All File Changes

v358_preview to v358_preview2 (2017-11-06 to 2017-11-13) v358

• src/hg/cirm/cdw/cdwFindSymlinkable/cdwFindSymlinkable.c
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    2956e9fa8365d70401240fb1626b17ea670d7e4a Tue Nov 7 12:38:05 2017 -0800
    Feedback from code review improvements.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 59, context: html, text, full: html, text
    2956e9fa8365d70401240fb1626b17ea670d7e4a Tue Nov 7 12:38:05 2017 -0800
    Feedback from code review improvements.
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/external/CESCG_CRP_Bioinformatics_Tasks_Document_v9.pdf
  • lines changed 0, context: html, text, full: html, text
    6ecf816dcc10bd226c988bf4605a72a36a7433a1 Thu Nov 9 10:21:57 2017 -0800
    Adding in some CIRM docs about sequencing costs and uniform processing pipeline, no redmine
• src/hg/cirm/gateway/htdocs/external/CESCG_SequencingInformaticsCosts-102914.pdf
  • lines changed 0, context: html, text, full: html, text
    6ecf816dcc10bd226c988bf4605a72a36a7433a1 Thu Nov 9 10:21:57 2017 -0800
    Adding in some CIRM docs about sequencing costs and uniform processing pipeline, no redmine
• src/hg/cirm/gateway/htdocs/footer.html
  • lines changed 85, context: html, text, full: html, text
    ac8c373cb5f5c64d0a6c48044f80e632616d4a29 Thu Nov 9 13:39:05 2017 -0800
    Moving included header/footer files into their own directory, no redmine
• src/hg/cirm/gateway/htdocs/header.html
  • lines changed 68, context: html, text, full: html, text
    ac8c373cb5f5c64d0a6c48044f80e632616d4a29 Thu Nov 9 13:39:05 2017 -0800
    Moving included header/footer files into their own directory, no redmine
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 28, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/help/cirmFAQ.html
  • lines changed 1, context: html, text, full: html, text
    95f6b2286f269c24a6bd5bddfa0c6e625be11360 Thu Nov 9 10:24:27 2017 -0800
    Commenting out line in table of contents to a FAQ that doesn't exist yet, no redmine
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 85, context: html, text, full: html, text
    ac8c373cb5f5c64d0a6c48044f80e632616d4a29 Thu Nov 9 13:39:05 2017 -0800
    Moving included header/footer files into their own directory, no redmine
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 68, context: html, text, full: html, text
    ac8c373cb5f5c64d0a6c48044f80e632616d4a29 Thu Nov 9 13:39:05 2017 -0800
    Moving included header/footer files into their own directory, no redmine
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 4, context: html, text, full: html, text
    f9123652b5c1d0bc67456f935147b2801f8ca045 Thu Nov 9 10:23:30 2017 -0800
    Adding announcement about CIRM blog post featuring CESCG stuff, no redmine
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 12, context: html, text, full: html, text
    6d0c8821a88f2edcdb04b1a4d0a6840a25189dba Thu Nov 9 10:29:38 2017 -0800
    Adding short description of Sample Psychic to tools page, no redmine
  • lines changed 2, context: html, text, full: html, text
    3d7184a4ec07bf71502bb9e52e81c7be2ce7cd3e Thu Nov 9 14:05:05 2017 -0800
    Updating docs to reflect that I've moved the header/footer files in a new inc directory, no redmine
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    46abb8c46b39e856ed63b7fb3a2f31d3f22c0b8f Thu Nov 9 10:34:19 2017 -0800
    fix problem in #19427=
• src/hg/hgSession/hgSession.c
  • lines changed 10, context: html, text, full: html, text
    7946c5e263cf909af673ecf7a7daa032d30fa11f Thu Nov 9 12:00:54 2017 -0800
    fix problem in #19914
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgTracks/encode.c
  • lines changed 72, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgTracks/encode.h
  • lines changed 2, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgTracks/simpleTracks.c
  • lines changed 9, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    9b24d5d85fe936a174eb7a6e3d9f83813a1d6a06 Mon Nov 6 16:17:04 2017 -0800
    Oops, check for track hub before trying to get a mysql connection. refs #19136
• src/hg/hgc/encodeClick.c
  • lines changed 105, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    17af3825ff150ad27d687ebc7f1ebfddab473035 Thu Nov 9 15:14:26 2017 -0800
    change error message for missing id in refLink #20505
  • lines changed 6, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    f7296d9b3f1119b3043058d7a0f851b27d47f03d Tue Nov 7 10:37:25 2017 -0800
    Adding newly released criGriChoV1 to static docs, refs #19228
  • lines changed 2, context: html, text, full: html, text
    0e1a50c0146ef62f97f1424a5fd9fb95a42356d2 Fri Nov 10 15:08:43 2017 -0800
    Static doc additions for releasing susScr11, refs #19859
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 4, context: html, text, full: html, text
    0e1a50c0146ef62f97f1424a5fd9fb95a42356d2 Fri Nov 10 15:08:43 2017 -0800
    Static doc additions for releasing susScr11, refs #19859
• src/hg/htdocs/goldenPath/help/bigNarrowPeak.html
  • lines changed 246, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    e096d7dd29f77b53d4bc9055d7ec9a5893ae9565 Tue Nov 7 13:51:40 2017 -0800
    Document new feature of pennantIcon (colored text label). refs #20270
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 1, context: html, text, full: html, text
    e096d7dd29f77b53d4bc9055d7ec9a5893ae9565 Tue Nov 7 13:51:40 2017 -0800
    Document new feature of pennantIcon (colored text label). refs #20270
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    e096d7dd29f77b53d4bc9055d7ec9a5893ae9565 Tue Nov 7 13:51:40 2017 -0800
    Document new feature of pennantIcon (colored text label). refs #20270
  • lines changed 5, context: html, text, full: html, text
    c61cee1901eb133f11b46b62dc9d0758cecdfc67 Wed Nov 8 16:04:41 2017 -0800
    Fixing bizarre typo in subgroups section of trackDbDoc
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 5, context: html, text, full: html, text
    f7296d9b3f1119b3043058d7a0f851b27d47f03d Tue Nov 7 10:37:25 2017 -0800
    Adding newly released criGriChoV1 to static docs, refs #19228
  • lines changed 37, context: html, text, full: html, text
    0e1a50c0146ef62f97f1424a5fd9fb95a42356d2 Fri Nov 10 15:08:43 2017 -0800
    Static doc additions for releasing susScr11, refs #19859
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 20, context: html, text, full: html, text
    2f1f97dd3d8a34a2d684699cc415d3d329bc7565 Tue Nov 7 12:49:30 2017 -0800
    Adding NAR paper and Braney paper to pubs.html page
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    f7296d9b3f1119b3043058d7a0f851b27d47f03d Tue Nov 7 10:37:25 2017 -0800
    Adding newly released criGriChoV1 to static docs, refs #19228
  • lines changed 11, context: html, text, full: html, text
    0e1a50c0146ef62f97f1424a5fd9fb95a42356d2 Fri Nov 10 15:08:43 2017 -0800
    Static doc additions for releasing susScr11, refs #19859
• src/hg/htdocs/style/HGStyle.css
  • lines changed 9, context: html, text, full: html, text
    a3c00a96548b7aa1a4f227008e3362a1674028c2 Tue Nov 7 10:02:00 2017 -0800
    Add styling for text-based pennantIcon. refs #20270
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/lib/customFactory.c
  • lines changed 18, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/lib/hui.c
  • lines changed 125, context: html, text, full: html, text
    0028868b72060a31d1ac6d35407f6d78c7ceb680 Tue Nov 7 10:00:48 2017 -0800
    Implement text pennantIcon (for 'New' tag). Simplify code while hood is up. refs #20270
  • lines changed 4, context: html, text, full: html, text
    55a3840bc0170b1211d8ddd4ca8c11aa2d125fcf Thu Nov 9 09:46:01 2017 -0800
    fix for #20281
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    5e88a1196c6be3d47f925d8d31e401ef0a65c1fc Fri Nov 10 14:40:51 2017 -0800
    add support for bigNarrowPeak in hubs and custom tracks
• src/hg/makeDb/doc/hg38/multiz30way.txt
  • lines changed 719, context: html, text, full: html, text
    0bad03b9bf82a3bdc76ad385fca8cc3944feac7f Mon Nov 6 18:55:19 2017 -0800
    ready for final README business refs #20216
  • lines changed 49, context: html, text, full: html, text
    24db880787d590d5498eaeb0ff8a48b9a0ca26d0 Tue Nov 7 14:31:49 2017 -0800
    marked QA Ready in redmine refs #20216
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    e1bba2795fb5442f6e093550273cf0a5f595c994 Thu Nov 9 12:42:35 2017 -0800
    Adding susScr11 to beta genbank updates, refs #19859
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    e2ede988f9fbcc2657c5e3e6eef627005167f61f Mon Nov 6 16:56:27 2017 -0800
    Adding criGriChoV1, refs #19228
  • lines changed 1, context: html, text, full: html, text
    3328eb258e6c1f95251ab1c1112e0c10b70cadea Fri Nov 10 15:15:44 2017 -0800
    Adding susScr11 to RR genebank updates, refs #19859
• src/hg/makeDb/trackDb/drosophila/dp3/twinscan.html
  • lines changed 1, context: html, text, full: html, text
    134351dc2046f8dd070558700ec41c9bd544c88a Mon Nov 13 09:39:58 2017 -0800
    Fixing broken links for dp3 found by the broken link report, no Remdine
• src/hg/makeDb/trackDb/guineaPig/cavPor3/nscanGene.html
  • lines changed 3, context: html, text, full: html, text
    a7a04e048b9f9ff371808102e4db1ca7872b6cc0 Thu Nov 9 07:43:59 2017 -0800
    Fixing broken links found by the broken link report for cavPor3, no Redmine.
• src/hg/makeDb/trackDb/human/bamSLDenisova.html
  • lines changed 1, context: html, text, full: html, text
    dbd96f7c976b90ac673eb340f2fa6f03c1828f67 Tue Nov 7 09:25:46 2017 -0800
    Fixing broken links for panTro2 found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 1609, context: html, text, full: html, text
    5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 374, context: html, text, full: html, text
    5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
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    483bd226bd99ba10c031dc94bfd7836906214bb6 Wed Nov 8 19:01:57 2017 -0800
    do not need gorGor1 or the older RBest definitions refs #20216
• src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra
  • lines changed 2, context: html, text, full: html, text
    6f2548f27be2cb58f3182f666247187915966fbd Wed Nov 8 11:02:24 2017 -0800
    correct case Primates on short/long labels refs #20216
  • lines changed 450, context: html, text, full: html, text
    5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra
  • lines changed 2, context: html, text, full: html, text
    6f2548f27be2cb58f3182f666247187915966fbd Wed Nov 8 11:02:24 2017 -0800
    correct case Primates on short/long labels refs #20216
  • lines changed 450, context: html, text, full: html, text
    5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 871, context: html, text, full: html, text
    5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 2, context: html, text, full: html, text
    aebb5c716cf6f8e2a5479c9860f84a15525389f2 Mon Nov 6 12:03:07 2017 -0800
    Make eQTL find more specific and catch the non-dbSNP variants. Fixes issue noted by Brian Lee in note #101. refs #15646
  • lines changed 14, context: html, text, full: html, text
    1f1d2e01dcbeff9a9082d7871fa6c6d50e4841fe Tue Nov 7 09:57:18 2017 -0800
    Add 'new' tag to GTEx eQTL track. refs #20270
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    ee48295c6a2004c7565638e79dfca2d7780dadf8 Wed Nov 8 18:46:33 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    ee48295c6a2004c7565638e79dfca2d7780dadf8 Wed Nov 8 18:46:33 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/hg38/bismap.html
  • lines changed 77, context: html, text, full: html, text
    457e2146d5e7b6577656243561a0a765c9280f30 Thu Nov 9 12:50:59 2017 -0800
    Combining the Bismap and Umap HTML pages so it can be shared between all three pages (super track and composites), refs #19154
  • lines changed 62, context: html, text, full: html, text
    fc386f90029de2ecef527724c666f8adc31dc4b8 Thu Nov 9 12:52:13 2017 -0800
    Renaming the shared HTML page from 'bismap.html' to 'mappability.html', refs #19154
• src/hg/makeDb/trackDb/human/hg38/cancerExpr.ra
  • lines changed 2, context: html, text, full: html, text
    793784b72ff28b3ceabdbdd480f1d3d84f2bf5c2 Mon Nov 6 16:52:59 2017 -0800
    Staging the TCGA transcript and gene expression tracks on hgwbeta, refs #19155
  • lines changed 2, context: html, text, full: html, text
    ed39f3444d93ee5ab35c60f69a2d1bee7df19192 Tue Nov 7 10:26:47 2017 -0800
    Removing the release tag, refs #19155
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 67, context: html, text, full: html, text
    f09149e29bf74efbf44a86fcba0fc20c8eede012 Mon Nov 6 16:28:15 2017 -0800
    Updating the track names to match our MySQL table naming scheme. Adding missing release tags in the view stanza. Removing underscores from the shortLable as well. refs #19154
  • lines changed 25, context: html, text, full: html, text
    644ce0151823516d795832c96d581a2775171a25 Mon Nov 6 16:40:59 2017 -0800
    Moving 'release alpha' tag to the include directive to avoid having a release tag on every stanza. refs #19154
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    061ed9d49208a5e2f9870cfb3562ef0e88a1d1e5 Thu Nov 9 12:57:57 2017 -0800
    Making Bismap and Umap composites use the shared HTML page. Removing the 'umap.html' as it is not needed anymore. refs #19154
  • lines changed 0, context: html, text, full: html, text
    6b05c0697e4481ae282625070999aa5a6dba2688 Thu Nov 9 15:32:29 2017 -0800
    Replacing all tabs with spaces as per code review, refs #20494
• src/hg/makeDb/trackDb/human/hg38/mappability.html
  • lines changed 62, context: html, text, full: html, text
    fc386f90029de2ecef527724c666f8adc31dc4b8 Thu Nov 9 12:52:13 2017 -0800
    Renaming the shared HTML page from 'bismap.html' to 'mappability.html', refs #19154
  • lines changed 13, context: html, text, full: html, text
    0a2a534d7677160cddf60fed43add246901de5e4 Thu Nov 9 14:04:32 2017 -0800
    Adding a link to the original Umap repository and adding a References section. refs #19154
  • lines changed 12, context: html, text, full: html, text
    8b08b7d451c2a1901e090d10f5fd697d640f9ea5 Thu Nov 9 14:11:11 2017 -0800
    Making all links open in a new tab by adding the target=_blank attribute, refs #19154
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    644ce0151823516d795832c96d581a2775171a25 Mon Nov 6 16:40:59 2017 -0800
    Moving 'release alpha' tag to the include directive to avoid having a release tag on every stanza. refs #19154
  • lines changed 5, context: html, text, full: html, text
    b028072ddb1514f01b1a344c82f0301ad7f2f863 Wed Nov 8 18:47:13 2017 -0800
    all definitions RR, Dev, old, new in one file refs #20216
• src/hg/makeDb/trackDb/human/hg38/umap.html
  • lines changed 48, context: html, text, full: html, text
    061ed9d49208a5e2f9870cfb3562ef0e88a1d1e5 Thu Nov 9 12:57:57 2017 -0800
    Making Bismap and Umap composites use the shared HTML page. Removing the 'umap.html' as it is not needed anymore. refs #19154
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 118, context: html, text, full: html, text
    483bd226bd99ba10c031dc94bfd7836906214bb6 Wed Nov 8 19:01:57 2017 -0800
    do not need gorGor1 or the older RBest definitions refs #20216
• src/hg/makeDb/trackDb/nscanGene.html
  • lines changed 1, context: html, text, full: html, text
    dbd96f7c976b90ac673eb340f2fa6f03c1828f67 Tue Nov 7 09:25:46 2017 -0800
    Fixing broken links for panTro2 found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/ntSeqContigs.html
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    dbd96f7c976b90ac673eb340f2fa6f03c1828f67 Tue Nov 7 09:25:46 2017 -0800
    Fixing broken links for panTro2 found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/ntSeqReads.html
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    dbd96f7c976b90ac673eb340f2fa6f03c1828f67 Tue Nov 7 09:25:46 2017 -0800
    Fixing broken links for panTro2 found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    7fb26d0f921500423931f0633d54db3c0d872827 Wed Nov 8 19:24:57 2017 -0800
    correct comment label on gorGor4 entry refs #20216
• src/hg/utils/automation/doRecipBest.pl
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    55307ac92fbd30177b01d37d223762b6a23a52d5 Wed Nov 8 14:05:55 2017 -0800
    indicate in the option help message about the load option refs #20216
• src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
    add listings for use with constructing Primates Placentals and Vertebrates chainNet composites refs #20216
• src/hg/utils/phyloTrees/chainNetComposites/afrotheria.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/amphibia.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/carnivora.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/cercopithecinae.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/cetartiodactyla.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/chiroptera.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/coelancanthimorpha.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/cryptodira.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/dinosauria.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/euarchontoglires.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/haplorrhini.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/hominidae.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/hyperoartia.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/laurasiatheria.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/lepidosauria.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/makefile
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/mammalia.list
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• src/hg/utils/phyloTrees/chainNetComposites/neopterygii.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/perissodactyla.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/strepsirrhini.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
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• src/hg/utils/phyloTrees/chainNetComposites/xenarthra.list
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    093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800
    add listings for use with constructing Primates Placentals and Vertebrates chainNet composites refs #20216
• src/hg/utils/phyloTrees/vertebrates.txt
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    d267cc65008bc191852edb2ef1cbd10909c7bf4c Wed Nov 8 16:55:24 2017 -0800
    updating entries for pseHum cheMyd apaSpi pelSin chrPic xipMac lepOcu astMex neoBri hapBur mayZeb punNye oreNil takFla refs #20216
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    903f8a8111fda2a1609710db6e9f96f715496e99 Mon Nov 6 13:43:12 2017 -0800
    fixed typo in help
• src/inc/filePath.h
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    2956e9fa8365d70401240fb1626b17ea670d7e4a Tue Nov 7 12:38:05 2017 -0800
    Feedback from code review improvements.
• src/lib/filePath.c
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    2956e9fa8365d70401240fb1626b17ea670d7e4a Tue Nov 7 12:38:05 2017 -0800
    Feedback from code review improvements.
• src/product/installer/browserSetup.sh
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    a4d87b5fb99e06580013311ae4bf433befded103 Tue Nov 7 12:22:13 2017 -0800
    GBIC rsync from hgdownload-euro if closer, also added an option to download from hgdownload-euro if regular or san diego hgdownload are down, refs #20353
• src/utils/qa/weeklybld/buildEnv.csh
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    15bcb203326a8118ac315da58157c63f6123c978 Mon Nov 13 09:47:46 2017 -0800
    v358 preview2 refs #20479

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