All File Changes

v379_preview to v379_preview2 (2019-03-04 to 2019-03-11) v379

• confs/preview.hg.conf
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    955b4c2e07d6a6c824607ac86a929a715817a5e0 Sun Mar 10 01:11:43 2019 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
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    0cd83f85a32961ed1a7c0313147c6985fda34fc6 Tue Mar 5 12:11:12 2019 -0800
    added a reminder to the end of the cdwMakeFileTags output to remind users to update the full text index too.
• src/hg/cirm/cdw/lib/cdwPageHeader.h
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    25586e2ae42040573c77989ab86db4a57d3c29a3 Mon Mar 4 16:43:10 2019 -0800
    Updating header to match static header based on feedback in CR, refs #22817
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
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    4b2f0b08db3863d454798b4b24c810971d8153d9 Mon Mar 4 16:30:51 2019 -0800
    Minor corrections in Pasca and Weissman lab desc. Adding Will to the page.
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 25, context: html, text, full: html, text
    c8901b6383c22eec5573992e4686bfe4d3700e73 Mon Mar 4 16:35:37 2019 -0800
    Adding a few missing pubs. Adding links to pubs, GEO, and dbGaP for a few daatsets. Adding new shortlinks to summary pages for a few datasets. refs #22852
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 5, context: html, text, full: html, text
    d70c49143f19ace315cd63186e55057c4dfaf089 Mon Mar 4 16:29:02 2019 -0800
    Whitespace-only changes to footer. no redmine
• src/hg/cirm/gateway/htdocs/inc/header.html
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    068250f4e8f6525cfb114b77a23c7fdb70939772 Wed Mar 6 18:32:12 2019 -0800
    Including new FontAwesome v5 in header. Updating legend at top of page to include other icons now on page. refs #23079
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 48, context: html, text, full: html, text
    9ef29a0661196c532e881816ca6ddf67b0205770 Mon Mar 4 16:31:33 2019 -0800
    Adding Jim's updated homepage text to the site, no redmine.
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 73, context: html, text, full: html, text
    c8901b6383c22eec5573992e4686bfe4d3700e73 Mon Mar 4 16:35:37 2019 -0800
    Adding a few missing pubs. Adding links to pubs, GEO, and dbGaP for a few daatsets. Adding new shortlinks to summary pages for a few datasets. refs #22852
  • lines changed 58, context: html, text, full: html, text
    068250f4e8f6525cfb114b77a23c7fdb70939772 Wed Mar 6 18:32:12 2019 -0800
    Including new FontAwesome v5 in header. Updating legend at top of page to include other icons now on page. refs #23079
• src/hg/hgSession/backup.c
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    9ae36bf63931b4a9d8a5a66e0d4696ead3a86eac Tue Mar 5 15:46:24 2019 -0800
    Fixing race condition where background is slow starting up. Found by Daniel.
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    0dc41ec22723a16550fc1aebc0970192a410aed0 Wed Mar 6 17:40:05 2019 -0800
    Strip commas before parsing positions in all 4 position parsing routines in hgTracks.c. Back in 4a03019 (hgFind cleanup), making hgTracks.c's parseVirtPosition strip commas wasn't sufficient; parseNonVirtPosition also needs to strip commas. Just to be safe, I'm making parseVPosition and parseNVPosition strip commas too. I think it would be better to make use of hdb's parsePosition rather than duplicate the core parsing code in 4 new places, but will leave that for another day.
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 7, context: html, text, full: html, text
    583ec14dfa16d1d2b276d8def704d81c78d4e599 Wed Mar 6 15:19:20 2019 -0800
    Fixing a typo and adding better quotes ref#23057
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 5, context: html, text, full: html, text
    b3d65174671cb91e04061d4e6004b945fdb43b55 Tue Mar 5 16:24:24 2019 -0800
    Editing customTrackText.html for grammar, no redmine
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 27, context: html, text, full: html, text
    61ef6598e71f0ca126ee10f62cc8d2ba787d2bd4 Mon Mar 4 17:19:35 2019 -0800
    Final draft of hgVcfTrackHelp page with images #22039
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    0001c7a0bb8143e431569d54b7ba369410c994f7 Tue Mar 5 12:16:00 2019 -0800
    Added more info on default SNP behavior #22039
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    225975e8b5126b8d541768d808631da98a946362 Mon Mar 4 11:52:05 2019 -0800
    Adding (public version) to RefSeq HGMD newsarch.html, refs #22659
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    43f2f9f2a3afe3bd1ec19e9677c6e6257a928acd Mon Mar 4 14:50:51 2019 -0800
    Announcing the Tabula Muris track for mm10, refs #21811
  • lines changed 1, context: html, text, full: html, text
    b5ad01c681965fb53c422609dbca58a2257f3037 Mon Mar 4 15:07:56 2019 -0800
    Shortening the title of the announcement on newsarch.html and adding an entry to indexNews.html, refs #21811
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    717f81142096530680a394f26a0f25f17917c4ae Tue Mar 5 16:08:53 2019 -0800
    Adding acknowledgements for CZI folk in the news announcement, refs #21811
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    e099b19ec84eafd20f53609ca018b414be21f6fe Tue Mar 5 16:18:56 2019 -0800
    Clarifying that Max and I are from UCSC, refs #21811
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    34c80bd1b2c379c57d9a7982ed6df75a15067b0d Wed Mar 6 10:14:19 2019 -0800
    Fixing a minor typo in my news announcement, no Redmine.
  • lines changed 3, context: html, text, full: html, text
    29905fd6126687df37882b64d015de8a55b44392 Wed Mar 6 16:00:22 2019 -0800
    Adding more credits to the Tabula Muris announcement, refs #21811
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    b024ff47774adcf85b8532e3d4c8c28b5e973196 Fri Mar 8 15:59:17 2019 -0800
    Archive news update for patchwork ref#18855
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 6, context: html, text, full: html, text
    73e9e776ba39981580128c7c4440b8af53cef403 Thu Mar 7 16:37:15 2019 -0800
    Adding PMC PMID entry to NAR paper
• src/hg/htdocs/history.html
  • lines changed 109, context: html, text, full: html, text
    cedb0272e341325a68b3a71acfd18103c84562f4 Wed Mar 6 11:54:45 2019 -0800
    Adding 'Genome' to a title and removing the 'Reflections' section. refs #20314
• src/hg/htdocs/images/patches.jpg
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    07d09bea7ae4d0e3f8d27f5e8b823af70bfd7b3a Mon Mar 11 09:56:02 2019 -0700
    Adding new image for patchwork announcement ref#18855
• src/hg/htdocs/images/vcfDefault.png
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    0001c7a0bb8143e431569d54b7ba369410c994f7 Tue Mar 5 12:16:00 2019 -0800
    Added more info on default SNP behavior #22039
• src/hg/htdocs/images/vcfFilters.png
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    5d6c6d4b49cc1e17fb2001a6ab6aa6edfe6abd43 Mon Mar 4 17:14:53 2019 -0800
    Adding images for hgVcfHelp page #22039
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    61ef6598e71f0ca126ee10f62cc8d2ba787d2bd4 Mon Mar 4 17:19:35 2019 -0800
    Final draft of hgVcfTrackHelp page with images #22039
• src/hg/htdocs/images/vcfOptions.png
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    5d6c6d4b49cc1e17fb2001a6ab6aa6edfe6abd43 Mon Mar 4 17:14:53 2019 -0800
    Adding images for hgVcfHelp page #22039
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    61ef6598e71f0ca126ee10f62cc8d2ba787d2bd4 Mon Mar 4 17:19:35 2019 -0800
    Final draft of hgVcfTrackHelp page with images #22039
• src/hg/htdocs/images/vcfSquare.png
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    5d6c6d4b49cc1e17fb2001a6ab6aa6edfe6abd43 Mon Mar 4 17:14:53 2019 -0800
    Adding images for hgVcfHelp page #22039
• src/hg/htdocs/images/vcfTree.png
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    ac1eeffd0f87001aff459944c7b67bb6ae5ed0fe Mon Mar 4 16:34:59 2019 -0800
    vcfTree image adding
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    b5ad01c681965fb53c422609dbca58a2257f3037 Mon Mar 4 15:07:56 2019 -0800
    Shortening the title of the announcement on newsarch.html and adding an entry to indexNews.html, refs #21811
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    b024ff47774adcf85b8532e3d4c8c28b5e973196 Fri Mar 8 15:59:17 2019 -0800
    Archive news update for patchwork ref#18855
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/README
  • lines changed 41, context: html, text, full: html, text
    77c5f0d7827add5913ef3535a147d650cb2cffb1 Wed Mar 6 15:35:51 2019 -0800
    Adding some documentation to the track matrix crawler and adding a script for extracting sub-matrices out of the giant matrix, refs #21785
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/cooccurrenceCounts.c
  • lines changed 12, context: html, text, full: html, text
    77c5f0d7827add5913ef3535a147d650cb2cffb1 Wed Mar 6 15:35:51 2019 -0800
    Adding some documentation to the track matrix crawler and adding a script for extracting sub-matrices out of the giant matrix, refs #21785
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/filterTop.py
  • lines changed 176, context: html, text, full: html, text
    77c5f0d7827add5913ef3535a147d650cb2cffb1 Wed Mar 6 15:35:51 2019 -0800
    Adding some documentation to the track matrix crawler and adding a script for extracting sub-matrices out of the giant matrix, refs #21785
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 69, context: html, text, full: html, text
    0d2c1dd4e883a4f2a530ea773427cdeef39f001e Mon Mar 4 13:49:17 2019 -0800
    lastz/chain/net to mouse GRCm38B refs #22271
• src/hg/makeDb/doc/mm10.txt
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    92464f409eeaa76ae789edca3bf933b0ca4dd092 Mon Mar 4 13:50:28 2019 -0800
    liftOver to GRCm38B refs #22271
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes18.sh
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    26523fb7b1f2ed70674392cbdf91daed1996fa68 Fri Mar 8 13:07:53 2019 -0800
    all built except for the blastTabs
• src/hg/makeDb/genbank/etc/build-genbank
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    3fa11fa12b7a1942cd984b15a9e06d117d2e3319 Mon Mar 4 10:24:57 2019 -0800
    We haven't been loading ESTs for a while. Oops.
• src/hg/makeDb/genbank/etc/genbank.conf
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    2d6413ac73ce99f46b980f3f0085c862314645d6 Tue Mar 5 09:09:25 2019 -0800
    don't build extra bells and whistles for GRCm38B
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    fc6634d646c87b153f46bf6e8f79db403d9c950b Sat Mar 9 14:07:31 2019 -0800
    don't load est decription:wq
• src/hg/makeDb/trackDb/chainDm3.html
  • lines changed 1, context: html, text, full: html, text
    bd31c73a2b7735d399ec275f964a7ac52fdca4d1 Wed Mar 6 08:48:50 2019 -0800
    Updating http to https for dp3, uiLinks cronjob
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
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    6ac86774faa00cca4618355ed6c3bcf7693a1f74 Mon Mar 11 10:20:40 2019 -0700
    Updating http to https for droAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dp3/genewise.html
  • lines changed 1, context: html, text, full: html, text
    bd31c73a2b7735d399ec275f964a7ac52fdca4d1 Wed Mar 6 08:48:50 2019 -0800
    Updating http to https for dp3, uiLinks cronjob
• src/hg/makeDb/trackDb/human/hg19/mastermind.html
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    77b94cf78689332bfeef8c06d6f95fc39520c84b Mon Mar 4 11:53:26 2019 -0800
    editing mastermind.html for CRv379, refs #23056
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    c97d5652b201e2483079e29171a54cb006498fb3 Mon Mar 11 08:58:40 2019 -0700
    Adding beta release tag for mastermind track on hg19, refs #21895
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
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    a357a07d42e78fdbe39d53e7fb0a498d97f7fd24 Mon Mar 4 11:09:53 2019 -0800
    Adding pennantIcons for the hg38 patchwork tracks ref#18855
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.ra
  • lines changed 1, context: html, text, full: html, text
    abf51fa097a71a6b7e15c423ad77c13c7b800208 Thu Mar 7 16:49:18 2019 -0800
    Releasing patchwork, changing visibilities and removing an old track with the same name ref#18855
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    a357a07d42e78fdbe39d53e7fb0a498d97f7fd24 Mon Mar 4 11:09:53 2019 -0800
    Adding pennantIcons for the hg38 patchwork tracks ref#18855
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    a357a07d42e78fdbe39d53e7fb0a498d97f7fd24 Mon Mar 4 11:09:53 2019 -0800
    Adding pennantIcons for the hg38 patchwork tracks ref#18855
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 53, context: html, text, full: html, text
    a357a07d42e78fdbe39d53e7fb0a498d97f7fd24 Mon Mar 4 11:09:53 2019 -0800
    Adding pennantIcons for the hg38 patchwork tracks ref#18855
  • lines changed 39, context: html, text, full: html, text
    abf51fa097a71a6b7e15c423ad77c13c7b800208 Thu Mar 7 16:49:18 2019 -0800
    Releasing patchwork, changing visibilities and removing an old track with the same name ref#18855
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    a357a07d42e78fdbe39d53e7fb0a498d97f7fd24 Mon Mar 4 11:09:53 2019 -0800
    Adding pennantIcons for the hg38 patchwork tracks ref#18855
• src/hg/makeDb/trackDb/mouse/GRCm38B/trackDb.ra
  • lines changed 75, context: html, text, full: html, text
    881d4ab8b17acb26d26ca500540795811247c6ae Wed Mar 6 11:40:25 2019 -0800
    adding display of mm10 liftOver chain (and psl) refs #22271
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    d1799c0f6759b1f15e900d7258a305346a38fc62 Wed Mar 6 15:47:44 2019 -0800
    adding BED file for chainLinks refs #22271
  • lines changed 44, context: html, text, full: html, text
    3c498d3795a5ecbf3b7bfab6c6c158e736d99b36 Thu Mar 7 00:40:58 2019 -0800
    added tracks to GRCm38
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    d323ab11c53c9f7ff8581762d6a7b295e0e96d76 Thu Mar 7 12:25:10 2019 -0800
    added tracks to GRCm38B preview browser
  • lines changed 2, context: html, text, full: html, text
    d2b661e1cc5c6d801b6f8fe35647389553840572 Fri Mar 8 09:22:21 2019 -0800
    specific db name for Mm10 chainNet refs #22271
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.ra
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    af0c026a91a0ead1e9200c30f2aa4c8269ed5b42 Thu Mar 7 08:05:33 2019 -0800
    Making UCSC Genes the first track under 'Genes and Gene Predictions' for mm10, ToDo #23084
• src/hg/makeDb/trackDb/mouse/mm10/tabulaMuris.html
  • lines changed 7, context: html, text, full: html, text
    1a58016f38772fcc887fdf7e2b67b392fa8a52b0 Mon Mar 4 15:15:59 2019 -0800
    Removing a line about views since this track no longer has views. Rephrasing the barchart display description. refs #21811
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    fb501c08f1d1d077e79277a611e3fc2c8336623a Thu Mar 7 11:37:20 2019 -0800
    Updating the link to the Tabula Muris downloads from the gbdb server, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
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    b7e8aa7680ad82537c25fe3b2e17e3628e0e657f Mon Mar 4 15:20:45 2019 -0800
    Shortening the shortLabels for the composite tracks. Adding the pennantIcon for the newly released tracks. Removing alpha and beta release tags. refs #21811
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    c782e5a28cf7caa5c16b5e1547a57a8a37064f90 Mon Mar 4 15:31:43 2019 -0800
    Changing the pennantIcon from 'Updated' to 'New', refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    b7e8aa7680ad82537c25fe3b2e17e3628e0e657f Mon Mar 4 15:20:45 2019 -0800
    Shortening the shortLabels for the composite tracks. Adding the pennantIcon for the newly released tracks. Removing alpha and beta release tags. refs #21811
• src/hg/makeDb/trackDb/netDm2.html
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    6ac86774faa00cca4618355ed6c3bcf7693a1f74 Mon Mar 11 10:20:40 2019 -0700
    Updating http to https for droAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/netDm3.html
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    bd31c73a2b7735d399ec275f964a7ac52fdca4d1 Wed Mar 6 08:48:50 2019 -0800
    Updating http to https for dp3, uiLinks cronjob
• src/hg/visiGene/knownToVisiGene/knownToVisiGene.c
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    822ada4e994ebf9a9087442a10a56e6f3c66b149 Fri Mar 8 12:55:05 2019 -0800
    change table indices to cover whole string.
• src/lib/annoStreamVcf.c
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    d9aba93eae9c9c1ba3f09055db42843cec8d63ba Wed Mar 6 17:09:07 2019 -0800
    Restoring a line incorrectly deleted in 49a9e46 -- thanks Braney for spotting! refs #23051
• src/utils/findMotif/findMotif.c
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/makefile
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    1e988e55a113409b757e34250b93e17bc0a3580d Thu Mar 7 14:11:59 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test1.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test10.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test11.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test2.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test3.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test4.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test5.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test6.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test7.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test8.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/expected/test9.txt.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/hg19.chrM.fa.gz
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
• src/utils/findMotif/tests/makefile
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    4b8a6c52d6c082137831ab42d67505c8d7c78a93 Thu Mar 7 14:08:47 2019 -0800
    expand findMotif to 32 character motifs and allow count of mis matches no redmine
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    269fad91bedc7b9555069a97efbeac142982a750 Sat Mar 9 17:19:06 2019 -0800
    adding clean target no redmine
• src/utils/qa/backupCentral.csh
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    16d9c22e94d9e76761aa2c93215b03aa91ec3ad9 Tue Mar 5 12:29:51 2019 -0800
    adding hubPublic to backup table in backupCentral.csh script
• src/utils/qa/weeklybld/buildEnv.csh
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    549109fbb63726d52bc0d3ed23482709c6b27795 Mon Mar 11 10:36:19 2019 -0700
    v379 preview2, refs #TICKETID

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