All File Changes
v350_preview to v350_preview2 (2017-05-22 to 2017-05-29) v350
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- confs/hgwdev.hg.conf
- lines changed 1, context: html, text, full: html, text
c7e5b57ca1142f8bd0c97cd62229cf07f9388df2 Sun May 28 01:12:02 2017 -0700
Installing updated hg.conf files from UCSC servers
- confs/rr.hg.conf
- lines changed 1, context: html, text, full: html, text
c7e5b57ca1142f8bd0c97cd62229cf07f9388df2 Sun May 28 01:12:02 2017 -0700
Installing updated hg.conf files from UCSC servers
- python/lib/ucscGb/qa/tables/checkGapOverlap.py
- lines changed 129, context: html, text, full: html, text
d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
- python/lib/ucscGb/qa/tables/factory.py
- lines changed 32, context: html, text, full: html, text
d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
- python/lib/ucscGb/qa/tables/positionalQa.py
- lines changed 41, context: html, text, full: html, text
d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
- python/lib/ucscGb/qa/tables/tableTypeUtils.py
- lines changed 89, context: html, text, full: html, text
d540dfe0694290a9b534284091d7a8d4af96f467 Wed May 24 09:31:52 2017 -0700
Adding two new library files: checkGapOverlap and tableTypeUtils. checkGapOverlap contains functions needed to create a bed3 file out of a given table, check overlap of items in this bed3 with gaps both bridged and not, and output urls to the first three of these overlaps. tableTypeUtils contains functions and sets moved from factory.py and positionalQa.py as well as access functions for these sets. refs #18828
- src/hca/LICENSE
- lines changed 18, context: html, text, full: html, text
3160a4f9e2924dbc4c828706a30c6a8112b587f1 Thu May 18 23:19:16 2017 -0700
Making directory for Human Cell Atlas work.
- src/hca/README
- lines changed 1, context: html, text, full: html, text
3160a4f9e2924dbc4c828706a30c6a8112b587f1 Thu May 18 23:19:16 2017 -0700
Making directory for Human Cell Atlas work.
- src/hca/oneShot/hcaTsvToJson1/hcaTsvToJson1.c
- lines changed 181, context: html, text, full: html, text
f26f0a56e8e42e7a5861dab0922af4455ceb5d56 Fri May 19 07:02:46 2017 -0700
First cut of utility to convert tab-separated-file to json files for HCA.
- lines changed 4, context: html, text, full: html, text
95778c97815df7fa4d8d05d41df9dc579fffebbd Fri May 19 07:05:22 2017 -0700
Improving usage message.
- src/hca/oneShot/hcaTsvToJson2/hcaTsvToJson2.c
- lines changed 212, context: html, text, full: html, text
0a0567053d3755a321545b62a5475ab3a52d9711 Wed May 24 00:05:02 2017 -0700
Adding some uuids in.
- src/hca/oneShot/hcaTsvToJson2/makefile
- lines changed 4, context: html, text, full: html, text
0a0567053d3755a321545b62a5475ab3a52d9711 Wed May 24 00:05:02 2017 -0700
Adding some uuids in.
- lines changed 2, context: html, text, full: html, text
2b7dcf8cbbabd34aee0ff9a8e064b662fbc51213 Wed May 24 09:02:08 2017 -0700
Moving -luuid line in makefile as per Hiram's advice and now it actually links!
- src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
- lines changed 18, context: html, text, full: html, text
7be45023c3d59745679040ef16b91842ce338d41 Thu May 25 10:00:43 2017 -0700
Adding support for csv, fixing format string compare for tsv and text. Addresses link issues on cdwWebBrowse Data Sets page where it has html, text, tsv, and csv links.
- src/hg/hgGene/hgGene.c
- lines changed 11, context: html, text, full: html, text
1d851880b8a9d745cfed02d9e7893c210fd7bc70 Wed May 24 13:56:28 2017 -0700
print out Gencode Gene Id if Gencode version of knownGene
- src/hg/hgGeneGraph/hgGeneGraph
- lines changed 73, context: html, text, full: html, text
33d37d6a60180fdc11fbdd59641c822579f85995 Wed May 24 15:04:20 2017 -0700
adding help page for mirrors where graphviz may not work, refs #13634
- lines changed 1, context: html, text, full: html, text
97d07cc944f4b5032f41134c52d7cf3d20a541de Thu May 25 13:56:17 2017 -0700
changing the hash bang line of hgGeneGraph inspired by hgwbeta, refs #13634
- lines changed 1, context: html, text, full: html, text
b88380414ddecaab81f5c19b9f0cf06dbbedc787 Fri May 26 06:36:28 2017 -0700
changing python hash bang again for hgGeneGraph, tiny wrangling fix, refs #13634
- lines changed 5, context: html, text, full: html, text
f788f52a37e301179d324c0d73d24570588e950c Fri May 26 16:57:00 2017 -0700
outputting a better error message when tables are missing, after a hgwbeta experience, refs #13634
- lines changed 3, context: html, text, full: html, text
9ca067c40fe32a9d42db9c3f1451907062950149 Fri May 26 17:06:39 2017 -0700
adding pointer to help page, refs #13634
- src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
- lines changed 1, context: html, text, full: html, text
a93b8c3821b6c637246f68c1fdfeceed8a49b4d3 Wed May 24 09:06:12 2017 -0700
Remove apparently unnecessary CSS. refs #19462
- src/hg/hgTables/bigWig.c
- lines changed 30, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTables/hgTables.h
- lines changed 5, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTables/wiggle.c
- lines changed 2, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTracks/barChartTrack.c
- lines changed 2, context: html, text, full: html, text
c8665892cbf049e6e8ff5596464440556bed55a2 Mon May 22 10:46:06 2017 -0700
Set useScore so dense mode displays well. No longer need the setting in trackDb). refs #18736
- lines changed 4, context: html, text, full: html, text
7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
- src/hg/hgTracks/bigWigTrack.c
- lines changed 115, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTracks/gencodeTracks.c
- lines changed 284, context: html, text, full: html, text
ab0308eb01ad28724dc672e898ec16dcb68ec248 Wed May 24 20:05:39 2017 -0700
Fixed bug where enabmling highlighting could cause duplication of some items.
This was caused by an attemt to optimized number of SQL queries constructing
queries that joined with tables that have a many to one relationship to the
gene annotations.
RM 17215
RM 19166
- lines changed 19, context: html, text, full: html, text
d611f39a00ac8d8a6385834aa1b2ea8dbe65d574 Thu May 25 15:26:39 2017 -0700
fixed bug in gencode highlight code where no highlights specified results in all being highlights
- src/hg/hgTracks/gtexTracks.c
- lines changed 2, context: html, text, full: html, text
7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTracks/hgTracks.h
- lines changed 4, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTracks/simpleTracks.c
- lines changed 7, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/hgTracks/wigCommon.h
- lines changed 4, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/htdocs/goldenPath/credits.html
- lines changed 7525, context: html, text, full: html, text
97f6bf1fdebee5f72438176ed67f5c58524030a0 Wed May 24 14:22:24 2017 -0700
Applied new style, reworked some sections. Refs #18504
- lines changed 51, context: html, text, full: html, text
9765eb186a69578209358244b112453dc901184b Wed May 24 15:03:08 2017 -0700
Converted the TOC to collapsible lists.
- lines changed 5, context: html, text, full: html, text
cc19ca1e4026cfcc952c55b010e29c461689a519 Wed May 24 19:07:56 2017 -0700
Pulled out Human as its own standalone link in TOC, per suggestion from Kate.
- src/hg/htdocs/goldenPath/help/barChart.html
- lines changed 33, context: html, text, full: html, text
89ee08eb69a19f1f8ea8abc4269dbd27699ee184 Tue May 23 15:46:37 2017 -0700
Edits to barChart track description, refs #18736
- lines changed 17, context: html, text, full: html, text
01fce10e07b2ed9dfdf14601061cac80e3bba77e Wed May 24 16:58:53 2017 -0700
Mostly minor changes to barChart description, refs #18736
- lines changed 43, context: html, text, full: html, text
5e4747757fc39669af3a6e9576fc44e7ffdd3d6b Thu May 25 15:41:56 2017 -0700
Some edits suggested by BrianL, refs #18736
- src/hg/htdocs/goldenPath/help/hgCompositeHelp.html
- lines changed 24, context: html, text, full: html, text
1a3556f2017f62ae3f5da613f2b9bf1a6f57ec28 Tue May 23 10:27:17 2017 -0700
Minor edits to hgComposite help, refs #11630
- src/hg/htdocs/goldenPath/help/hgGeneGraph.html
- lines changed 3, context: html, text, full: html, text
326daa8d8909356a7bd10545c3525ff285cb40b1 Mon May 22 14:54:04 2017 -0700
Correction to URL for hgGeneGraph stats page, changing URL to database that's now disappeared, minor spelling correction, refs #13634
- lines changed 1, context: html, text, full: html, text
d01f09a32c56f6b042ca2a921196593f8c7bb265 Tue May 23 12:20:42 2017 -0700
fixing mpidb link, refs #13534
- lines changed 34, context: html, text, full: html, text
0658be300780cc55fcf9fe9bcde68b77ee867ca0 Thu May 25 16:18:54 2017 -0700
adding data access section, refs #13634
- src/hg/htdocs/goldenPath/help/multiRegionHelp.html
- lines changed 5, context: html, text, full: html, text
6d477b5c13c2913f7ab1e8738abafa413e5d14db Mon May 22 12:03:26 2017 -0700
added info on new feature for custom regions in BED format, refs #17358
- lines changed 2, context: html, text, full: html, text
05d2c619e5a3fb5af3e94568d2068e76467d1308 Tue May 23 08:48:45 2017 -0700
added new screenshot of multi-region menu, refs #17358
- src/hg/htdocs/images/MultiRegionConfigurationWindow2.PNG
- lines changed 0, context: html, text, full: html, text
05d2c619e5a3fb5af3e94568d2068e76467d1308 Tue May 23 08:48:45 2017 -0700
added new screenshot of multi-region menu, refs #17358
- lines changed 0, context: html, text, full: html, text
f80cb480b03f9fdade8e8cbea179360d64348a90 Wed May 24 09:41:58 2017 -0700
dropped extra multiconfig snapshot
- src/hg/htdocs/images/MultiRegionConfigurationWindow2.png
- lines changed 0, context: html, text, full: html, text
5f3348494a51665660ac9650a28336ea95d48b26 Tue May 23 08:53:31 2017 -0700
corrected .png extension
- src/hg/htdocs/inc/gbPageStart.html
- lines changed 12, context: html, text, full: html, text
b038c9efbd0006a4ef85b0d4709663aae16a2080 Wed May 17 21:30:03 2017 -0700
Add option to include JS for dynamic behavior.
- src/hg/htdocs/inc/globalNavBar.inc
- lines changed 1, context: html, text, full: html, text
6e5534d6e49c698643817a5745f19dea156e3157 Wed May 24 15:32:08 2017 -0700
take out "Make Composite" from blue bar menu
- src/hg/htdocs/staticStyle/gbStatic.css
- lines changed 31, context: html, text, full: html, text
ec5a82a0f026c41041f9df33cdf98efec297a092 Mon May 22 16:00:49 2017 -0700
Support for collapsible sections, initial use table of contents type pages. refs #18504
- src/hg/htdocs/testToc.html
- lines changed 35, context: html, text, full: html, text
ec5a82a0f026c41041f9df33cdf98efec297a092 Mon May 22 16:00:49 2017 -0700
Support for collapsible sections, initial use table of contents type pages. refs #18504
- src/hg/inc/mathWig.h
- lines changed 13, context: html, text, full: html, text
e4dc5f0504182a78676676ea772abfd3df806c51 Wed May 24 14:11:58 2017 -0700
oops, left out mathWig.h
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/js/hgTracks.js
- lines changed 7, context: html, text, full: html, text
ea3693ba624c2bc0e7849cac3dba48ee6a1ddd30 Tue May 23 21:49:46 2017 -0700
fixing multi-highlights not moving during pannings, refs #19463
- src/hg/lib/barChartGeneExp.as
- lines changed 15, context: html, text, full: html, text
89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
Fixing the issues identified in this weeks code review, refs #19445
- src/hg/lib/barChartTranscExp.as
- lines changed 15, context: html, text, full: html, text
189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
- lines changed 1, context: html, text, full: html, text
d37ad664c3fd2bb2c1888f658b1fb81c9db4f0c3 Wed May 24 09:34:29 2017 -0700
Updating the table name in the .as file, refs #18736
- src/hg/lib/customFactory.c
- lines changed 11, context: html, text, full: html, text
917916ac4ed3c2b7e4cdcdb4e03edd42ae5b450d Mon May 22 11:38:54 2017 -0700
Allow barChart custom tracks without matrix fields (dataOffset, len). refs #18736
- src/hg/lib/hdb.c
- lines changed 2, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/lib/mathWig.c
- lines changed 111, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/lib/trackDbCustom.c
- lines changed 2, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/lib/trackHub.c
- lines changed 7, context: html, text, full: html, text
677b513b231891e30d32024de7ded7766ef72058 Wed May 24 14:09:42 2017 -0700
add mathWig track type which is an arithmetic combination of bigWi.
- src/hg/makeDb/doc/hg19.txt
- lines changed 3, context: html, text, full: html, text
2c0b08d7df94e0cb6a8b3dfdc47c6eec25ba2ba7 Thu May 25 11:34:12 2017 -0700
updating table change date in clinvar otto update, refs #19458
- lines changed 42, context: html, text, full: html, text
58fbbd0e2fc10b717d69ebc6a24e056c7946fbab Thu May 25 15:46:13 2017 -0700
adding makedoc for interactions track, refs #13634
- lines changed 33, context: html, text, full: html, text
f8088604628eb6ff492531c438614fa92211b432 Fri May 26 09:59:15 2017 -0700
adding more details to interactions track makedoc, refs #13634
- src/hg/makeDb/doc/hg38/hg38.txt
- lines changed 48, context: html, text, full: html, text
189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
- lines changed 6, context: html, text, full: html, text
89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
Fixing the issues identified in this weeks code review, refs #19445
- src/hg/makeDb/doc/hg38/interactions.txt
- lines changed 7, context: html, text, full: html, text
58fbbd0e2fc10b717d69ebc6a24e056c7946fbab Thu May 25 15:46:13 2017 -0700
adding makedoc for interactions track, refs #13634
- lines changed 20, context: html, text, full: html, text
f8088604628eb6ff492531c438614fa92211b432 Fri May 26 09:59:15 2017 -0700
adding more details to interactions track makedoc, refs #13634
- src/hg/makeDb/doc/mm10.txt
- lines changed 76, context: html, text, full: html, text
97cdff9ff0ae3fbf72798fd2d1b660afdc619741 Fri May 26 11:31:42 2017 -0700
ncbiRefSeq gene track build instructions refs #18997
- src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes18.sh
- lines changed 951, context: html, text, full: html, text
17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
gencode v26 version of knownGene
- src/hg/makeDb/doc/wikipediaScrape.txt
- lines changed 3, context: html, text, full: html, text
17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
gencode v26 version of knownGene
- src/hg/makeDb/trackDb/human/clinvar.html
- lines changed 3, context: html, text, full: html, text
da58c5408b67bdbcfe91b6a7e4a5051c5dea827c Tue May 23 12:11:43 2017 -0700
clinVar has changed their format again, refs #19458
- src/hg/makeDb/trackDb/human/hg38/Bismap.html
- lines changed 11, context: html, text, full: html, text
89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
Fixing the issues identified in this weeks code review, refs #19445
- src/hg/makeDb/trackDb/human/hg38/Umap.html
- lines changed 10, context: html, text, full: html, text
89b0dff94a9b96866a35b9bc0afff49c8ea9150a Wed May 24 13:44:53 2017 -0700
Fixing the issues identified in this weeks code review, refs #19445
- src/hg/makeDb/trackDb/human/hg38/barCharts.ra
- lines changed 67, context: html, text, full: html, text
189d6ab935888dfdaf05199e7caeb3ec9553571e Tue May 23 12:23:38 2017 -0700
TrackDb changes, custom as file and doc for GTEX transcript track, refs #19350
- lines changed 2, context: html, text, full: html, text
7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
- lines changed 1, context: html, text, full: html, text
84aba1336c8995f2e830823096229bdef57c80c6 Tue May 23 15:50:15 2017 -0700
Adding alpha tag in new hg38/barCharts.ra for track gtexGene to restore GTEx on beta.
- src/hg/makeDb/trackDb/human/hg38/gtexExpr.html
- lines changed 126, context: html, text, full: html, text
2a7ba03ee1c1439b724eeb52f5ddd00efc5dd715 Tue May 23 15:02:48 2017 -0700
Adding in the html files for gtex supertrack , refs #19350
- src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html
- lines changed 124, context: html, text, full: html, text
2a7ba03ee1c1439b724eeb52f5ddd00efc5dd715 Tue May 23 15:02:48 2017 -0700
Adding in the html files for gtex supertrack , refs #19350
- src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
- lines changed 40, context: html, text, full: html, text
17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
gencode v26 version of knownGene
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 1, context: html, text, full: html, text
7d342854b5719897461428785269775c06727326 Tue May 23 12:39:07 2017 -0700
Remove need for spectrum setting in trackDb for barChart and gtexGene tracks
- lines changed 2, context: html, text, full: html, text
17a1ac964849e17fa9c4391e5995d13dc3787e64 Mon May 29 08:44:52 2017 -0700
gencode v26 version of knownGene
- src/hg/makeDb/trackDb/interactions.html
- lines changed 1, context: html, text, full: html, text
3427fa112813f798972aeba31f388459fc9007a2 Tue May 23 15:07:04 2017 -0700
Fixing URL typo, refs #13634
- src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
- lines changed 53, context: html, text, full: html, text
11dbfd831cc086a17bc981529ff050a587f36d28 Tue May 23 13:42:15 2017 -0700
Fixing the References section on the strainSNPs.html page for mm10, refs #18305
- lines changed 3, context: html, text, full: html, text
75bc49bac47e2a3dbf88a1516f3cfabce74b35b6 Tue May 23 15:33:51 2017 -0700
Making the preprint reference a hyperlink to the paper in the strainSNPs description page, refs #18305
- lines changed 6, context: html, text, full: html, text
05a57d765221544f83ea7070f00faa9d84f42ab7 Wed May 24 13:21:17 2017 -0700
Adding periods to the end of sentences in the strainSNPs description page, refs #18305
- src/hg/makeDb/trackDb/tanDups.html
- lines changed 95, context: html, text, full: html, text
35bebcf1469bc20222200f35aa69e8d119bfd7d3 Tue May 23 14:52:46 2017 -0700
adding composite for gapOverlaps and tandemDups refs #13553
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 15, context: html, text, full: html, text
35bebcf1469bc20222200f35aa69e8d119bfd7d3 Tue May 23 14:52:46 2017 -0700
adding composite for gapOverlaps and tandemDups refs #13553
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
451a2448e7969d3cdb6edb16125dd09373c461d1 Mon May 22 17:26:32 2017 -0700
adding pyLib directory to the build makefile, refs #13634
- src/hg/pyLib/makefile
- lines changed 8, context: html, text, full: html, text
f3658c9efc9e9121a4f03f1055e8e8bdfb7db5e7 Wed May 24 17:13:02 2017 -0700
removing the copy instructions of graphviz from the makefile, refs #13634
- src/hg/utils/automation/doAssemblyHub.pl
- lines changed 1, context: html, text, full: html, text
1fba77124671c29b4e773929733015e036167960 Fri May 26 19:52:30 2017 -0700
fix up type for photoCredits.txt refs #19450
- src/hg/utils/automation/doTandemDup.pl
- lines changed 1, context: html, text, full: html, text
1026d424d15e26e1138aaaa5f371e9180bd7533e Tue May 23 22:40:06 2017 -0700
include the remove of the batch /err/ directories in cleanup refs #13553
- src/hg/utils/otto/clinvar/clinVarToBed
- lines changed 1, context: html, text, full: html, text
da58c5408b67bdbcfe91b6a7e4a5051c5dea827c Tue May 23 12:11:43 2017 -0700
clinVar has changed their format again, refs #19458
- lines changed 8, context: html, text, full: html, text
2c0b08d7df94e0cb6a8b3dfdc47c6eec25ba2ba7 Thu May 25 11:34:12 2017 -0700
updating table change date in clinvar otto update, refs #19458
- src/inc/tagToSql.h
- lines changed 4, context: html, text, full: html, text
8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
- src/lib/https.c
- lines changed 9, context: html, text, full: html, text
a13302691fc41d6ff9a561685f4af33ef2921d51 Wed May 24 14:32:19 2017 -0700
Problem discovered handle leak. Reported by Jonathan. We just need to close it ourselves at the end since we use BIO_noclose flag. This is good for future if we someday re-use a connection.
- src/lib/net.c
- lines changed 1, context: html, text, full: html, text
f42e23773a5fd7a5d3f0fd1c1a6f183ab1175772 Wed May 24 11:25:16 2017 -0700
File descriptor leak in netLineFileMayOpen when error-condition occurs. Reported by Jonathan.
- src/lib/tagToSql.c
- lines changed 98, context: html, text, full: html, text
8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
- lines changed 1, context: html, text, full: html, text
11a457ee3cba6ca5739c8b2607533d597c20e774 Fri May 26 12:50:35 2017 -0700
Fixing a refactoring induced bug. Subtle one!
- src/makefile
- lines changed 1, context: html, text, full: html, text
1e640abe5f2d2cb1b5e9797db12427893b2d4bec Fri May 26 13:34:28 2017 -0700
Adding tabFile to make dirs.
- src/tabFile/LICENSE
- lines changed 18, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tabFile/README
- lines changed 3, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tabFile/makefile
- lines changed 32, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tabFile/tabInfo/makefile
- lines changed 3, context: html, text, full: html, text
3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
Making a tagInfo utility that parallels tagStormInfo.
- src/tabFile/tabInfo/tabInfo.c
- lines changed 165, context: html, text, full: html, text
3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
Making a tagInfo utility that parallels tagStormInfo.
- src/tabFile/tabInfo/test.in
- lines changed 3370, context: html, text, full: html, text
3ab2c488f953187a6f6849b3d75f40126bb02703 Fri May 26 12:51:46 2017 -0700
Making a tagInfo utility that parallels tagStormInfo.
- src/tabFile/tabQuery/makefile
- lines changed 3, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tabFile/tabQuery/tabQuery.c
- lines changed 157, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tagStorm/LICENSE
- lines changed 1, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/tagStorm/README
- lines changed 12, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- lines changed 1, context: html, text, full: html, text
7b319f59e8c9183d7938f5e4e8b2b43caaa77d8d Fri May 26 13:25:48 2017 -0700
Referencing LICENSE file in README file.
- src/tagStorm/tagStormFromTab/tagStormFromTab.c
- lines changed 200, context: html, text, full: html, text
f39997389acdbf7e4da32594c892938edabfcdf9 Thu May 11 12:50:42 2017 -0700
Adding -spec option.
- lines changed 3, context: html, text, full: html, text
bff6ae7c3087d5ed8b47dc77a6eae593d475603b Tue May 23 13:37:21 2017 -0700
Removing some debugging set.
- src/tagStorm/tagStormInfo/tagStormInfo.c
- lines changed 91, context: html, text, full: html, text
8baf466781afe94e75e47aafe7e123b63284450c Fri May 26 12:37:53 2017 -0700
Refactoring to move routine to print a tagStorm schema line from tagStormInfo to tagToSql.c for reuse in tabInfo.
- src/tagStorm/tagStormInfo/tests/expected.out
- lines changed 1, context: html, text, full: html, text
cc384aecda6ac58a6236790d7cb3c89ffd084987 Fri May 26 12:32:50 2017 -0700
Updating expected test set results.
- src/tagStorm/tagStormInfo/tests/expected.schema
- lines changed 2, context: html, text, full: html, text
cc384aecda6ac58a6236790d7cb3c89ffd084987 Fri May 26 12:32:50 2017 -0700
Updating expected test set results.
- lines changed 2, context: html, text, full: html, text
52bfb2c4a2b1d876e2d4a57625d7752fb1e0f8cd Fri May 26 12:50:00 2017 -0700
Fixing expected schema again
- src/tagStorm/tagStormQuery/tagStormQuery.c
- lines changed 17, context: html, text, full: html, text
7e03b72e0c404ba2d76a28e43f2a3e8774e783a6 Fri May 26 13:26:57 2017 -0700
Dealing with consequences of librarification of tagStormQuery.
- src/tagStorm/tagStormScalarToArray/makefile
- lines changed 7, context: html, text, full: html, text
5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
- src/tagStorm/tagStormScalarToArray/tagStormScalarToArray.c
- lines changed 99, context: html, text, full: html, text
5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
- src/tagStorm/tagStormScalarToArray/test.expected
- lines changed 12, context: html, text, full: html, text
5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
- src/tagStorm/tagStormScalarToArray/test.in
- lines changed 12, context: html, text, full: html, text
5ca9a01cf702e61fb67b56694ff9999b43ebe149 Wed May 24 22:00:30 2017 -0700
Making utility to convert older tagStorms to format that can support comma separated values similar to the csv format for array values.
- src/tagStorm/tagStormToCsv/makefile
- lines changed 3, context: html, text, full: html, text
1891c9ec6b79cfca974922dc1232985ca8d9529c Thu May 25 10:16:14 2017 -0700
Adding tagStormToCsv which never got commited, no redmine
- src/tagStorm/tagStormToCsv/tagStormToCsv.c
- lines changed 47, context: html, text, full: html, text
1891c9ec6b79cfca974922dc1232985ca8d9529c Thu May 25 10:16:14 2017 -0700
Adding tagStormToCsv which never got commited, no redmine
- src/userApps/README
- lines changed 11, context: html, text, full: html, text
601f2b5984448488bd26aead6be30b50503fa05b Thu May 25 13:59:53 2017 -0700
indicate rsync instructions no redmine
- lines changed 2, context: html, text, full: html, text
16dbc21b173a5cc54d4d7cb31ac30a0f2b3b0087 Thu May 25 14:05:12 2017 -0700
make userApps README point to new mirror instruction page, no redmine
- src/utils/addCols/addCols.c
- lines changed 25, context: html, text, full: html, text
11b5d7088f505cdc4f678d3451d63bed4a3019f9 Fri May 26 13:28:25 2017 -0700
Adding maxCols option so can handle more than 16.
- src/utils/ggTables
- lines changed 17, context: html, text, full: html, text
b88380414ddecaab81f5c19b9f0cf06dbbedc787 Fri May 26 06:36:28 2017 -0700
changing python hash bang again for hgGeneGraph, tiny wrangling fix, refs #13634
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/utils/qa/makefile
- lines changed 1, context: html, text, full: html, text
00be53fdc64136b82e946142ed54230a8a092a34 Wed May 24 10:30:42 2017 -0700
Add new runBits to makefile. Removing old version, refs #18828
- src/utils/qa/runBits
- lines changed 51, context: html, text, full: html, text
dfa38476ce393fb3ae03ed7ba8f6845596e26b73 Wed May 24 10:29:08 2017 -0700
New version of runBits based on Python. Runs featureBits to check percent coverage on genome plus percent overlap with gaps. Will also output links to genome-test for first three overlapped gaps. Can also output overlap with unbridged gaps. refs #18828
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
9e8b279a2d38ec77cac7c2a39022614b2e94c830 Mon May 29 09:55:23 2017 -0700
v350 preview2 refs #19473
- src/utils/tabQuery/makefile
- lines changed 3, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- src/utils/tabQuery/tabQuery.c
- lines changed 157, context: html, text, full: html, text
c1702f4d7e442e45db8d6f40d581f70b975d1340 Fri May 26 10:59:08 2017 -0700
Creating a new directory for tab-separated-file utilities and seeding it with tabQuery formerly in the utils directory.
- lines changed: 15729
- files changed: 138