All File Changes

v350_preview2 to v350_base (2017-05-29 to 2017-06-05) v350

• confs/hgwbeta.hg.conf
  • lines changed 6, context: html, text, full: html, text
    6d0a466542547e8a0e5a237762c5c5ca24462ec3 Sun Jun 4 01:11:49 2017 -0700
    Installing updated hg.conf files from UCSC servers
• python/lib/ucscGb/qa/tables/checkGapOverlap.py
  • lines changed 6, context: html, text, full: html, text
    df4198ad15ecffbf65495d54ac680a8937aaca71 Wed May 31 14:22:13 2017 -0700
    Correcting minor typo in checkSplit function. Adding hideTracks=1 to output URL to hide all tracks but those you're looking at. Adding short comments to the beginning of each function. All part of Code Review, refs #19495
• src/browserbox/root/updateBrowser.sh
  • lines changed 8, context: html, text, full: html, text
    3b2e14c90156120b53c5031856842de0c57ca58c Tue May 30 17:34:02 2017 -0700
    gene interactions track: add to hgGene, patch GBIC/GBIB for it, refs #13634
• src/hca/reformat/geoSoftToRaDir/geoSoftToRaDir.c
  • lines changed 181, context: html, text, full: html, text
    6a91b99fc3df6010238394485667d076310d502e Sat May 27 12:58:01 2017 -0700
    Converter from geo soft files to something easier for us to deal with.
  • lines changed 44, context: html, text, full: html, text
    444eadfd092a6813d4d9fd8991a3d3e1776c2e93 Sat May 27 13:12:48 2017 -0700
    Changing handling of data_processing from array to separate tags with a numerical suffix.
• src/hca/reformat/geoSoftToRaDir/makefile
  • lines changed 3, context: html, text, full: html, text
    6a91b99fc3df6010238394485667d076310d502e Sat May 27 12:58:01 2017 -0700
    Converter from geo soft files to something easier for us to deal with.
• src/hca/reformat/geoToTagStorm/geoToHca.delete
  • lines changed 23, context: html, text, full: html, text
    d2e0a48caf4f5bacc50391fb4beb757b7f9634c7 Tue May 30 18:20:49 2017 -0700
    Adding a few more tags not needed in hca.
• src/hca/reformat/geoToTagStorm/geoToHca.remove
  • lines changed 20, context: html, text, full: html, text
    52e0757df85856092b1311bad3190a7e71e326e2 Tue May 30 13:56:27 2017 -0700
    Adding some geo/hca renames.
  • lines changed 20, context: html, text, full: html, text
    d2e0a48caf4f5bacc50391fb4beb757b7f9634c7 Tue May 30 18:20:49 2017 -0700
    Adding a few more tags not needed in hca.
• src/hca/reformat/geoToTagStorm/geoToHca.rename
  • lines changed 40, context: html, text, full: html, text
    52e0757df85856092b1311bad3190a7e71e326e2 Tue May 30 13:56:27 2017 -0700
    Adding some geo/hca renames.
• src/hca/reformat/geoToTagStorm/geoToTagStorm.c
  • lines changed 196, context: html, text, full: html, text
    3dfc14978b8284e72c0585737bd748941bf260bb Mon May 29 15:55:00 2017 -0700
    Making utility to go from GEO soft file to a three level tag storm
  • lines changed 112, context: html, text, full: html, text
    d97205bb3891dca78de17e0d94e6e614b586c55d Mon May 29 18:59:52 2017 -0700
    Removing some useless tags, and simplifying ones that appear at several levels to a single unprefixed tag.
  • lines changed 82, context: html, text, full: html, text
    093a3424a93c80ebaf1cfd9cb0546828920f67fb Mon May 29 19:05:13 2017 -0700
    Moving some useful stuff to library.
  • lines changed 93, context: html, text, full: html, text
    52b344f174fdc221794197c3117f72c0972ce375 Mon May 29 21:56:02 2017 -0700
    Adding array indexes to multi-tags. Adding to subs list. Removing data_processing special case.
  • lines changed 14, context: html, text, full: html, text
    c2dda7acfe760d9723e350f5a0bb60814fd1b9cf Tue May 30 18:20:02 2017 -0700
    Making series a child of top rather than merging fields.
• src/hca/reformat/geoToTagStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    3dfc14978b8284e72c0585737bd748941bf260bb Mon May 29 15:55:00 2017 -0700
    Making utility to go from GEO soft file to a three level tag storm
• src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
  • lines changed 1, context: html, text, full: html, text
    61c875f5f8c8efad55583dad62553fc331ea3363 Wed May 31 09:44:40 2017 -0700
    Existing bug noticed by Braney. Thanks.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 7, context: html, text, full: html, text
    3b2e14c90156120b53c5031856842de0c57ca58c Tue May 30 17:34:02 2017 -0700
    gene interactions track: add to hgGene, patch GBIC/GBIB for it, refs #13634
  • lines changed 3, context: html, text, full: html, text
    f4290c666c7402ed2ecbbd7f4058ba76e7988bb5 Wed May 31 17:00:43 2017 -0700
    renaming hgGene links to protein interactions, refs #13634
• src/hg/hgGeneGraph/README.txt
  • lines changed 2, context: html, text, full: html, text
    7727c24e06341a267e7561409f7bf7a3293d88ab Fri Jun 2 11:54:51 2017 -0700
    changes after code review, refs #19510
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 7, context: html, text, full: html, text
    6a0e43196a3a99808b3c26252ce6ca30ee2c574f Wed May 31 13:43:38 2017 -0700
    fixing bug when no links are left, refs #13634
  • lines changed 13, context: html, text, full: html, text
    6c3389d97b58ad04533a072efa1858dcadcf00e1 Thu Jun 1 09:22:08 2017 -0700
    allowing default gene and removing assembly if not known, refs #13634
  • lines changed 12, context: html, text, full: html, text
    c3ad8f42fcb9df72943c002404152f77c5802a98 Thu Jun 1 09:57:29 2017 -0700
    fixing incorrect db counts on the low level menu, refs #13634
  • lines changed 2, context: html, text, full: html, text
    ed43585bcfb32162fecd950fe59b99483b59a5bb Thu Jun 1 13:51:06 2017 -0700
    changing it to gene interactions, refs #13634
  • lines changed 2, context: html, text, full: html, text
    5576f303e5975afc8c096289bbe58231bc0afc7d Fri Jun 2 11:25:35 2017 -0700
    fixing biocarta links, refs #13634
  • lines changed 40, context: html, text, full: html, text
    d87311a4a4a25c703fff51e32d5a52574feaceb5 Fri Jun 2 14:44:21 2017 -0700
    adding the evidence field to the ggEventDb, refs #13634
  • lines changed 1, context: html, text, full: html, text
    c9cedab62ccadf62530d2586f9d771c289d3ea86 Fri Jun 2 17:16:50 2017 -0700
    adding openBel as a data source, refs #13634
  • lines changed 11, context: html, text, full: html, text
    71495d97a500eb0b1f176584e677c0d3965bf9ae Fri Jun 2 17:22:25 2017 -0700
    improving layout of evidence a bit, refs #13634
  • lines changed 8, context: html, text, full: html, text
    8f07ea1e9137dc164688def8459f6784879ebbeb Sun Jun 4 08:09:48 2017 -0700
    fixes for openbel dataset in hgGeneGraph, refs #13634
  • lines changed 2, context: html, text, full: html, text
    884a11762453d7f4141aed366f3d1eaa2a428a20 Sun Jun 4 23:59:50 2017 -0700
    a few more fixes for openbel and gpml, refs #13634
• src/hg/hgSession/hgSession.c
  • lines changed 25, context: html, text, full: html, text
    e50eb37345c15103c27e279de68e0837bf96d434 Tue May 30 14:26:23 2017 -0700
    fixing hgSession bug after my last change, refs #19430
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    3ac146126c6b73e2870939c95e62e843dc09f2d3 Tue May 30 22:31:24 2017 -0700
    Fixes problem where http header gets output twice when calling web.c::webAbort() from hgc.c. fixes #19470
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 30, context: html, text, full: html, text
    b5aa368068ad5b8f383c2ab25848ff10771c613b Wed May 31 18:20:49 2017 -0700
    Adding FAQ for UCSC RefSeq vs NCBI RefSeq, refs #19436
  • lines changed 7, context: html, text, full: html, text
    84ddb94a1607049e5d330226faae850531452c07 Fri Jun 2 13:14:25 2017 -0700
    Changing wording slighly based on reviewer input, refs #19436
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 45, context: html, text, full: html, text
    c6b8947de918ffc8106d284117ec07e115e6776c Wed May 31 16:07:57 2017 -0700
    More edits to barChart doc, refs #18736
  • lines changed 75, context: html, text, full: html, text
    6a5902fb12b7ba80c89a3ff4ce0504565b80ebc5 Thu Jun 1 15:11:03 2017 -0700
    Some additional explanation/correction to barChart doc. refs #18736
  • lines changed 8, context: html, text, full: html, text
    c956618114230cacf7f4d980ae709df5a53a1346 Fri Jun 2 09:05:05 2017 -0700
    Minor typo fixes to barChart help page, also committing imagem refs #18736
  • lines changed 30, context: html, text, full: html, text
    76f5efcf3e8e7ecb40c6796aa3d60dd25d055fd9 Fri Jun 2 10:40:31 2017 -0700
    Adding examples to barChart doc, should be ready for review now, refs #18736
  • lines changed 4, context: html, text, full: html, text
    c68ea0e7d12d6a10b930543ec158a703ff553552 Fri Jun 2 10:51:10 2017 -0700
    Fixing link typos in barChart doc, refs #18736
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 1, context: html, text, full: html, text
    7727c24e06341a267e7561409f7bf7a3293d88ab Fri Jun 2 11:54:51 2017 -0700
    changes after code review, refs #19510
  • lines changed 3, context: html, text, full: html, text
    96d63c692fc15357af3800b6a0c363a18d33db89 Sat Jun 3 08:45:23 2017 -0700
    adding support and converter for the openbel dataset, refs #13634
  • lines changed 30, context: html, text, full: html, text
    884a11762453d7f4141aed366f3d1eaa2a428a20 Sun Jun 4 23:59:50 2017 -0700
    a few more fixes for openbel and gpml, refs #13634
  • lines changed 5, context: html, text, full: html, text
    9c45aaa0203cbae28af9a39501d4b00d948be9ed Mon Jun 5 00:04:11 2017 -0700
    renaming protein to gene interaction viewer in the help doc, refs #13634
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 15, context: html, text, full: html, text
    c1cf8a154bce82c9a26f5b41ff64ee30d613eccc Fri Jun 2 14:25:10 2017 -0700
    Adding announcement about changes to default tracks for hg19, hg38, and mm10. refs #19441
  • lines changed 2, context: html, text, full: html, text
    1d0ca075529e51e5ab10dc6eee304a2e24b76175 Fri Jun 2 14:39:48 2017 -0700
    Minor spelling corrections to default track announcement, no redmine
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    723419848aa95ea0f05f1c6af9e5983160a72dd7 Mon Jun 5 09:16:14 2017 -0700
    Updating to permanent url, no refs
• src/hg/htdocs/images/exampleBoxPlot.png
  • lines changed 0, context: html, text, full: html, text
    c956618114230cacf7f4d980ae709df5a53a1346 Fri Jun 2 09:05:05 2017 -0700
    Minor typo fixes to barChart help page, also committing imagem refs #18736
• src/hg/htdocs/images/hbv1.jpg
  • lines changed 0, context: html, text, full: html, text
    21f21b680a87dd29fe29ac63945d256a78102748 Fri Jun 2 10:38:23 2017 -0700
    WikiMedia Commons: Dr. Graham Beards refs #19533
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    651345208376ec49d6ba1a4a037f43cab89ad4ff Thu Jun 1 09:10:07 2017 -0700
    adding gene interactions to tools menu, refs #13634
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    c1cf8a154bce82c9a26f5b41ff64ee30d613eccc Fri Jun 2 14:25:10 2017 -0700
    Adding announcement about changes to default tracks for hg19, hg38, and mm10. refs #19441
• src/hg/htdocs/training/index.html
  • lines changed 23, context: html, text, full: html, text
    646181929c38f35b4c47eea9721fa08b258d0a8b Tue May 30 11:37:27 2017 -0700
    dropped mention of completed ESHG workshop
• src/hg/inc/genePred.h
  • lines changed 16, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b75b79c29bfa4b7ddfd08654d4e26b944de26dc6 Mon Jun 5 10:29:06 2017 -0700
    New version number v350
• src/hg/inc/web.h
  • lines changed 7, context: html, text, full: html, text
    3ac146126c6b73e2870939c95e62e843dc09f2d3 Tue May 30 22:31:24 2017 -0700
    Fixes problem where http header gets output twice when calling web.c::webAbort() from hgc.c. fixes #19470
• src/hg/lib/genePred.c
  • lines changed 155, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/hg/lib/ggEventDb.as
  • lines changed 1, context: html, text, full: html, text
    96d63c692fc15357af3800b6a0c363a18d33db89 Sat Jun 3 08:45:23 2017 -0700
    adding support and converter for the openbel dataset, refs #13634
• src/hg/lib/ggSymbol.as
  • lines changed 5, context: html, text, full: html, text
    3b2e14c90156120b53c5031856842de0c57ca58c Tue May 30 17:34:02 2017 -0700
    gene interactions track: add to hgGene, patch GBIC/GBIB for it, refs #13634
• src/hg/lib/vcfUi.c
  • lines changed 3, context: html, text, full: html, text
    d93220dc80a6f12eb516471427167283b20ccecd Wed May 31 14:40:58 2017 -0700
    Don't name buttons "submit" when we're going to invoke the function document.formName.submit() because document.formName.submit will point to the button instead of the function. refs #18305 note-47
• src/hg/lib/web.c
  • lines changed 38, context: html, text, full: html, text
    3ac146126c6b73e2870939c95e62e843dc09f2d3 Tue May 30 22:31:24 2017 -0700
    Fixes problem where http header gets output twice when calling web.c::webAbort() from hgc.c. fixes #19470
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    7727c24e06341a267e7561409f7bf7a3293d88ab Fri Jun 2 11:54:51 2017 -0700
    changes after code review, refs #19510
• src/hg/makeDb/doc/mm10.txt
  • lines changed 91, context: html, text, full: html, text
    feee9fb437652a80d3439c22c8ce5d6669b95d41 Tue May 30 15:11:20 2017 -0700
    clean up featureBits and pslCheck for ncbiRefSeq track refs #18997
  • lines changed 30, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes18.sh
  • lines changed 38, context: html, text, full: html, text
    b150d0a746a428e9f51c293232c848304c14f02d Thu Jun 1 14:02:20 2017 -0700
    redo protein predictions and downstream tables for UCSC genes based on Gencode V26
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    e213343353ff9a815bb331d87494c5ffb992569d Fri Jun 2 11:27:34 2017 -0700
    adding hbv1 Hepatitis B virus - refs #19533
  • lines changed 5, context: html, text, full: html, text
    4a0f96d37d88cd9d5d041d9af59330f99c16c22f Sat Jun 3 09:53:10 2017 -0700
    trying mrna.xeno on hbv1 to see what loads refs #19533
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    e213343353ff9a815bb331d87494c5ffb992569d Fri Jun 2 11:27:34 2017 -0700
    adding hbv1 Hepatitis B virus - refs #19533
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 6, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    54746c4cc1d3b1e5c0adb66cad9b90db33f7f5a8 Wed May 31 10:32:15 2017 -0700
    fixing up all.joiner, refs #13634
  • lines changed 91, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/HBV/hbv1/description.html
  • lines changed 64, context: html, text, full: html, text
    2795f6243d87343bb5ad075b26e173499332ca1b Fri Jun 2 10:45:12 2017 -0700
    initial files from makeGenomeDb.pl refs #19533
• src/hg/makeDb/trackDb/HBV/hbv1/gap.html
  • lines changed 29, context: html, text, full: html, text
    2795f6243d87343bb5ad075b26e173499332ca1b Fri Jun 2 10:45:12 2017 -0700
    initial files from makeGenomeDb.pl refs #19533
• src/hg/makeDb/trackDb/HBV/hbv1/gold.html
  • lines changed 33, context: html, text, full: html, text
    2795f6243d87343bb5ad075b26e173499332ca1b Fri Jun 2 10:45:12 2017 -0700
    initial files from makeGenomeDb.pl refs #19533
• src/hg/makeDb/trackDb/HBV/hbv1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    2795f6243d87343bb5ad075b26e173499332ca1b Fri Jun 2 10:45:12 2017 -0700
    initial files from makeGenomeDb.pl refs #19533
  • lines changed 5, context: html, text, full: html, text
    0b1372f0d80b7cf84f7fb4ffedf5fd7be50c032c Fri Jun 2 10:55:31 2017 -0700
    adding gold search rule refs #19533
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 1, context: html, text, full: html, text
    5017a9ca5894a90ea4f50f3979c76b3bcf7b6b13 Wed May 31 13:33:48 2017 -0700
    removed status about current release, as UCSC browser might be behind
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
  • lines changed 18, context: html, text, full: html, text
    7161b1a97cfa0619c5e137926b3732a47c1dd708 Wed May 31 11:06:52 2017 -0700
    Fixing some issues spotted in the code review and a supertrack show issue Brian spotted, refs #19350 and #19500
  • lines changed 1, context: html, text, full: html, text
    662ee5ac1a18f5d52625a77dadbd74adb196d78c Fri Jun 2 15:16:36 2017 -0700
    Adding visibility pack to the gene subtrack, making it show on default, refs #19350
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    5790ff91a82d46fd9d1ac4f8fcdc282a5b9379b9 Fri Jun 2 08:15:35 2017 -0700
    Changing OMIM SNPs from pack to dense at Jim's recommendation, no redmine
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 1, context: html, text, full: html, text
    5017a9ca5894a90ea4f50f3979c76b3bcf7b6b13 Wed May 31 13:33:48 2017 -0700
    removed status about current release, as UCSC browser might be behind
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    90701f1d81093d39cae0eb8fdb6a5f3af403e23f Tue May 30 10:39:30 2017 -0700
    Adding beta release tag for Gene Interactions track, refs #13634
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    5345308e020c18d503e5d07ec3784c65e29fe9b0 Thu Jun 1 09:16:17 2017 -0700
    Initial descriptions for danRer11.
  • lines changed 1, context: html, text, full: html, text
    2795f6243d87343bb5ad075b26e173499332ca1b Fri Jun 2 10:45:12 2017 -0700
    initial files from makeGenomeDb.pl refs #19533
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    f720a1886d0e56e134f32d3f2c6b168027c02b4d Tue May 30 14:14:59 2017 -0700
    turn on NCBI RefSeq composite track ready for QA refs #18997
  • lines changed 1, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM13.ra
  • lines changed 1, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.html
  • lines changed 30, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.ra
  • lines changed 266, context: html, text, full: html, text
    34ca9a98d8d7667085278ce2f91e78d5912f66fa Wed May 31 14:17:34 2017 -0700
    load of GENCODE VM14
• src/hg/makeDb/trackDb/trackDb.chainNet.other.ra
  • lines changed 5, context: html, text, full: html, text
    52511b5b43706da590e218d1bad9780cd63ba350 Thu Jun 1 13:24:20 2017 -0700
    change release tag on ci3 chain net per refs #16628
• src/hg/makeDb/trackDb/zebrafish/danRer11/description.html
  • lines changed 64, context: html, text, full: html, text
    5345308e020c18d503e5d07ec3784c65e29fe9b0 Thu Jun 1 09:16:17 2017 -0700
    Initial descriptions for danRer11.
• src/hg/makeDb/trackDb/zebrafish/danRer11/gap.html
  • lines changed 31, context: html, text, full: html, text
    5345308e020c18d503e5d07ec3784c65e29fe9b0 Thu Jun 1 09:16:17 2017 -0700
    Initial descriptions for danRer11.
• src/hg/makeDb/trackDb/zebrafish/danRer11/gold.html
  • lines changed 38, context: html, text, full: html, text
    5345308e020c18d503e5d07ec3784c65e29fe9b0 Thu Jun 1 09:16:17 2017 -0700
    Initial descriptions for danRer11.
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    5345308e020c18d503e5d07ec3784c65e29fe9b0 Thu Jun 1 09:16:17 2017 -0700
    Initial descriptions for danRer11.
• src/hg/pyLib/hgLib.py
  • lines changed 7, context: html, text, full: html, text
    6c3389d97b58ad04533a072efa1858dcadcf00e1 Thu Jun 1 09:22:08 2017 -0700
    allowing default gene and removing assembly if not known, refs #13634
• src/hg/pyLib/makefile
  • lines changed 8, context: html, text, full: html, text
    7727c24e06341a267e7561409f7bf7a3293d88ab Fri Jun 2 11:54:51 2017 -0700
    changes after code review, refs #19510
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 269, context: html, text, full: html, text
    4f2f38aa1f1493c1f374a4408d5f126155448f2b Thu Jun 1 13:59:51 2017 -0700
    adding v89 listings refs #19526
• src/hg/utils/automation/doTandemDup.pl
  • lines changed 2, context: html, text, full: html, text
    eedb43ce075e8caba280bad4507b477d84f434aa Fri May 26 20:01:55 2017 -0700
    fixup usage message for kmerPrint.pl refs #19450
• src/hg/utils/automation/kmerPrint.pl
  • lines changed 1, context: html, text, full: html, text
    eedb43ce075e8caba280bad4507b477d84f434aa Fri May 26 20:01:55 2017 -0700
    fixup usage message for kmerPrint.pl refs #19450
• src/hg/utils/automation/ucscAltAgp
  • lines changed 111, context: html, text, full: html, text
    168884f8b1c050c20a5adbec2442b8d5959f6699 Fri Jun 2 10:52:15 2017 -0700
    Python script to generate agp and fasta files for alternate sequences during the initial build process for new assemblies, refs #19459
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 49, context: html, text, full: html, text
    e2a3d55832ce65193efa1b07d1666565ff5cdbed Wed May 31 12:25:58 2017 -0700
    add the ability to get cds out of a file in genePredToBigGenePred
• src/hg/utils/genePredToBigGenePred/makeBigKnown
  • lines changed 2, context: html, text, full: html, text
    e2a3d55832ce65193efa1b07d1666565ff5cdbed Wed May 31 12:25:58 2017 -0700
    add the ability to get cds out of a file in genePredToBigGenePred
• src/hg/utils/genePredToProt/genePredToProt.c
  • lines changed 226, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl
  • lines changed 25, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl
  • lines changed 25, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/hg/utils/genePredToProt/tests/makefile
  • lines changed 42, context: html, text, full: html, text
    f7792e45d8c710b375ed418f55f759a13c545421 Thu Jun 1 23:11:14 2017 -0700
    Moved guts of genePredToProt to library to allow Brian to use it in CGIs. Removed unnecessary PSL creation from genePredToProt.
• src/inc/csv.h
  • lines changed 17, context: html, text, full: html, text
    a7e4140d8466c8dee5118c7480f4b116072cd7b1 Tue May 30 18:12:50 2017 -0700
    Adding csv module.
• src/inc/hash.h
  • lines changed 6, context: html, text, full: html, text
    5f2a0e390ae8a849b5d987fbcd86d8dda453c14c Tue May 30 18:15:29 2017 -0700
    Adding two functions that build hashes out of arrays of strings.
• src/inc/tagStorm.h
  • lines changed 25, context: html, text, full: html, text
    ea844c8ebc1c3bf693b81e5ba1f6a08c8bd46aa8 Tue May 30 18:17:10 2017 -0700
    Adding some functions for editing tagStorms, either deleting all tags of a given name or renaming them.
• src/lib/csv.c
  • lines changed 62, context: html, text, full: html, text
    a7e4140d8466c8dee5118c7480f4b116072cd7b1 Tue May 30 18:12:50 2017 -0700
    Adding csv module.
• src/lib/hash.c
  • lines changed 21, context: html, text, full: html, text
    5f2a0e390ae8a849b5d987fbcd86d8dda453c14c Tue May 30 18:15:29 2017 -0700
    Adding two functions that build hashes out of arrays of strings.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    a7e4140d8466c8dee5118c7480f4b116072cd7b1 Tue May 30 18:12:50 2017 -0700
    Adding csv module.
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    3503f8667486a2b5ff657fd2a73de829dbae0138 Tue May 30 10:21:08 2017 -0700
    Un-doing change that was not needed. netSkipHttpHeaderLinesHandlingRedirect has already closed the file descriptor itself on failure. No need for us to close it.
• src/lib/tagStorm.c
  • lines changed 96, context: html, text, full: html, text
    ea844c8ebc1c3bf693b81e5ba1f6a08c8bd46aa8 Tue May 30 18:17:10 2017 -0700
    Adding some functions for editing tagStorms, either deleting all tags of a given name or renaming them.
• src/product/installer/browserSetup.sh
  • lines changed 4, context: html, text, full: html, text
    3b2e14c90156120b53c5031856842de0c57ca58c Tue May 30 17:34:02 2017 -0700
    gene interactions track: add to hgGene, patch GBIC/GBIB for it, refs #13634
• src/product/minimal.hg.conf
  • lines changed 3, context: html, text, full: html, text
    66644c5805972d024cb88a08fa3be553975e60fd Wed May 31 14:06:40 2017 -0700
    Documenting udc.cacheDir option in minimal.hg.conf for vai.pl usage, refs #12216
• src/tabFile/makefile
  • lines changed 3, context: html, text, full: html, text
    72d331125b6436857a882ac41a4588810da20651 Fri May 26 14:36:55 2017 -0700
    Adding new utility to collapse fields with same name into a single comma-separated field.
• src/tabFile/tabRepeatedFieldsToArrayField/expected.out
  • lines changed 5, context: html, text, full: html, text
    72d331125b6436857a882ac41a4588810da20651 Fri May 26 14:36:55 2017 -0700
    Adding new utility to collapse fields with same name into a single comma-separated field.
• src/tabFile/tabRepeatedFieldsToArrayField/makefile
  • lines changed 3, context: html, text, full: html, text
    72d331125b6436857a882ac41a4588810da20651 Fri May 26 14:36:55 2017 -0700
    Adding new utility to collapse fields with same name into a single comma-separated field.
• src/tabFile/tabRepeatedFieldsToArrayField/tabRepeatedFieldsToArrayField.c
  • lines changed 139, context: html, text, full: html, text
    72d331125b6436857a882ac41a4588810da20651 Fri May 26 14:36:55 2017 -0700
    Adding new utility to collapse fields with same name into a single comma-separated field.
  • lines changed 4, context: html, text, full: html, text
    5d4616290454b29ef09230e5332b086ba5dea764 Fri May 26 14:38:30 2017 -0700
    Adding a little verbose diagnostic message.
  • lines changed 34, context: html, text, full: html, text
    0c33463d9eea1c6cfa5b641de752b05d517c9b64 Tue May 30 18:18:04 2017 -0700
    Moving useful function to csv module in library.
• src/tabFile/tabRepeatedFieldsToArrayField/test.in
  • lines changed 4, context: html, text, full: html, text
    72d331125b6436857a882ac41a4588810da20651 Fri May 26 14:36:55 2017 -0700
    Adding new utility to collapse fields with same name into a single comma-separated field.
• src/tagStorm/makefile
  • lines changed 4, context: html, text, full: html, text
    2de6d7adfd3e3252d093e162a8e953b4fc36d10a Tue May 30 18:14:21 2017 -0700
    Adding to tagStorm utilities build.
• src/tagStorm/softToTagStorm.py
  • lines changed 137, context: html, text, full: html, text
    20eadd2fdbd9f96d196121a3b6d0937fa544bf43 Wed May 31 09:47:07 2017 -0700
    A python script which converts GEO soft files into a tagStorm format, no redmine and old
• src/tagStorm/tagStormArrayToCsv/makefile
  • lines changed 3, context: html, text, full: html, text
    bce8502f7c0ec3b1ae0e5d336fee5835d49984f6 Tue May 30 18:12:27 2017 -0700
    Adding csv module.
• src/tagStorm/tagStormArrayToCsv/tagStormArrayToCsv.c
  • lines changed 147, context: html, text, full: html, text
    bce8502f7c0ec3b1ae0e5d336fee5835d49984f6 Tue May 30 18:12:27 2017 -0700
    Adding csv module.
• src/userApps/README
  • lines changed 1, context: html, text, full: html, text
    7727c24e06341a267e7561409f7bf7a3293d88ab Fri Jun 2 11:54:51 2017 -0700
    changes after code review, refs #19510
• src/utils/ggBelCsvToTab
  • lines changed 277, context: html, text, full: html, text
    96d63c692fc15357af3800b6a0c363a18d33db89 Sat Jun 3 08:45:23 2017 -0700
    adding support and converter for the openbel dataset, refs #13634
  • lines changed 21, context: html, text, full: html, text
    8f07ea1e9137dc164688def8459f6784879ebbeb Sun Jun 4 08:09:48 2017 -0700
    fixes for openbel dataset in hgGeneGraph, refs #13634
  • lines changed 56, context: html, text, full: html, text
    884a11762453d7f4141aed366f3d1eaa2a428a20 Sun Jun 4 23:59:50 2017 -0700
    a few more fixes for openbel and gpml, refs #13634
• src/utils/ggGpmlToTab
  • lines changed 329, context: html, text, full: html, text
    884a11762453d7f4141aed366f3d1eaa2a428a20 Sun Jun 4 23:59:50 2017 -0700
    a few more fixes for openbel and gpml, refs #13634
• src/utils/ggGpmlToTag
  • lines changed 325, context: html, text, full: html, text
    884a11762453d7f4141aed366f3d1eaa2a428a20 Sun Jun 4 23:59:50 2017 -0700
    a few more fixes for openbel and gpml, refs #13634
• src/utils/ggPidToTab
  • lines changed 10, context: html, text, full: html, text
    96d63c692fc15357af3800b6a0c363a18d33db89 Sat Jun 3 08:45:23 2017 -0700
    adding support and converter for the openbel dataset, refs #13634
• src/utils/ggTables
  • lines changed 14, context: html, text, full: html, text
    3b2e14c90156120b53c5031856842de0c57ca58c Tue May 30 17:34:02 2017 -0700
    gene interactions track: add to hgGene, patch GBIC/GBIB for it, refs #13634
  • lines changed 12, context: html, text, full: html, text
    96d63c692fc15357af3800b6a0c363a18d33db89 Sat Jun 3 08:45:23 2017 -0700
    adding support and converter for the openbel dataset, refs #13634
• src/utils/newPythonProg/newPythonProg.c
  • lines changed 14, context: html, text, full: html, text
    a0db214e86c3f7080b9e2a5f9ac6c76c8610f1af Fri Jun 2 12:42:24 2017 -0700
    Some small updates to the python script skeleton, removing some things that were unnecessary, refs #16156
• src/utils/qa/runBits
  • lines changed 1, context: html, text, full: html, text
    16799e3e99bcb6bea9f904e1c217f5334fb38313 Thu Jun 1 15:09:07 2017 -0700
    Adding missing space in command output, refs #19495
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    13023473a24aa1ba3dacfe08d667502941c838c0 Mon Jun 5 10:28:34 2017 -0700
    v350 final build refs #19473

• lines changed: 4965
• files changed: 138