All File Changes

v350_preview to v350_preview2 (2017-05-22 to 2017-05-29) v350

• confs/hgwdev.hg.conf
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    c7e5b57ca1142f8bd0c97cd62229cf07f9388df2 Sun May 28 01:12:02 2017 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    c7e5b57ca1142f8bd0c97cd62229cf07f9388df2 Sun May 28 01:12:02 2017 -0700
    Installing updated hg.conf files from UCSC servers
• python/lib/ucscGb/qa/tables/checkGapOverlap.py
  • lines changed 129, context: html, text, full: html, text
    d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
    Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 32, context: html, text, full: html, text
    d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
    Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 41, context: html, text, full: html, text
    d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
    Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
• python/lib/ucscGb/qa/tables/tableTypeUtils.py
  • lines changed 89, context: html, text, full: html, text
    d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
    Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
• src/hca/LICENSE
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    3160a4f9e2924dbc4c828706a30c6a8112b587f1 Thu May 18 23:19:16 2017 -0700
    Making directory for Human Cell Atlas work.
• src/hca/README
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    3160a4f9e2924dbc4c828706a30c6a8112b587f1 Thu May 18 23:19:16 2017 -0700
    Making directory for Human Cell Atlas work.
• src/hca/oneShot/hcaTsvToJson1/hcaTsvToJson1.c
  • lines changed 181, context: html, text, full: html, text
    f26f0a56e8e42e7a5861dab0922af4455ceb5d56 Fri May 19 07:02:46 2017 -0700
    First cut of utility to convert tab-separated-file to json files for HCA.
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    95778c97815df7fa4d8d05d41df9dc579fffebbd Fri May 19 07:05:22 2017 -0700
    Improving usage message.
• src/hca/oneShot/hcaTsvToJson2/hcaTsvToJson2.c
  • lines changed 212, context: html, text, full: html, text
    0a0567053d3755a321545b62a5475ab3a52d9711 Wed May 24 00:05:02 2017 -0700
    Adding some uuids in.
• src/hca/oneShot/hcaTsvToJson2/makefile
  • lines changed 4, context: html, text, full: html, text
    0a0567053d3755a321545b62a5475ab3a52d9711 Wed May 24 00:05:02 2017 -0700
    Adding some uuids in.
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    2b7dcf8cbbabd34aee0ff9a8e064b662fbc51213 Wed May 24 09:02:08 2017 -0700
    Moving -luuid line in makefile as per Hiram's advice and now it actually links!
• src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
  • lines changed 18, context: html, text, full: html, text
    7be45023c3d59745679040ef16b91842ce338d41 Thu May 25 10:00:43 2017 -0700
    Adding support for csv, fixing format string compare for tsv and text. Addresses link issues on cdwWebBrowse Data Sets page where it has html, text, tsv, and csv links.
• src/hg/hgGene/hgGene.c
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    1d851880b8a9d745cfed02d9e7893c210fd7bc70 Wed May 24 13:56:28 2017 -0700
    print out Gencode Gene Id if Gencode version of knownGene
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 73, context: html, text, full: html, text
    33d37d6a60180fdc11fbdd59641c822579f85995 Wed May 24 15:04:20 2017 -0700
    adding help page for mirrors where graphviz may not work, refs #13634
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    97d07cc944f4b5032f41134c52d7cf3d20a541de Thu May 25 13:56:17 2017 -0700
    changing the hash bang line of hgGeneGraph inspired by hgwbeta, refs #13634
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    b88380414ddecaab81f5c19b9f0cf06dbbedc787 Fri May 26 06:36:28 2017 -0700
    changing python hash bang again for hgGeneGraph, tiny wrangling fix, refs #13634
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    f788f52a37e301179d324c0d73d24570588e950c Fri May 26 16:57:00 2017 -0700
    outputting a better error message when tables are missing, after a hgwbeta experience, refs #13634
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    9ca067c40fe32a9d42db9c3f1451907062950149 Fri May 26 17:06:39 2017 -0700
    adding pointer to help page, refs #13634
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 1, context: html, text, full: html, text
    a93b8c3821b6c637246f68c1fdfeceed8a49b4d3 Wed May 24 09:06:12 2017 -0700
    Remove apparently unnecessary CSS. refs #19462
• src/hg/hgTables/bigWig.c
  • lines changed 30, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTables/hgTables.h
  • lines changed 5, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTables/wiggle.c
  • lines changed 2, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTracks/barChartTrack.c
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    c8665892cbf049e6e8ff5596464440556bed55a2 Mon May 22 10:46:06 2017 -0700
    Set useScore so dense mode displays well. No longer need the setting in trackDb). refs #18736
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    7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
    Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 115, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 284, context: html, text, full: html, text
    ab0308eb01ad28724dc672e898ec16dcb68ec248 Wed May 24 20:05:39 2017 -0700
    Fixed bug where enabmling highlighting could cause duplication of some items. This was caused by an attemt to optimized number of SQL queries constructing queries that joined with tables that have a many to one relationship to the gene annotations. RM 17215 RM 19166
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    d611f39a00ac8d8a6385834aa1b2ea8dbe65d574 Thu May 25 15:26:39 2017 -0700
    fixed bug in gencode highlight code where no highlights specified results in all being highlights
• src/hg/hgTracks/gtexTracks.c
  • lines changed 2, context: html, text, full: html, text
    7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
    Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTracks/simpleTracks.c
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/hgTracks/wigCommon.h
  • lines changed 4, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/htdocs/goldenPath/credits.html
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    97f6bf1fdebee5f72438176ed67f5c58524030a0 Wed May 24 14:22:24 2017 -0700
    Applied new style, reworked some sections. Refs #18504
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    9765eb186a69578209358244b112453dc901184b Wed May 24 15:03:08 2017 -0700
    Converted the TOC to collapsible lists.
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    cc19ca1e4026cfcc952c55b010e29c461689a519 Wed May 24 19:07:56 2017 -0700
    Pulled out Human as its own standalone link in TOC, per suggestion from Kate.
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 33, context: html, text, full: html, text
    89ee08eb69a19f1f8ea8abc4269dbd27699ee184 Tue May 23 15:46:37 2017 -0700
    Edits to barChart track description, refs #18736
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    01fce10e07b2ed9dfdf14601061cac80e3bba77e Wed May 24 16:58:53 2017 -0700
    Mostly minor changes to barChart description, refs #18736
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    5e4747757fc39669af3a6e9576fc44e7ffdd3d6b Thu May 25 15:41:56 2017 -0700
    Some edits suggested by BrianL, refs #18736
• src/hg/htdocs/goldenPath/help/hgCompositeHelp.html
  • lines changed 24, context: html, text, full: html, text
    1a3556f2017f62ae3f5da613f2b9bf1a6f57ec28 Tue May 23 10:27:17 2017 -0700
    Minor edits to hgComposite help, refs #11630
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 3, context: html, text, full: html, text
    326daa8d8909356a7bd10545c3525ff285cb40b1 Mon May 22 14:54:04 2017 -0700
    Correction to URL for hgGeneGraph stats page, changing URL to database that's now disappeared, minor spelling correction, refs #13634
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    d01f09a32c56f6b042ca2a921196593f8c7bb265 Tue May 23 12:20:42 2017 -0700
    fixing mpidb link, refs #13534
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    0658be300780cc55fcf9fe9bcde68b77ee867ca0 Thu May 25 16:18:54 2017 -0700
    adding data access section, refs #13634
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
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    6d477b5c13c2913f7ab1e8738abafa413e5d14db Mon May 22 12:03:26 2017 -0700
    added info on new feature for custom regions in BED format, refs #17358
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    05d2c619e5a3fb5af3e94568d2068e76467d1308 Tue May 23 08:48:45 2017 -0700
    added new screenshot of multi-region menu, refs #17358
• src/hg/htdocs/images/MultiRegionConfigurationWindow2.PNG
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    05d2c619e5a3fb5af3e94568d2068e76467d1308 Tue May 23 08:48:45 2017 -0700
    added new screenshot of multi-region menu, refs #17358
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    f80cb480b03f9fdade8e8cbea179360d64348a90 Wed May 24 09:41:58 2017 -0700
    dropped extra multiconfig snapshot
• src/hg/htdocs/images/MultiRegionConfigurationWindow2.png
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    5f3348494a51665660ac9650a28336ea95d48b26 Tue May 23 08:53:31 2017 -0700
    corrected .png extension
• src/hg/htdocs/inc/gbPageStart.html
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    b038c9efbd0006a4ef85b0d4709663aae16a2080 Wed May 17 21:30:03 2017 -0700
    Add option to include JS for dynamic behavior.
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    6e5534d6e49c698643817a5745f19dea156e3157 Wed May 24 15:32:08 2017 -0700
    take out "Make Composite" from blue bar menu
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 31, context: html, text, full: html, text
    ec5a82a0f026c41041f9df33cdf98efec297a092 Mon May 22 16:00:49 2017 -0700
    Support for collapsible sections, initial use table of contents type pages. refs #18504
• src/hg/htdocs/testToc.html
  • lines changed 35, context: html, text, full: html, text
    ec5a82a0f026c41041f9df33cdf98efec297a092 Mon May 22 16:00:49 2017 -0700
    Support for collapsible sections, initial use table of contents type pages. refs #18504
• src/hg/inc/mathWig.h
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    e4dc5f0504182a78676676ea772abfd3df806c51 Wed May 24 14:11:58 2017 -0700
    oops, left out mathWig.h
• src/hg/inc/trackDb.h
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/js/hgTracks.js
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    ea3693ba624c2bc0e7849cac3dba48ee6a1ddd30 Tue May 23 21:49:46 2017 -0700
    fixing multi-highlights not moving during pannings, refs #19463
• src/hg/lib/barChartGeneExp.as
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    89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
    Fixing the issues identified in this weeks code review, refs #19445
• src/hg/lib/barChartTranscExp.as
  • lines changed 15, context: html, text, full: html, text
    189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
    TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
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    d37ad664c3fd2bb2c1888f658b1fb81c9db4f0c3 Wed May 24 09:34:29 2017 -0700
    Updating the table name in the .as file, refs #18736
• src/hg/lib/customFactory.c
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    917916ac4ed3c2b7e4cdcdb4e03edd42ae5b450d Mon May 22 11:38:54 2017 -0700
    Allow barChart custom tracks without matrix fields (dataOffset, len). refs #18736
• src/hg/lib/hdb.c
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/lib/makefile
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/lib/mathWig.c
  • lines changed 111, context: html, text, full: html, text
    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/lib/trackDbCustom.c
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/lib/trackHub.c
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    677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
    add mathWig track type which is an arithmetic combination of bigWi.
• src/hg/makeDb/doc/hg19.txt
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    2c0b08d7df94e0cb6a8b3dfdc47c6eec25ba2ba7 Thu May 25 11:34:12 2017 -0700
    updating table change date in clinvar otto update, refs #19458
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    58fbbd0e2fc10b717d69ebc6a24e056c7946fbab Thu May 25 15:46:13 2017 -0700
    adding makedoc for interactions track, refs #13634
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    f8088604628eb6ff492531c438614fa92211b432 Fri May 26 09:59:15 2017 -0700
    adding more details to interactions track makedoc, refs #13634
• src/hg/makeDb/doc/hg38/hg38.txt
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    189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
    TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
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    89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
    Fixing the issues identified in this weeks code review, refs #19445
• src/hg/makeDb/doc/hg38/interactions.txt
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    58fbbd0e2fc10b717d69ebc6a24e056c7946fbab Thu May 25 15:46:13 2017 -0700
    adding makedoc for interactions track, refs #13634
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    f8088604628eb6ff492531c438614fa92211b432 Fri May 26 09:59:15 2017 -0700
    adding more details to interactions track makedoc, refs #13634
• src/hg/makeDb/doc/mm10.txt
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    97cdff9ff0ae3fbf72798fd2d1b660afdc619741 Fri May 26 11:31:42 2017 -0700
    ncbiRefSeq gene track build instructions refs #18997
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes18.sh
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    17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
    gencode v26 version of knownGene
• src/hg/makeDb/doc/wikipediaScrape.txt
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    17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
    gencode v26 version of knownGene
• src/hg/makeDb/trackDb/human/clinvar.html
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    da58c5408b67bdbcfe91b6a7e4a5051c5dea827c Tue May 23 12:11:43 2017 -0700
    clinVar has changed their format again, refs #19458
• src/hg/makeDb/trackDb/human/hg38/Bismap.html
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    89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
    Fixing the issues identified in this weeks code review, refs #19445
• src/hg/makeDb/trackDb/human/hg38/Umap.html
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    89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
    Fixing the issues identified in this weeks code review, refs #19445
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
  • lines changed 67, context: html, text, full: html, text
    189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
    TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
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    7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
    Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
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    84aba1336c8995f2e830823096229bdef57c80c6 Tue May 23 15:50:15 2017 -0700
    Adding alpha tag in new hg38/barCharts.ra for track gtexGene to restore GTEx on beta.
• src/hg/makeDb/trackDb/human/hg38/gtexExpr.html
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    2a7ba03ee1c1439b724eeb52f5ddd00efc5dd715 Tue May 23 15:02:48 2017 -0700
    Adding in the html files for gtex supertrack , refs #19350
• src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html
  • lines changed 124, context: html, text, full: html, text
    2a7ba03ee1c1439b724eeb52f5ddd00efc5dd715 Tue May 23 15:02:48 2017 -0700
    Adding in the html files for gtex supertrack , refs #19350
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 40, context: html, text, full: html, text
    17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
    gencode v26 version of knownGene
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
    Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
  • lines changed 2, context: html, text, full: html, text
    17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
    gencode v26 version of knownGene
• src/hg/makeDb/trackDb/interactions.html
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    3427fa112813f798972aeba31f388459fc9007a2 Tue May 23 15:07:04 2017 -0700
    Fixing URL typo, refs #13634
• src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
  • lines changed 53, context: html, text, full: html, text
    11dbfd831cc086a17bc981529ff050a587f36d28 Tue May 23 13:42:15 2017 -0700
    Fixing the References section on the strainSNPs.html page for mm10, refs #18305
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    75bc49bac47e2a3dbf88a1516f3cfabce74b35b6 Tue May 23 15:33:51 2017 -0700
    Making the preprint reference a hyperlink to the paper in the strainSNPs description page, refs #18305
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    05a57d765221544f83ea7070f00faa9d84f42ab7 Wed May 24 13:21:17 2017 -0700
    Adding periods to the end of sentences in the strainSNPs description page, refs #18305
• src/hg/makeDb/trackDb/tanDups.html
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    35bebcf1469bc20222200f35aa69e8d119bfd7d3 Tue May 23 14:52:46 2017 -0700
    adding composite for gapOverlaps and tandemDups refs #13553
• src/hg/makeDb/trackDb/trackDb.ra
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    35bebcf1469bc20222200f35aa69e8d119bfd7d3 Tue May 23 14:52:46 2017 -0700
    adding composite for gapOverlaps and tandemDups refs #13553
• src/hg/makefile
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    451a2448e7969d3cdb6edb16125dd09373c461d1 Mon May 22 17:26:32 2017 -0700
    adding pyLib directory to the build makefile, refs #13634
• src/hg/pyLib/makefile
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    f3658c9efc9e9121a4f03f1055e8e8bdfb7db5e7 Wed May 24 17:13:02 2017 -0700
    removing the copy instructions of graphviz from the makefile, refs #13634
• src/hg/utils/automation/doAssemblyHub.pl
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    1fba77124671c29b4e773929733015e036167960 Fri May 26 19:52:30 2017 -0700
    fix up type for photoCredits.txt refs #19450
• src/hg/utils/automation/doTandemDup.pl
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    1026d424d15e26e1138aaaa5f371e9180bd7533e Tue May 23 22:40:06 2017 -0700
    include the remove of the batch /err/ directories in cleanup refs #13553
• src/hg/utils/otto/clinvar/clinVarToBed
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    da58c5408b67bdbcfe91b6a7e4a5051c5dea827c Tue May 23 12:11:43 2017 -0700
    clinVar has changed their format again, refs #19458
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    2c0b08d7df94e0cb6a8b3dfdc47c6eec25ba2ba7 Thu May 25 11:34:12 2017 -0700
    updating table change date in clinvar otto update, refs #19458
• src/inc/tagToSql.h
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    8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
    Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
• src/lib/https.c
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    a13302691fc41d6ff9a561685f4af33ef2921d51 Wed May 24 14:32:19 2017 -0700
    Problem discovered handle leak. Reported by Jonathan. We just need to close it ourselves at the end since we use BIO_noclose flag. This is good for future if we someday re-use a connection.
• src/lib/net.c
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    f42e23773a5fd7a5d3f0fd1c1a6f183ab1175772 Wed May 24 11:25:16 2017 -0700
    File descriptor leak in netLineFileMayOpen when error-condition occurs. Reported by Jonathan.
• src/lib/tagToSql.c
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    8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
    Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
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    11a457ee3cba6ca5739c8b2607533d597c20e774 Fri May 26 12:50:35 2017 -0700
    Fixing a refactoring induced bug. Subtle one!
• src/makefile
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    1e640abe5f2d2cb1b5e9797db12427893b2d4bec Fri May 26 13:34:28 2017 -0700
    Adding tabFile to make dirs.
• src/tabFile/LICENSE
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tabFile/README
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tabFile/makefile
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tabFile/tabInfo/makefile
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    3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
    Making a tagInfo utility that parallels tagStormInfo.
• src/tabFile/tabInfo/tabInfo.c
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    3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
    Making a tagInfo utility that parallels tagStormInfo.
• src/tabFile/tabInfo/test.in
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    3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
    Making a tagInfo utility that parallels tagStormInfo.
• src/tabFile/tabQuery/makefile
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tabFile/tabQuery/tabQuery.c
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tagStorm/LICENSE
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/tagStorm/README
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
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    7b319f59e8c9183d7938f5e4e8b2b43caaa77d8d Fri May 26 13:25:48 2017 -0700
    Referencing LICENSE file in README file.
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
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    f39997389acdbf7e4da32594c892938edabfcdf9 Thu May 11 12:50:42 2017 -0700
    Adding -spec option.
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    bff6ae7c3087d5ed8b47dc77a6eae593d475603b Tue May 23 13:37:21 2017 -0700
    Removing some debugging set.
• src/tagStorm/tagStormInfo/tagStormInfo.c
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    8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
    Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
• src/tagStorm/tagStormInfo/tests/expected.out
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    cc384aecda6ac58a6236790d7cb3c89ffd084987 Fri May 26 12:32:50 2017 -0700
    Updating expected test set results.
• src/tagStorm/tagStormInfo/tests/expected.schema
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    cc384aecda6ac58a6236790d7cb3c89ffd084987 Fri May 26 12:32:50 2017 -0700
    Updating expected test set results.
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    52bfb2c4a2b1d876e2d4a57625d7752fb1e0f8cd Fri May 26 12:50:00 2017 -0700
    Fixing expected schema again
• src/tagStorm/tagStormQuery/tagStormQuery.c
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    7e03b72e0c404ba2d76a28e43f2a3e8774e783a6 Fri May 26 13:26:57 2017 -0700
    Dealing with consequences of librarification of tagStormQuery.
• src/tagStorm/tagStormScalarToArray/makefile
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    5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
    Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
• src/tagStorm/tagStormScalarToArray/tagStormScalarToArray.c
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    5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
    Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
• src/tagStorm/tagStormScalarToArray/test.expected
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    5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
    Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
• src/tagStorm/tagStormScalarToArray/test.in
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    5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
    Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
• src/tagStorm/tagStormToCsv/makefile
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    1891c9ec6b79cfca974922dc1232985ca8d9529c Thu May 25 10:16:14 2017 -0700
    Adding tagStormToCsv which never got commited, no redmine
• src/tagStorm/tagStormToCsv/tagStormToCsv.c
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    1891c9ec6b79cfca974922dc1232985ca8d9529c Thu May 25 10:16:14 2017 -0700
    Adding tagStormToCsv which never got commited, no redmine
• src/userApps/README
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    601f2b5984448488bd26aead6be30b50503fa05b Thu May 25 13:59:53 2017 -0700
    indicate rsync instructions no redmine
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    16dbc21b173a5cc54d4d7cb31ac30a0f2b3b0087 Thu May 25 14:05:12 2017 -0700
    make userApps README point to new mirror instruction page, no redmine
• src/utils/addCols/addCols.c
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    11b5d7088f505cdc4f678d3451d63bed4a3019f9 Fri May 26 13:28:25 2017 -0700
    Adding maxCols option so can handle more than 16.
• src/utils/ggTables
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    b88380414ddecaab81f5c19b9f0cf06dbbedc787 Fri May 26 06:36:28 2017 -0700
    changing python hash bang again for hgGeneGraph, tiny wrangling fix, refs #13634
• src/utils/makefile
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/utils/qa/makefile
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    00be53fdc64136b82e946142ed54230a8a092a34 Wed May 24 10:30:42 2017 -0700
    Add new runBits to makefile. Removing old version, refs #18828
• src/utils/qa/runBits
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    dfa38476ce393fb3ae03ed7ba8f6845596e26b73 Wed May 24 10:29:08 2017 -0700
    New version of runBits based on Python. Runs featureBits to check percent coverage on genome plus percent overlap with gaps. Will also output links to genome-test for first three overlapped gaps. Can also output overlap with unbridged gaps. refs #18828
• src/utils/qa/weeklybld/buildEnv.csh
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    9e8b279a2d38ec77cac7c2a39022614b2e94c830 Mon May 29 09:55:23 2017 -0700
    v350 preview2 refs #19473
• src/utils/tabQuery/makefile
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
• src/utils/tabQuery/tabQuery.c
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    c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
    Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.

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