 -0700
    fix calculation for protein blat on negative strand refs #25538
• src/utils/pslScore/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    725a8349dd0337b68ba8bedf10cf9fe1ab7492d3 Mon May 11 09:48:12 2020 -0700
    fix calculation for protein blat on negative strand refs #25538
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    3726607cd42c30454406b0da7bb7fe0504a9478a Mon May 11 10:36:41 2020 -0700
    v398 final build

• lines changed: 1085
• files changed: 91