All File Changes

v349_preview to v349_preview2 (2017-05-01 to 2017-05-08) v349

• confs/hgwdev.hg.conf
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    a7679698d97e5107745daced62cce321bb814c58 Sun May 7 01:11:47 2017 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    a7679698d97e5107745daced62cce321bb814c58 Sun May 7 01:11:47 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 91, context: html, text, full: html, text
    e709a27cb8ef46571408976408ac5985cdd3c554 Fri May 5 10:15:59 2017 -0700
    CIRM: a few changes to cdwSummary for the new Seurat version
• src/hg/cirm/cdw/httpsGatewayConfig/README.txt
  • lines changed 11, context: html, text, full: html, text
    519c6ccc64a40c5c3d154c773a3e0c7047078d90 Thu May 4 12:02:25 2017 -0700
    CIRM: allowing users to login without a VPN. Documenting how this works in a README file and adding the magic Apache config file for it.
• src/hg/cirm/cdw/httpsGatewayConfig/proxy-host.conf
  • lines changed 39, context: html, text, full: html, text
    519c6ccc64a40c5c3d154c773a3e0c7047078d90 Thu May 4 12:02:25 2017 -0700
    CIRM: allowing users to login without a VPN. Documenting how this works in a README file and adding the magic Apache config file for it.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 2, context: html, text, full: html, text
    fa4766bae7b4b6256e2c72d07da8867d7da130f3 Fri May 5 12:49:02 2017 -0700
    CIRM: my last commit had a bug in the case where returnto was set. Fixing this and also fixing the returnto URLs of the CDW. Also documenting the new hg.conf option.
• src/hg/hgComposite/hgComposite.c
  • lines changed 846, context: html, text, full: html, text
    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
  • lines changed 8, context: html, text, full: html, text
    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
  • lines changed 13, context: html, text, full: html, text
    3bd303d90463041294d0879f7a3ef64c6f8dcaf4 Sun May 7 17:44:39 2017 -0700
    ongoing work on custom composites
• src/hg/hgComposite/makefile
  • lines changed 17, context: html, text, full: html, text
    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    1020ed9ae2ad60e3ec36657f14029485bb2ae0f7 Wed May 3 11:13:57 2017 -0700
    Get bigBarChart custom track support mostly working. refs #18736
  • lines changed 1, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/hgLogin/hgLogin.c
  • lines changed 16, context: html, text, full: html, text
    0cbc15777c7929e94bfb8d37526ec7ce8eabe8fe Fri May 5 10:07:10 2017 -0700
    CIRM: fixing a bug in hgLogin that appears only when using it through a reverse-proxy. Adding login.relativeLink to hg.conf for this case.
  • lines changed 5, context: html, text, full: html, text
    fa4766bae7b4b6256e2c72d07da8867d7da130f3 Fri May 5 12:49:02 2017 -0700
    CIRM: my last commit had a bug in the case where returnto was set. Fixing this and also fixing the returnto URLs of the CDW. Also documenting the new hg.conf option.
• src/hg/hgTracks/barChartTrack.c
  • lines changed 5, context: html, text, full: html, text
    c8834b5b67c2b983e3c7736a2ce2342448b536f2 Tue May 2 16:13:27 2017 -0700
    A little more robust to bad trackDb. refs #18736
  • lines changed 5, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/hgTracks/bedTrack.c
  • lines changed 12, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 3, context: html, text, full: html, text
    2679cdd794ef4fbc2ff87ec0f919bc0e93784b0c Wed May 3 15:11:45 2017 -0700
    fix default track colors on bigGenePred type
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    b24581fff3eb64801b297ad8b3ad260d1c2cbd15 Thu May 4 02:23:26 2017 -0700
    Added errCatch around bed validation which can errAbort. Minor tweak to textarea improves whitespace newline handling for BED input.
• src/hg/hgTracks/gtexTracks.c
  • lines changed 3, context: html, text, full: html, text
    ffa6bd5dfd1cc374ce42d970a504f1dc9688935f Mon May 1 13:37:56 2017 -0700
    Allow custom labeling of bar chart values on details page. And update file that should have been in previous commit (viewlimits fix). refs #18736
• src/hg/hgTracks/hgTracks.c
  • lines changed 38, context: html, text, full: html, text
    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
  • lines changed 13, context: html, text, full: html, text
    b24581fff3eb64801b297ad8b3ad260d1c2cbd15 Thu May 4 02:23:26 2017 -0700
    Added errCatch around bed validation which can errAbort. Minor tweak to textarea improves whitespace newline handling for BED input.
  • lines changed 6, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
  • lines changed 4, context: html, text, full: html, text
    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
  • lines changed 64, context: html, text, full: html, text
    3bd303d90463041294d0879f7a3ef64c6f8dcaf4 Sun May 7 17:44:39 2017 -0700
    ongoing work on custom composites
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/hgTracks/multiWig.c
  • lines changed 10, context: html, text, full: html, text
    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
  • lines changed 58, context: html, text, full: html, text
    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
  • lines changed 2, context: html, text, full: html, text
    3bd303d90463041294d0879f7a3ef64c6f8dcaf4 Sun May 7 17:44:39 2017 -0700
    ongoing work on custom composites
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    2679cdd794ef4fbc2ff87ec0f919bc0e93784b0c Wed May 3 15:11:45 2017 -0700
    fix default track colors on bigGenePred type
  • lines changed 24, context: html, text, full: html, text
    f90ad219df60f60f805f555eee38239aa2aa3d1a Sat May 6 06:37:31 2017 -0700
    make density graphs use exons instead of the length of the whole feature #19300
• src/hg/hgc/barChartClick.c
  • lines changed 7, context: html, text, full: html, text
    ffa6bd5dfd1cc374ce42d970a504f1dc9688935f Mon May 1 13:37:56 2017 -0700
    Allow custom labeling of bar chart values on details page. And update file that should have been in previous commit (viewlimits fix). refs #18736
  • lines changed 25, context: html, text, full: html, text
    0490db6e85ca2bdf98e3bf71df2b04d7582a08de Mon May 1 14:21:50 2017 -0700
    Add links to matrix and sample files on details page. refs #18738
  • lines changed 3, context: html, text, full: html, text
    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
  • lines changed 36, context: html, text, full: html, text
    3810604d5c77948f1eb2d1dc7605aa4fdda5f3e2 Mon May 1 16:56:54 2017 -0700
    Use .as comments to label item name and name2. Also add name2 to boxplot. refs #18736
  • lines changed 6, context: html, text, full: html, text
    5593175b35ed5abf3ac564ab716869c64593cb40 Wed May 3 08:44:31 2017 -0700
    Make data download link more useful ? It now retrieves data frame. The full matrix and sample file urls can live in track description. refs #18736
  • lines changed 8, context: html, text, full: html, text
    1020ed9ae2ad60e3ec36657f14029485bb2ae0f7 Wed May 3 11:13:57 2017 -0700
    Get bigBarChart custom track support mostly working. refs #18736
  • lines changed 9, context: html, text, full: html, text
    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    1020ed9ae2ad60e3ec36657f14029485bb2ae0f7 Wed May 3 11:13:57 2017 -0700
    Get bigBarChart custom track support mostly working. refs #18736
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 6, context: html, text, full: html, text
    3810604d5c77948f1eb2d1dc7605aa4fdda5f3e2 Mon May 1 16:56:54 2017 -0700
    Use .as comments to label item name and name2. Also add name2 to boxplot. refs #18736
  • lines changed 14, context: html, text, full: html, text
    9569f017fa4f55a12ecd82aa9270091ccc939883 Tue May 2 16:16:18 2017 -0700
    Fix ordering problem on boxplot (thanks Chris L). refs #18736
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
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    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQcite.html
  • lines changed 4, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 14, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQdisplay.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
  • lines changed 5, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
  • lines changed 36, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 6, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 8, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 7, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 4, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
  • lines changed 15, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQtables.html
  • lines changed 3, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 6, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
  • lines changed 21, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/FAQ/index.html
  • lines changed 14, context: html, text, full: html, text
    707b2a3388e207eb215d665d6d029829470d5e1f Wed May 3 13:00:41 2017 -0700
    Converted the TOCs for FAQ pages into bulleted lists in the absence of better TOC-specific styling.
• src/hg/htdocs/contacts.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/axt.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 6, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/bigWig.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/customColumn.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
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    dc752033797c349eb80897d5042eb48010e2772e Tue May 2 08:00:49 2017 -0700
    Correcting spelling of URL, no redmine
• src/hg/htdocs/goldenPath/help/fileSearch.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 1, context: html, text, full: html, text
    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/haplotypes.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hgCodonColoringMrna.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hgCompositeHelpText.html
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    9c8cfc5f5d90d882743d66d2ebcae92f97ac816f Sun May 7 18:24:35 2017 -0700
    check in hgComposite help file
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    9628c8db891b3ccaf98da25d398f5f082040c4d1 Wed May 3 11:38:02 2017 -0700
    Announcing and documenting enhanced highlighting, refs #19118
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/mirror.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/mysql.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/net.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/phastCons.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/query.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    ca0eced9d495e2bf4850da62f94e64e74ad74b1e Wed May 3 11:27:56 2017 -0700
    Additional setting for bigBarChart. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
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    ca0eced9d495e2bf4850da62f94e64e74ad74b1e Wed May 3 11:27:56 2017 -0700
    Additional setting for bigBarChart. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    ca0eced9d495e2bf4850da62f94e64e74ad74b1e Wed May 3 11:27:56 2017 -0700
    Additional setting for bigBarChart. refs #18736
• src/hg/htdocs/goldenPath/help/trix.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/help/vcf.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/goldenPath/newsarch.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
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    effe09be5a6b95f283664bc823bb524855d29bf2 Tue May 2 18:11:50 2017 -0700
    Staging newsarch annoucement for highlighting, refs #19118
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    9628c8db891b3ccaf98da25d398f5f082040c4d1 Wed May 3 11:38:02 2017 -0700
    Announcing and documenting enhanced highlighting, refs #19118
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    935d721e6e1964b837326dfa1edbf0bf4dc5af68 Wed May 3 16:00:13 2017 -0700
    Staging blat custom tracks announcement, refs #2811
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    63bdf7d96962b3eba4c0aacadc5d30277071c283 Thu May 4 08:45:55 2017 -0700
    More edits to blat ct announcement, refs #2811
• src/hg/htdocs/goldenPath/pubs.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/htdocs/images/highlightScreenshot2017.png
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    59758a2c8034827297bf62b741b36b1ccf9a319b Tue May 2 16:18:12 2017 -0700
    Adding new image file for highlight annoucement, refs #19118
• src/hg/htdocs/indexNews.html
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    9628c8db891b3ccaf98da25d398f5f082040c4d1 Wed May 3 11:38:02 2017 -0700
    Announcing and documenting enhanced highlighting, refs #19118
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    935d721e6e1964b837326dfa1edbf0bf4dc5af68 Wed May 3 16:00:13 2017 -0700
    Staging blat custom tracks announcement, refs #2811
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    63bdf7d96962b3eba4c0aacadc5d30277071c283 Thu May 4 08:45:55 2017 -0700
    More edits to blat ct announcement, refs #2811
• src/hg/htdocs/staticStyle/gbStatic.css
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    0a10375725ed97f08a5f555ba687a7eb8710c1b9 Thu May 4 11:44:08 2017 -0700
    Adding a section to gbStatic.css for all <a links></a> to be font-weight bold to improve visability refs #18502
• src/hg/htdocs/style/gb.css
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    857182c9dd3165d550b0246da56a7b64f9697517 Mon May 1 12:25:35 2017 -0700
    Gray out text in a disabled control (as in HGStyle). Not standard in boostrap/jQuery UI. Affects GTEx UI as well as barchart. Older GTEx UI has this appearance as it uses HGStyle. refs #18736
• src/hg/inc/barChartBed.h
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    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
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    3810604d5c77948f1eb2d1dc7605aa4fdda5f3e2 Mon May 1 16:56:54 2017 -0700
    Use .as comments to label item name and name2. Also add name2 to boxplot. refs #18736
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    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
• src/hg/inc/barChartUi.h
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    ffa6bd5dfd1cc374ce42d970a504f1dc9688935f Mon May 1 13:37:56 2017 -0700
    Allow custom labeling of bar chart values on details page. And update file that should have been in previous commit (viewlimits fix). refs #18736
• src/hg/inc/customComposite.h
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    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/inc/gtexUi.h
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    bf18fbc459d663c8559dcfec513675ec165bcbc3 Mon May 1 12:23:14 2017 -0700
    Fix problem with GTEx viewLimits input box noted by QA during review of this track (similar controls). Id name was changed for barchart in JS -- needed update in GTEx. refs #18736
• src/hg/inc/hui.h
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    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/lib/barChartBed.as
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    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
• src/hg/lib/barChartBed.c
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    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
• src/hg/lib/barChartBed.sql
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    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
• src/hg/lib/barChartUi.c
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    1020ed9ae2ad60e3ec36657f14029485bb2ae0f7 Wed May 3 11:13:57 2017 -0700
    Get bigBarChart custom track support mostly working. refs #18736
• src/hg/lib/customComposite.c
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/lib/customFactory.c
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    70dd30683fe3a9795bb81067da75d34521265577 Thu May 4 16:41:16 2017 -0700
    Add custom track suport for type barChart. refs #18736
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    3bb3a5c8edd08f85940d6358484dbe3343f34338 Fri May 5 10:01:15 2017 -0700
    Left out registration of barChart type in last round of cleanup. refs #18736
• src/hg/lib/gtexUi.c
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    bf18fbc459d663c8559dcfec513675ec165bcbc3 Mon May 1 12:23:14 2017 -0700
    Fix problem with GTEx viewLimits input box noted by QA during review of this track (similar controls). Id name was changed for barchart in JS -- needed update in GTEx. refs #18736
• src/hg/lib/hdb.c
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    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/lib/hui.c
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    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/lib/makefile
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    f8de331fce87ec0df45e71399f7450c0dd69d189 Sat May 6 17:31:44 2017 -0700
    on going work on custom composites
• src/hg/lib/tablesTables.c
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    02d89176305ef7972e33c058db73d82056134a92 Fri May 5 17:07:32 2017 -0700
    CIRM: adding a clear button to the files table.
• src/hg/lib/trackHub.c
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    c46be5cebadbe532ca7f7fc2a5cde930554c7ae7 Tue May 2 11:20:34 2017 -0700
    first check in of hgComposite code.
• src/hg/makeDb/crisprTrack/createBigBed.py
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    9461be66d6eaec3f2fd8da2b0d5470fa8a944e71 Mon May 1 21:57:34 2017 -0700
    fixing a bug in the crispr track pipeline for the regeneron contract things, refs #18968
• src/hg/makeDb/doc/falPer1.txt
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    b895408e8689768bc133e3940cad6e22eb6e55a3 Mon May 1 11:32:33 2017 -0700
    document lastz/chainNet runs between falPer1, geoFor1, galGao5 and melGal5 refs #15096
• src/hg/makeDb/doc/galGal5/lastzRuns.txt
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    b895408e8689768bc133e3940cad6e22eb6e55a3 Mon May 1 11:32:33 2017 -0700
    document lastz/chainNet runs between falPer1, geoFor1, galGao5 and melGal5 refs #15096
• src/hg/makeDb/doc/geoFor1.txt
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    b895408e8689768bc133e3940cad6e22eb6e55a3 Mon May 1 11:32:33 2017 -0700
    document lastz/chainNet runs between falPer1, geoFor1, galGao5 and melGal5 refs #15096
• src/hg/makeDb/doc/melGal5/lastzRuns.txt
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    b895408e8689768bc133e3940cad6e22eb6e55a3 Mon May 1 11:32:33 2017 -0700
    document lastz/chainNet runs between falPer1, geoFor1, galGao5 and melGal5 refs #15096
• src/hg/makeDb/doc/monDom5.txt
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    8878c78f2453d94e3853edf42f03260720cd8304 Mon May 8 09:43:11 2017 -0700
    wrap up lastz/chainNet runs to xentro9 refs #19151
• src/hg/makeDb/doc/mouseStrains/hubIndex.html
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    178ac45080c1c1389ddf7088c7aed96e5f565e98 Wed May 3 10:12:48 2017 -0700
    remove caroli and pahari, incorrect assemblies, refs #13553
• src/hg/makeDb/doc/mouseStrains/makefile
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    178ac45080c1c1389ddf7088c7aed96e5f565e98 Wed May 3 10:12:48 2017 -0700
    remove caroli and pahari, incorrect assemblies, refs #13553
• src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt
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    178ac45080c1c1389ddf7088c7aed96e5f565e98 Wed May 3 10:12:48 2017 -0700
    remove caroli and pahari, incorrect assemblies, refs #13553
• src/hg/makeDb/doc/xenTro9/lastzRuns.txt
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    8878c78f2453d94e3853edf42f03260720cd8304 Mon May 8 09:43:11 2017 -0700
    wrap up lastz/chainNet runs to xentro9 refs #19151
• src/hg/makeDb/doc/xenTro9/multiz11way.txt
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    f4cacabb4a338e580925100cbd8e32951c049d0c Tue May 2 11:21:32 2017 -0700
    starting 11-way conservation track refs #19151
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    13d2c4facad57a5f7a52735c887a193ee728f1ec Tue May 2 16:06:38 2017 -0700
    working on download documents refs #19151
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    7c68ef88e7e6e24487c569ed98548dacd20407ed Tue May 2 17:16:46 2017 -0700
    completed xenTro9 11-way multiz refs #19151
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    18013ec2828115838f4861b578dc1cbaa561f223 Wed May 3 07:38:45 2017 -0700
    alias Notamacropus eugenii
• src/hg/makeDb/hgLoadBed/makefile
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    9e83875382b580eea449c0f9fe83b3686b506409 Thu May 4 14:59:09 2017 -0700
    Add schema for barChart custom track type. refs #18736
• src/hg/makeDb/trackDb/birds/aptMan1/description.html
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    4c92536454705c0357df9276d681889d5f8d912d Tue May 2 00:57:33 2017 -0700
    Fixed typos found via spellchecker.
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.chainNet.ra
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    6ae35c704fb3253f71f58e0a42b138f0ed325a67 Tue May 2 15:02:27 2017 -0700
    Adding chain/net overrides to fix matrix and chain lines for aquChr2, refs #15096
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra
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    6ae35c704fb3253f71f58e0a42b138f0ed325a67 Tue May 2 15:02:27 2017 -0700
    Adding chain/net overrides to fix matrix and chain lines for aquChr2, refs #15096
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.chainNet.ra
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    9c25a4f0bd7f99fa1a63afe34161f133efbb5166 Wed May 3 11:34:24 2017 -0700
    Adding overrides to get the correct matrix lines for aquChr2, refs #15096
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
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    f65374e5887f291e576d7773aaee8938e33b7c17 Thu May 4 15:08:04 2017 -0700
    Fixing the order of the chain/net composite tracks for the Comparative Genomics group for hg19 and hg38, refs #19187
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    f65374e5887f291e576d7773aaee8938e33b7c17 Thu May 4 15:08:04 2017 -0700
    Fixing the order of the chain/net composite tracks for the Comparative Genomics group for hg19 and hg38, refs #19187
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
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    18094e3938581feae122c7624cebd2024083284f Wed May 3 14:28:54 2017 -0700
    Adding the aquChr2 chain/net tracks to the Vertebrate composite track for hg38, refs #15096
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    f65374e5887f291e576d7773aaee8938e33b7c17 Thu May 4 15:08:04 2017 -0700
    Fixing the order of the chain/net composite tracks for the Comparative Genomics group for hg19 and hg38, refs #19187
• src/hg/makeDb/trackDb/human/hg16/trackDb.chainNet.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    6710f8ee1f7a5c393c3f832d33a14d65bbd282de Thu May 4 14:30:48 2017 -0700
    Changing the priority values to resemble the output from the 209wayChainNet.pl script for the chain/net tracks in hg16, hg17, and hg18. refs #19187
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
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    1f1cfcb9463be6caae0d7e1e70db07b05d293da2 Thu May 4 15:09:12 2017 -0700
    Removing the melGal1 override since it will be added to the Vertebrate chain/net composite for hg19, refs #19187
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    ffa6bd5dfd1cc374ce42d970a504f1dc9688935f Mon May 1 13:37:56 2017 -0700
    Allow custom labeling of bar chart values on details page. And update file that should have been in previous commit (viewlimits fix). refs #18736
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    0490db6e85ca2bdf98e3bf71df2b04d7582a08de Mon May 1 14:21:50 2017 -0700
    Add links to matrix and sample files on details page. refs #18738
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    30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 Mon May 1 15:54:05 2017 -0700
    Add name2 to schema, to support alternate names. refs #18736
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    c67885b1bc7b28fd26dfcc1cd622a6e0b5240438 Mon May 1 15:56:32 2017 -0700
    Clean up tests
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    69455e12fc029cc2f68e05dbc91c144eaa801e9c Wed May 3 11:53:47 2017 -0700
    Adding the Golden eagle to the vertebrate chain/net composite on mm10, refs #15096
• src/hg/makeDb/trackDb/refSeqComposite.html
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    b15640218a0268ac831c05d4e98e352df9bcb557 Tue May 2 16:24:37 2017 -0700
    Change awkward wording based on Max's feedback, no redmine
• src/hg/makeDb/trackDb/tagTypes.tab
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    ffa6bd5dfd1cc374ce42d970a504f1dc9688935f Mon May 1 13:37:56 2017 -0700
    Allow custom labeling of bar chart values on details page. And update file that should have been in previous commit (viewlimits fix). refs #18736
• src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra
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    cc3d9c426f37bfea013408fcf3d14f546cce0d71 Wed May 3 09:36:47 2017 -0700
    adding aquChr2 chainNet refs #15096
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    5ac2f527434d4a64f5c1598d34406a6148781098 Mon May 8 09:49:46 2017 -0700
    do not need release alpha on aquChr2 lastz/chainNet refs #15096
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
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    f46daea640675e1f0518f415873091ec47f1e48e Fri May 5 16:59:50 2017 -0700
    Updating wallably scientific name on gateway page, refs #19346
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
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    ba069899569331408e747ac80e04aeb2535e3119 Tue May 2 11:19:18 2017 -0700
    starting 11-way conservation track refs #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.11way.ra
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    ba069899569331408e747ac80e04aeb2535e3119 Tue May 2 11:19:18 2017 -0700
    starting 11-way conservation track refs #19151
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    f539ae993f701e834ae8a57865b60b88785a1a00 Thu May 4 13:52:21 2017 -0700
    setting viewLimits for phyloP refs #19151
• src/hg/makefile
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    360e8cec003eeef6cdd6be49a75c74518bc6492a Sun May 7 18:19:45 2017 -0700
    add hgComposite to hg makefile
• src/hg/utils/otto/omim/doOmimGene2/doOmimGene2.c
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    af94707f3aae87c8d208f6ee290f61e38bbee389 Fri May 5 11:18:09 2017 -0700
    Reorganized MySQL queries in doOmimGene2 so they're less likely to time out
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    6d4369ec871bba9f9889b3a97cb7accac6f4904d Wed May 3 15:42:11 2017 -0700
    need to cgiDecode the dataPt to detect the multi region files refs #17358
• src/inc/rbTree.h
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    d762c6dd610c1983daf0e73f3696960f286cdaf9 Sat May 6 11:30:17 2017 -0700
    make rangeTree functions thread safe.
• src/lib/rangeTree.c
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    d762c6dd610c1983daf0e73f3696960f286cdaf9 Sat May 6 11:30:17 2017 -0700
    make rangeTree functions thread safe.
• src/lib/rbTree.c
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    d762c6dd610c1983daf0e73f3696960f286cdaf9 Sat May 6 11:30:17 2017 -0700
    make rangeTree functions thread safe.
• src/product/ex.hg.conf
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    fa4766bae7b4b6256e2c72d07da8867d7da130f3 Fri May 5 12:49:02 2017 -0700
    CIRM: my last commit had a bug in the case where returnto was set. Fixing this and also fixing the returnto URLs of the CDW. Also documenting the new hg.conf option.
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    bd7b3d34bfc78957316f16a13a2e0033194b3867 Wed May 3 12:32:10 2017 -0700
    Changing the group calculation of tpm from mean to median, refs #19155
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    26e07f7ed288daa8fd41e2ecdffc721d98a11432 Thu May 4 08:43:31 2017 -0700
    Adding a new option, useMean, that lets the user choose mean or median as the middle calculation. refs #19155
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    07f5a53daad64ef67f2ce77de0d5d7076f0548ff Thu May 4 15:34:55 2017 -0700
    Fixing an error in documentation spotted by Chris Lee, refs 18736
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    69e7bc29592bfd70f29d30ef9da060f91d3621be Fri May 5 10:20:14 2017 -0700
    Fixing an output column error spotted by Chris Lee and updating documentation, refs #18736 and #19155
• src/utils/expMatrixToBarchartBed/tests/makefile
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    26e07f7ed288daa8fd41e2ecdffc721d98a11432 Thu May 4 08:43:31 2017 -0700
    Adding a new option, useMean, that lets the user choose mean or median as the middle calculation. refs #19155
• src/utils/expMatrixToBarchartBed/tests/test.output
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    bd7b3d34bfc78957316f16a13a2e0033194b3867 Wed May 3 12:32:10 2017 -0700
    Changing the group calculation of tpm from mean to median, refs #19155
  • lines changed 11, context: html, text, full: html, text
    69e7bc29592bfd70f29d30ef9da060f91d3621be Fri May 5 10:20:14 2017 -0700
    Fixing an output column error spotted by Chris Lee and updating documentation, refs #18736 and #19155
• src/utils/expMatrixToBarchartBed/tests/test.output2
  • lines changed 8, context: html, text, full: html, text
    bd7b3d34bfc78957316f16a13a2e0033194b3867 Wed May 3 12:32:10 2017 -0700
    Changing the group calculation of tpm from mean to median, refs #19155
  • lines changed 8, context: html, text, full: html, text
    26e07f7ed288daa8fd41e2ecdffc721d98a11432 Thu May 4 08:43:31 2017 -0700
    Adding a new option, useMean, that lets the user choose mean or median as the middle calculation. refs #19155
  • lines changed 11, context: html, text, full: html, text
    69e7bc29592bfd70f29d30ef9da060f91d3621be Fri May 5 10:20:14 2017 -0700
    Fixing an output column error spotted by Chris Lee and updating documentation, refs #18736 and #19155
• src/utils/makefile
  • lines changed 39, context: html, text, full: html, text
    4abf44177745692dfda0cc4f93b2b20f2dd39ea2 Thu May 4 10:40:43 2017 -0700
    Add tools for making barChart files (expMatrixToBarchartBed and bedJoinTabOffset) to user apps. Cleanup ws and provide for scripts in subdirs. refs #18736
• src/utils/qa/weeklybld/buildEnv.csh
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    160666320fb932336184de867eff5147b797079e Mon May 8 10:01:34 2017 -0700
    v349 preview2 refs #19342'

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