All File Changes

v344_preview to v344_preview2 (2017-01-16 to 2017-01-23) v344

• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    2aafbbca21aee2147bdabe2f3e56a76299d6bc5c Sun Jan 22 01:11:45 2017 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    b57fa67c3b39df42ccbcfe7557256189e394ccc2 Thu Jan 19 15:19:41 2017 -0800
    fixes #18696 crashing trying to revComp missing sequence
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 19, context: html, text, full: html, text
    f04df66eae07dfd571642966b1d787256ffaf825 Wed Jan 18 14:32:49 2017 -0800
    cytoBandIdeogram on assembly hubs
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    023ca09ffc8c0e6a943ff5c33ea60fc4b31ef88a Mon Jan 16 15:06:46 2017 -0800
    changing zoom steps to multiples of 5, refs #18635
  • lines changed 1, context: html, text, full: html, text
    f04df66eae07dfd571642966b1d787256ffaf825 Wed Jan 18 14:32:49 2017 -0800
    cytoBandIdeogram on assembly hubs
  • lines changed 1, context: html, text, full: html, text
    1432d3cfdf4bc0a283005bd95a523a954bce9d94 Thu Jan 19 12:15:05 2017 -0800
    Fixing a stray <br> that appeared in a warning message, refs #18693
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    f04df66eae07dfd571642966b1d787256ffaf825 Wed Jan 18 14:32:49 2017 -0800
    cytoBandIdeogram on assembly hubs
• src/hg/htdocs/admin/mirror.html
  • lines changed 273, context: html, text, full: html, text
    e72388fea323de454d3560ac26f1b5aab39915ee Thu Jan 19 16:09:09 2017 -0800
    Fixing one last typo with markdown to html conversion, as well as typo in mirrorDocs makefile. Adding updated mirror.html page to htdocs as well, refs #16007, #18619
• src/hg/htdocs/admin/mirrorManual.html
  • lines changed 1444, context: html, text, full: html, text
    e72388fea323de454d3560ac26f1b5aab39915ee Thu Jan 19 16:09:09 2017 -0800
    Fixing one last typo with markdown to html conversion, as well as typo in mirrorDocs makefile. Adding updated mirror.html page to htdocs as well, refs #16007, #18619
  • lines changed 0, context: html, text, full: html, text
    400406fb3cb15b6037e79081d3710c1fe4210121 Thu Jan 19 16:19:19 2017 -0800
    making mirrorManual.html executable so it picks up menubar
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 8, context: html, text, full: html, text
    cd7d619b719b47081e1f13943cd1dcd0d655fc6b Fri Jan 20 09:42:23 2017 -0800
    update bigPsl.html to specify that it's 12+13
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 79, context: html, text, full: html, text
    e72388fea323de454d3560ac26f1b5aab39915ee Thu Jan 19 16:09:09 2017 -0800
    Fixing one last typo with markdown to html conversion, as well as typo in mirrorDocs makefile. Adding updated mirror.html page to htdocs as well, refs #16007, #18619
• src/hg/htdocs/goldenPath/help/halSnake.html
  • lines changed 230, context: html, text, full: html, text
    1ca2e540f98dbccb901ef62e817134938490e283 Wed Jan 18 15:31:47 2017 -0800
    add halSnake.html placeholder file
  • lines changed 230, context: html, text, full: html, text
    dda7a3380df40e03883c7f87c550dfb0783a01c0 Wed Jan 18 15:42:42 2017 -0800
    remove halSnake.html for now
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 40, context: html, text, full: html, text
    a35afe62ec4dbfb53db298631a08465a00a6dd7a Mon Jan 23 09:28:22 2017 -0800
    adding story about GBiC to home and newsarch pages
• src/hg/htdocs/images/Aptenodytes_forsteri.jpg
  • lines changed 0, context: html, text, full: html, text
    815cc1bb7c76e07c5c1bd090444e87cc9e8b738b Wed Jan 18 13:53:17 2017 -0800
    Photo courtesy Ian Duffy, flickr/creative commons www.flickr.com/photos/38323841@N00/4322964957/ no redmine
• src/hg/htdocs/images/Camelus_ferus.jpg
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    d51d27e90ec53fb41f227be45c81e6ad283ea563 Wed Jan 18 15:07:24 2017 -0800
    Photo courtesy John Hill, Wikimedia Commons commons.wikimedia.org/wiki/File:Wild_Bactrian_camel_on_road_east_of_Yarkand.jpg
• src/hg/htdocs/images/Equus_przewalskii.jpg
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    68321a736315c8bd0697fe44e00d1992b20f1186 Wed Jan 18 14:01:38 2017 -0800
    Alina Zienowicz, Wikimedia Commons, commons.wikimedia.org/wiki/File:Przewalski_horse_Warsaw_zoo.JPG no redmine
• src/hg/htdocs/images/Panthera_tigris_altaica.jpg
  • lines changed 0, context: html, text, full: html, text
    860c8075d55c79e2ecaf7bbc90c30f9aa4436c6c Wed Jan 18 14:45:13 2017 -0800
    Photo courtesy Appaloosa, Wikimedia Commons commons.wikimedia.org/wiki/File:P.t.altaica_Tomak_Male.jpg no redmine
• src/hg/htdocs/images/phylo/rn6_20way.png
  • lines changed 0, context: html, text, full: html, text
    9e555f7e91265c04840dc591d64278382b3885d2 Sat Jan 21 11:36:40 2017 -0800
    phylo image for rn6 20way refs #18656
• src/hg/htdocs/indexNews.html
  • lines changed 15, context: html, text, full: html, text
    a35afe62ec4dbfb53db298631a08465a00a6dd7a Mon Jan 23 09:28:22 2017 -0800
    adding story about GBiC to home and newsarch pages
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    1ae65c6298ac909c2636306070c2e3d4a89fa971 Fri Jan 20 10:50:10 2017 -0800
    In hGetGenomeOptionsForClade, orderKey was added to the SELECT list in order to support MySQL 5.7. Jim pointed out in code review that adding another column to the output can cause extra rows if there are multiple values per distinct(whatever) -- in this case, multiple values of orderKey per genome. Adding 'group by genome' to the query removes the duplicates. refs #18673
• src/hg/makeDb/doc/galGal5/lastzRuns.txt
  • lines changed 178, context: html, text, full: html, text
    52ac476a2c9590707df3233614146d4b44f898ad Fri Jan 20 14:26:57 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 72, context: html, text, full: html, text
    218835549760828fe06e31e22be1e435e415fb84 Fri Jan 20 14:30:40 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 39, context: html, text, full: html, text
    ca618003f2631e20dc6ed8255fe5d28f5560cca0 Fri Jan 20 13:25:22 2017 -0800
    completed sequence for p8 version refs #13673
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 19, context: html, text, full: html, text
    8e7df7d2b7eeb9b8c97973b8333c3656e2e929b2 Wed Jan 18 08:12:36 2017 -0800
    liftOver to melGal5 refs #18656
• src/hg/makeDb/doc/melGal5/initialBuild.txt
  • lines changed 145, context: html, text, full: html, text
    77f43471b3d7ea5175c67703c6bb66d80c297fde Wed Jan 18 08:13:38 2017 -0800
    running up genbank refs #18656
  • lines changed 104, context: html, text, full: html, text
    70c4f652dfcc3850671155ffbd0f4c25e3bf65d9 Fri Jan 20 14:33:03 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/melGal5/lastzRuns.txt
  • lines changed 117, context: html, text, full: html, text
    70c4f652dfcc3850671155ffbd0f4c25e3bf65d9 Fri Jan 20 14:33:03 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/mm10.txt
  • lines changed 63, context: html, text, full: html, text
    218835549760828fe06e31e22be1e435e415fb84 Fri Jan 20 14:30:40 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 65, context: html, text, full: html, text
    218835549760828fe06e31e22be1e435e415fb84 Fri Jan 20 14:30:40 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/doc/rn6.txt
  • lines changed 625, context: html, text, full: html, text
    596bbd93460cad45a66a0394a7dcca29f21216f3 Wed Jan 18 08:13:11 2017 -0800
    continuing alignments for 20-way multiz refs #18656
  • lines changed 419, context: html, text, full: html, text
    1985315adcd0c698dfc42f66084085e5bbd1983f Thu Jan 19 11:34:10 2017 -0800
    running up syntenicNet refs #18656
  • lines changed 19, context: html, text, full: html, text
    a3fc9be264996bb181e9b0fc5d50043065716dbf Fri Jan 20 14:34:09 2017 -0800
    completed lastz alignments ready for 20-way refs #17168
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 60, context: html, text, full: html, text
    218835549760828fe06e31e22be1e435e415fb84 Fri Jan 20 14:30:40 2017 -0800
    wrapping up same set of alignments as melGal1 refs #17168
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    b1d1fc34969d1c7b1cb7ace2b5afe9751fec6b4a Wed Jan 18 19:56:32 2017 -0800
    adding melGal5 to the update alignments refs #18656
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    07b468142183b0aa5218384c64ef003f330e82d7 Tue Jan 17 10:38:59 2017 -0800
    Added melGal5; refs #18656
  • lines changed 1, context: html, text, full: html, text
    2ba4e9dee785ef979c410dbb5301f98be7483545 Tue Jan 17 20:32:11 2017 -0800
    was missing melGal5.refseq.mrna.native.pslCDnaFilter refs #18656
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    b1d1fc34969d1c7b1cb7ace2b5afe9751fec6b4a Wed Jan 18 19:56:32 2017 -0800
    adding melGal5 to the update alignments refs #18656
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    88dfe612b2d279ec6a964b4399215ef319f80b1c Wed Jan 18 20:04:56 2017 -0800
    adding melGal5 rules refs #18656
  • lines changed 6, context: html, text, full: html, text
    176f6c6de5aac4f766922556348e9a96e848cc41 Wed Jan 18 20:15:04 2017 -0800
    cleaner melGal5 keys check refs #18656
  • lines changed 25, context: html, text, full: html, text
    dddf90a21a081997714d5c21377a7d0c4aaa60ee Thu Jan 19 10:40:22 2017 -0800
    ignore Genbank tables in assembly databases
  • lines changed 1, context: html, text, full: html, text
    3bebf4ab36e95c7e6219b310a5b59d8335a7a35c Fri Jan 20 11:10:44 2017 -0800
    catching up chain net definitions for melGal5 and rn6 alignments refs #18656
  • lines changed 3, context: html, text, full: html, text
    ba33239d4e94b7da618beca11f61f7ac0559cd2f Fri Jan 20 13:23:18 2017 -0800
    fixup ncbiRefSeq rules refs #13673
• src/hg/makeDb/trackDb/cow/snp148.shared.html
  • lines changed 1, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 2, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
• src/hg/makeDb/trackDb/human/hg38/hg38Patch9.html
  • lines changed 1, context: html, text, full: html, text
    611eb695a7590e084148fd03ea510df1ba7429e0 Tue Jan 17 07:30:12 2017 -0800
    edited hg38Patch9 desc page per refs #18630
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 10, context: html, text, full: html, text
    7f3545e00af6cd43789922d10942b2987b7dd37c Fri Jan 20 10:38:24 2017 -0800
    fixup hgFindSpec for ncbiRefSeqProtein searches refs #13673
• src/hg/makeDb/trackDb/human/snp141.shared.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/human/snp144.shared.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/human/snp146.shared.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/human/snp147.shared.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/mouse/snp142.shared.html
  • lines changed 1, context: html, text, full: html, text
    78403992a2ac68acacd7178829664bbcf159f85b Wed Jan 18 10:17:44 2017 -0800
    edited mouse snp142.shared.html per refs #17960
• src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra
  • lines changed 97, context: html, text, full: html, text
    bfb1f3f57192f1cc6c6e34ab38911d4e02afea36 Fri Jan 20 11:00:27 2017 -0800
    adding chain net overrides to rn6 refs #18656
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    bfb1f3f57192f1cc6c6e34ab38911d4e02afea36 Fri Jan 20 11:00:27 2017 -0800
    adding chain net overrides to rn6 refs #18656
• src/hg/makeDb/trackDb/snp128.html
  • lines changed 3, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
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    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/makeDb/trackDb/snp137.shared.html
  • lines changed 1, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
• src/hg/makeDb/trackDb/snp138.shared.html
  • lines changed 7, context: html, text, full: html, text
    2081a51bd355eb7e90dac0279fc72bb3a431db23 Wed Jan 18 09:27:13 2017 -0800
    edited snp shared.html to include data access section per refs #17960
  • lines changed 2, context: html, text, full: html, text
    2a6dd47b1bee04b5247610b404a905ad3cb7ec84 Thu Jan 19 12:47:49 2017 -0800
    edited snp html files per refs #18675
• src/hg/utils/automation/prepConfig.pl
  • lines changed 26, context: html, text, full: html, text
    9964cf5f43a2052378e200e37e81968cef66e3a2 Fri Jan 20 11:20:19 2017 -0800
    indicate requirement of photoReference.txt refs #18706
• src/hg/utils/phyloTrees/191way.nh
  • lines changed 5, context: html, text, full: html, text
    1454e6da154a2d5f516ae7f18c6e8e2b5572c338 Fri Jan 20 14:49:54 2017 -0800
    updated versions to latest for rn6 20-way refs #18656
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
  • lines changed 1, context: html, text, full: html, text
    8c68e89af6e4c31c81b2a1ab5fe4c9b1f990525e Fri Jan 20 09:31:45 2017 -0800
    change usage message to point out that bigPsl is now bigBed 12+13
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    5eee234b477ed74599b35af7cbad1de195fae16b Sat Jan 21 14:18:32 2017 -0800
    Adding cmpStringOrder routine to force order to conform to a predefined explicit nonalphabetical order.
• src/inc/fieldedTable.h
  • lines changed 1, context: html, text, full: html, text
    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
• src/inc/tagStorm.h
  • lines changed 4, context: html, text, full: html, text
    cdfb695ee8fc4dcb613e443f602cd526b4d250aa Thu Jan 19 23:47:48 2017 -0800
    Adding tagStormHoist to tagSTorm.h, also making it so that the function will put in a single root node for forests, so can have a place to hoist tags shared by all in that case.
  • lines changed 6, context: html, text, full: html, text
    387fdf87c4514e568a9c4c4685fba8d0b0f3c7cd Sat Jan 21 14:19:54 2017 -0800
    Adding sort routines for fields in stanzas.
• src/inc/tagToSql.h
  • lines changed 9, context: html, text, full: html, text
    6762c9714af0d2d3fd83a9a10597d92ab6e170d6 Sat Jan 21 08:00:29 2017 -0800
    Exposing tagType functions tagTypeInfoNew and tagTypeInfoAdd to other modules and writing tagTypeInfoFree for benefit of tagStormFromTab.
• src/inc/twoBit.h
  • lines changed 3, context: html, text, full: html, text
    c84cfb3709fec4c63ae72505aba7cc32dd359039 Mon Jan 16 11:41:46 2017 -0800
    add maskBed option to twoBitInfo to get a bed file of masked regions
• src/lib/common.c
  • lines changed 19, context: html, text, full: html, text
    5eee234b477ed74599b35af7cbad1de195fae16b Sat Jan 21 14:18:32 2017 -0800
    Adding cmpStringOrder routine to force order to conform to a predefined explicit nonalphabetical order.
• src/lib/fieldedTable.c
  • lines changed 1, context: html, text, full: html, text
    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
• src/lib/tagStorm.c
  • lines changed 109, context: html, text, full: html, text
    cec3ab53880681ae1792a643f9c9e81fb9325571 Thu Jan 19 19:19:38 2017 -0800
    Moving tagStormHoist code to library.
  • lines changed 13, context: html, text, full: html, text
    cdfb695ee8fc4dcb613e443f602cd526b4d250aa Thu Jan 19 23:47:48 2017 -0800
    Adding tagStormHoist to tagSTorm.h, also making it so that the function will put in a single root node for forests, so can have a place to hoist tags shared by all in that case.
  • lines changed 1, context: html, text, full: html, text
    813873c75553cc797a25514a86e3d4f7d9511122 Sat Jan 21 09:32:39 2017 -0800
    Adjusting verbosity levels.
  • lines changed 49, context: html, text, full: html, text
    387fdf87c4514e568a9c4c4685fba8d0b0f3c7cd Sat Jan 21 14:19:54 2017 -0800
    Adding sort routines for fields in stanzas.
• src/lib/tagToSql.c
  • lines changed 13, context: html, text, full: html, text
    6762c9714af0d2d3fd83a9a10597d92ab6e170d6 Sat Jan 21 08:00:29 2017 -0800
    Exposing tagType functions tagTypeInfoNew and tagTypeInfoAdd to other modules and writing tagTypeInfoFree for benefit of tagStormFromTab.
• src/lib/twoBit.c
  • lines changed 14, context: html, text, full: html, text
    c84cfb3709fec4c63ae72505aba7cc32dd359039 Mon Jan 16 11:41:46 2017 -0800
    add maskBed option to twoBitInfo to get a bed file of masked regions
• src/product/README.txt
  • lines changed 181, context: html, text, full: html, text
    1be5f0b9a69d27a1dcdf7c59a3477dff6be473ef Wed Jan 18 09:29:06 2017 -0800
    adding new mirror instructions aka README.txt, ref #16007
  • lines changed 36, context: html, text, full: html, text
    056c6e989eb7453c77ade14806fab49e72f6419a Wed Jan 18 13:28:05 2017 -0800
    Initial edits to Max's new mirror page, plus incorporating feedback from Cath on gbic user guide. refs #18619 #16007
  • lines changed 4, context: html, text, full: html, text
    7b0482a5ae608c73e7d478f5dcef4f4c25363f0e Wed Jan 18 14:16:26 2017 -0800
    Making links to help pages absolute so they will work in ASCII mode and from other mirrors, refs #16007
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    1bc2ed316bd7698c150decc5405879eaaa4d3193 Thu Jan 19 08:43:37 2017 -0800
    Small changes to new mirror page based on feedback from Cath, refs #16007
• src/product/installer/README.md
  • lines changed 30, context: html, text, full: html, text
    056c6e989eb7453c77ade14806fab49e72f6419a Wed Jan 18 13:28:05 2017 -0800
    Initial edits to Max's new mirror page, plus incorporating feedback from Cath on gbic user guide. refs #18619 #16007
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    d2a4d9f32fadd62a03e3cc916c124c05f590119e Wed Jan 18 16:15:19 2017 -0800
    Fixing minor bug in script and typo in doc, refs #18619
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    f2ee875c3f9fc9fd071db392f70694946fc8828c Thu Jan 19 14:04:02 2017 -0800
    Incorporating feedback from Ann into gbic user guide, no refs
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    ca182e4619a5507f6e326f07dabe184e0d609ac5 Thu Jan 19 15:30:16 2017 -0800
    Fixing typo in gbic user guide, no refs
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    fb2dda4371176eb6960b7c8f39cea6c89363cb6f Thu Jan 19 15:57:00 2017 -0800
    Fixing typo in link that didn't quite convert well from markdown to html, no refs
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    e72388fea323de454d3560ac26f1b5aab39915ee Thu Jan 19 16:09:09 2017 -0800
    Fixing one last typo with markdown to html conversion, as well as typo in mirrorDocs makefile. Adding updated mirror.html page to htdocs as well, refs #16007, #18619
• src/product/installer/browserSetup.sh
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    44f8846ae142ec963859d5fa6ccba10f229a9ec9 Tue Jan 17 16:54:24 2017 -0800
    Make script only download external db's for model orgs, fixes bugs Cath found. These changes have been approved by Max, refs #18619
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    d2a4d9f32fadd62a03e3cc916c124c05f590119e Wed Jan 18 16:15:19 2017 -0800
    Fixing minor bug in script and typo in doc, refs #18619
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    4651082ce9ac7f1d5eac25e7aeb9c8837f0ef01d Thu Jan 19 12:01:52 2017 -0800
    Uncommenting line that creates empty hg18 db based on feedback from Cath, refs #18619
• src/product/mirrorDocs/makefile
  • lines changed 13, context: html, text, full: html, text
    056c6e989eb7453c77ade14806fab49e72f6419a Wed Jan 18 13:28:05 2017 -0800
    Initial edits to Max's new mirror page, plus incorporating feedback from Cath on gbic user guide. refs #18619 #16007
  • lines changed 2, context: html, text, full: html, text
    e72388fea323de454d3560ac26f1b5aab39915ee Thu Jan 19 16:09:09 2017 -0800
    Fixing one last typo with markdown to html conversion, as well as typo in mirrorDocs makefile. Adding updated mirror.html page to htdocs as well, refs #16007, #18619
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 112, context: html, text, full: html, text
    f410105db0b3a911e646540347a9f77eacd62923 Wed Jan 18 12:20:23 2017 -0800
    Improving according to Max's feedback. In particular this avoids outputting blank fields, and also weights fields in deciding which one to partition on first in a way that works better for the big data set Max found.
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    49d86cd9b0e9281c9f55cf2fe44291cdfe3cea2f Thu Jan 19 11:20:01 2017 -0800
    Cleaning up more memory. Better inclusion of fields.
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    1c59685f3b4193f062ea8c52c884593ee5dd5e8d Thu Jan 19 14:34:01 2017 -0800
    Put in a new method for calculating the divs, which is now default. Use the 'local' flag to get the old way. I'm likely to simplify the old way soon.
  • lines changed 99, context: html, text, full: html, text
    cd6894da275f1408964f9e42ba7490c0a4c2b622 Thu Jan 19 15:24:03 2017 -0800
    Cleaning up some memory.
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    4f252b105cea62a65ef611f1c122a53ea1b98e9f Thu Jan 19 23:49:18 2017 -0800
    Making it hoist by default at end (but adding a noHoist option). Also makinga debugging dump function go to stderr rather than stdout.
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    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
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    63969df56a4c7d3728052a8a8a1577ab0cef0c2d Fri Jan 20 11:13:57 2017 -0800
    Making local partitioning use same scoring scheme as global partitioning.
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    1a84329d8f1d64d817bb479e6475e64bb7b06eab Fri Jan 20 17:43:37 2017 -0800
    Calculating size of predictor chain to aid partitioning. Adding more info to dumps for debugging.
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    9f47439d246bdf7624581fb48e75edcceae8a3e0 Sat Jan 21 08:01:21 2017 -0800
    Discouraging partitioning on numerical fields, especially non-integer ones.
  • lines changed 117, context: html, text, full: html, text
    e9277b1493ec38adef034a36778b3353430e8f16 Sat Jan 21 08:07:56 2017 -0800
    Removing unused routines and making all routines except main static.
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    813873c75553cc797a25514a86e3d4f7d9511122 Sat Jan 21 09:32:39 2017 -0800
    Adjusting verbosity levels.
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    e3c2c344823583895d01c4ac539d18d96c2558fe Sat Jan 21 09:59:45 2017 -0800
    Fixing memory leaks
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    653d5099ccc1a73d3663e6b0b8ad8fcadb8e1c2f Sat Jan 21 14:22:06 2017 -0800
    Making it sort tags in stanzas alphabetically by default, and have an option that explicitly keeps same order as input tab-separated-file. It used to end up with order that largely followed input order, but had some random elements. Had to define a new sorting routine to get back old order in this case.
• src/tagStorm/tagStormHoist/expected.out
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    77325cc1b1dc7cde1a835f6163d5a17624d0c958 Thu Jan 19 19:16:02 2017 -0800
    updating test set
• src/tagStorm/tagStormHoist/tagStormHoist.c
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    d1ea4d0bc9a04dd97b213728eb9e6682b5826ad2 Thu Jan 19 19:17:19 2017 -0800
    Refactoring a bit in anticipation of moving code to library.
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    cec3ab53880681ae1792a643f9c9e81fb9325571 Thu Jan 19 19:19:38 2017 -0800
    Moving tagStormHoist code to library.
• src/tagStorm/tagStormHoist/test.in
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    77325cc1b1dc7cde1a835f6163d5a17624d0c958 Thu Jan 19 19:16:02 2017 -0800
    updating test set
• src/utils/qa/weeklybld/buildEnv.csh
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    fefe58073df93f30d4f6e1bf5bf04af38d9538f1 Mon Jan 23 10:06:35 2017 -0800
    v344 preview2 refs #18555
• src/utils/twoBitInfo/twoBitInfo.c
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    c84cfb3709fec4c63ae72505aba7cc32dd359039 Mon Jan 16 11:41:46 2017 -0800
    add maskBed option to twoBitInfo to get a bed file of masked regions

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