All File Changes
v337_preview2 to v337_base (2016-08-08 to 2016-08-15) v337
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- src/hg/cirm/cdw/cdwSummary/cdwSummary
- lines changed 2, context: html, text, full: html, text
4c0e94287baa7c92a6570c29273b7aacb243df1c Mon Aug 8 10:45:15 2016 -0700
fix strange R syntax problem with if...else in CIRM summary script
- src/hg/cirm/cdw/wrangle/kallistoToMatrix/kallistoToMatrix
- lines changed 30, context: html, text, full: html, text
1f08293747e8b617c85744f1e23433928b138ffb Fri Aug 12 22:49:00 2016 -0700
CIRM kallistoToMatrix: adding option to keep genes that are not expressed. adding option to recurse into subdirectories
- src/hg/hgGene/gad.c
- lines changed 9, context: html, text, full: html, text
b7bc2a330a4430adc400bac36a66701080382e47 Mon Aug 8 16:06:13 2016 -0700
Fixing links to Genetic Association Database (now archive-only), refs #15342
- src/hg/hgGene/hgGeneData/Human/links.ra
- lines changed 1, context: html, text, full: html, text
02e0b4574f516c369dd3210a68700eb3a767ab0d Thu Aug 11 10:56:04 2016 -0700
Updating link to HuGe literature search, refs #15342
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 1, context: html, text, full: html, text
8e0a4db9b5cf81ab6826ea086a6aca749934e5e9 Mon Aug 8 14:17:43 2016 -0700
Fixing typo caught by Christopher Lee. refs #17209 note-53
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
7c23357a1a7352445e138c74cc19931a70722761 Thu Aug 11 14:08:04 2016 -0700
Revert "Finishing touches on html-encoding of errors for warn/abort when using html output."
This reverts commit 4aa7141dedea619f3bc7d42316f886bcfd554349.
- lines changed 2, context: html, text, full: html, text
e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
- lines changed 71, context: html, text, full: html, text
1f6843501878c47ccba47c897077d2b5022f3e01 Sun Aug 14 15:55:17 2016 -0700
get bigPsl "alignment in window" to work
- src/hg/hgc/hgc.h
- lines changed 4, context: html, text, full: html, text
1f6843501878c47ccba47c897077d2b5022f3e01 Sun Aug 14 15:55:17 2016 -0700
get bigPsl "alignment in window" to work
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 1, context: html, text, full: html, text
a696f86fb9762450111e98537d782f09edfe577b Fri Aug 12 12:12:30 2016 -0700
Adding news item, release & credit info for galVar1, refs #17180
- src/hg/htdocs/goldenPath/credits.html
- lines changed 45, context: html, text, full: html, text
a696f86fb9762450111e98537d782f09edfe577b Fri Aug 12 12:12:30 2016 -0700
Adding news item, release & credit info for galVar1, refs #17180
- lines changed 1, context: html, text, full: html, text
3acb23ef2cd15b4df2a91e1a573caf71f2019b95 Fri Aug 12 12:19:58 2016 -0700
fixed a couple of typos
- src/hg/htdocs/goldenPath/help/bigPsl.html
- lines changed 1, context: html, text, full: html, text
03057acc147d8fa7bd171460eb20cd1977017779 Sun Aug 14 16:27:51 2016 -0700
change some wording bigPsl in response to code review
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 4, context: html, text, full: html, text
f5f1dd034547e97adab7551908f1b107d909b0aa Tue Aug 9 12:07:15 2016 -0700
Adding some wording about custom tracks per Max input MLQ refs #17867
- src/hg/htdocs/goldenPath/help/gbic.html
- lines changed 6, context: html, text, full: html, text
879a9e8f572d91aed8a1186d002e3ec49f24b8f6 Thu Aug 11 16:11:47 2016 -0700
Changes to gbic.html based on code review, refs #17860
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
- lines changed 1, context: html, text, full: html, text
3df2ce3e6bea2420c1910e2cdfb4090f7636366f Fri Aug 12 22:46:26 2016 -0700
fixing typo in trackDb docs
- lines changed 1, context: html, text, full: html, text
a8aed7d68a6f1f1fbbe4527a24293329f52e7e18 Fri Aug 12 22:50:25 2016 -0700
fixing a similar typo in trackDb docs
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 26, context: html, text, full: html, text
a696f86fb9762450111e98537d782f09edfe577b Fri Aug 12 12:12:30 2016 -0700
Adding news item, release & credit info for galVar1, refs #17180
- lines changed 2, context: html, text, full: html, text
3ba10b5896360ccec5fb391f7de64f3fb935de3f Fri Aug 12 12:15:47 2016 -0700
made a few corrections
- lines changed 3, context: html, text, full: html, text
fed8132dad3b51aa4c4cc7f25c85b9071082d9ed Fri Aug 12 12:17:36 2016 -0700
fixed typos
- src/hg/htdocs/indexNews.html
- lines changed 13, context: html, text, full: html, text
a696f86fb9762450111e98537d782f09edfe577b Fri Aug 12 12:12:30 2016 -0700
Adding news item, release & credit info for galVar1, refs #17180
- lines changed 1, context: html, text, full: html, text
3ba10b5896360ccec5fb391f7de64f3fb935de3f Fri Aug 12 12:15:47 2016 -0700
made a few corrections
- src/hg/inc/soTerm.h
- lines changed 3, context: html, text, full: html, text
e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
- src/hg/inc/versionInfo.h
- lines changed 1, context: html, text, full: html, text
97e40314ec4f1b7bc3ebac5f7d541b224057eae7 Mon Aug 15 10:32:02 2016 -0700
New version number v337
- src/hg/lib/bigPsl.as
- lines changed 1, context: html, text, full: html, text
03057acc147d8fa7bd171460eb20cd1977017779 Sun Aug 14 16:27:51 2016 -0700
change some wording bigPsl in response to code review
- src/hg/lib/cart.c
- lines changed 1, context: html, text, full: html, text
2160baec63f853659980b53f4cda17cd56ac31e7 Thu Aug 11 14:08:42 2016 -0700
Revert "Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan"
This reverts commit 4cfc3d3eb5486c004765de17570c548ea6c388d5.
- src/hg/lib/hdb.c
- lines changed 26, context: html, text, full: html, text
d185918b081b11e5e66133f6d147cf6220b54f81 Fri Aug 12 14:52:31 2016 -0700
Make hDbForTaxon more discerning about extra fluff in defaultDb and dbDb: order multiple matches in defaultDb by dbDb.orderKey, require active=1 and check database existence. refs #17886
- src/hg/lib/hgFind.c
- lines changed 1, context: html, text, full: html, text
7c23357a1a7352445e138c74cc19931a70722761 Thu Aug 11 14:08:04 2016 -0700
Revert "Finishing touches on html-encoding of errors for warn/abort when using html output."
This reverts commit 4aa7141dedea619f3bc7d42316f886bcfd554349.
- lines changed 10, context: html, text, full: html, text
00423dc0b59a930bd39fc75597abdf90752faf34 Thu Aug 11 21:00:42 2016 -0700
removing mention of gbStatus table
- src/hg/lib/snp125Ui.c
- lines changed 58, context: html, text, full: html, text
e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
- src/hg/lib/soTerm.c
- lines changed 55, context: html, text, full: html, text
e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
- src/hg/makeDb/doc/gorGor5/initialBuild.txt
- lines changed 83, context: html, text, full: html, text
a457316487907b46048bd9e48ff3f52f4a5acc6b Mon Aug 8 14:16:31 2016 -0700
gorGor5 in the pushQ 007874 refs #17580
- lines changed 2, context: html, text, full: html, text
07d48778f50cf173833664537688681b12ab6567 Mon Aug 8 14:49:30 2016 -0700
fix orderKey refs #17580
- src/hg/makeDb/doc/hg18.txt
- lines changed 13, context: html, text, full: html, text
955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
- src/hg/makeDb/doc/hg19.txt
- lines changed 24, context: html, text, full: html, text
955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
- lines changed 23, context: html, text, full: html, text
aad8186bd6883ae5debe29a690e36176d1a9e9a9 Thu Aug 11 10:20:51 2016 -0700
LRG tracks updated for hg19 and hg38. refs #13359
- src/hg/makeDb/doc/hg38/hg38.txt
- lines changed 20, context: html, text, full: html, text
aad8186bd6883ae5debe29a690e36176d1a9e9a9 Thu Aug 11 10:20:51 2016 -0700
LRG tracks updated for hg19 and hg38. refs #13359
- src/hg/makeDb/doc/hg38/variation.txt
- lines changed 24, context: html, text, full: html, text
955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
- src/hg/makeDb/doc/panTro3.txt
- lines changed 17, context: html, text, full: html, text
60fa030134dbf038678de2223b23c6494944788c Mon Aug 8 14:46:27 2016 -0700
liftOver to and from panTro3 panTro5 refs #17817
- src/hg/makeDb/doc/panTro5/initialBuild.txt
- lines changed 12, context: html, text, full: html, text
9d1a581154394267def6c37a74417768ad3fe14e Mon Aug 8 14:28:08 2016 -0700
panTro5 in the pushQ 007873 refs #17817
- lines changed 2, context: html, text, full: html, text
60fa030134dbf038678de2223b23c6494944788c Mon Aug 8 14:46:27 2016 -0700
liftOver to and from panTro3 panTro5 refs #17817
- src/hg/makeDb/doc/panTro5/lastzRuns.txt
- lines changed 6, context: html, text, full: html, text
19669f24e28a8eb75275b32db980cac9363c647c Mon Aug 8 13:09:21 2016 -0700
lastz to gorGor5 done refs #17817 #17580
- src/hg/makeDb/doc/worms/ancCey1.txt
- lines changed 65, context: html, text, full: html, text
80d45136bda37565ee89b89c57a3abcb34a82c67 Mon Aug 8 15:19:36 2016 -0700
done with genbank refs #15209
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
ec40f7a2d57f40c0b1a379f2d31453942223db37 Mon Aug 8 15:18:39 2016 -0700
Added ancCey1 - Ancylostoma ceylanicum refs #15209
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
ec40f7a2d57f40c0b1a379f2d31453942223db37 Mon Aug 8 15:18:39 2016 -0700
Added ancCey1 - Ancylostoma ceylanicum refs #15209
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
73ed8702043b81fdda04863534287bf7a163ef62 Tue Aug 9 11:25:02 2016 -0700
turning on genbank updates for galVar1
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
ccb8abef78edfb46e0b950ca3be7e2b245fae545 Tue Aug 9 12:53:00 2016 -0700
Adding GalGal5 to list of non-self chains, refs #17168
- src/hg/makeDb/trackDb/est.html
- lines changed 9, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 8, context: html, text, full: html, text
55ab91a9a8d5ed3b43d794b03085eaa93b120910 Fri Aug 12 15:12:03 2016 -0700
Correcting copy-pasted settings for linking to orthologous positions in chimp and macaque from SNPs tracks. HT Christopher Lee. refs #17209
- src/hg/makeDb/trackDb/human/snp147.html
- lines changed 1, context: html, text, full: html, text
f97a3ac1a11dea04e220df88ab301069f80150b4 Fri Aug 12 12:57:15 2016 -0700
Fixing link to ncbi from track desc page, refs #17209
- src/hg/makeDb/trackDb/human/snp147.shared.html
- lines changed 3, context: html, text, full: html, text
6f275e93dd1dad63fa37611e0f9572bec7185ebb Mon Aug 8 16:54:57 2016 -0700
Adding description of non-coding RNA coloring to snp147 description page, refs #17209
- src/hg/makeDb/trackDb/human/snp147Common.html
- lines changed 1, context: html, text, full: html, text
f97a3ac1a11dea04e220df88ab301069f80150b4 Fri Aug 12 12:57:15 2016 -0700
Fixing link to ncbi from track desc page, refs #17209
- src/hg/makeDb/trackDb/human/snp147Flagged.html
- lines changed 1, context: html, text, full: html, text
f97a3ac1a11dea04e220df88ab301069f80150b4 Fri Aug 12 12:57:15 2016 -0700
Fixing link to ncbi from track desc page, refs #17209
- src/hg/makeDb/trackDb/human/snp147Mult.html
- lines changed 1, context: html, text, full: html, text
f97a3ac1a11dea04e220df88ab301069f80150b4 Fri Aug 12 12:57:15 2016 -0700
Fixing link to ncbi from track desc page, refs #17209
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 19, context: html, text, full: html, text
955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
- lines changed 40, context: html, text, full: html, text
55ab91a9a8d5ed3b43d794b03085eaa93b120910 Fri Aug 12 15:12:03 2016 -0700
Correcting copy-pasted settings for linking to orthologous positions in chimp and macaque from SNPs tracks. HT Christopher Lee. refs #17209
- src/hg/makeDb/trackDb/intronEst.html
- lines changed 8, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/mouse/trackDb.ra
- lines changed 15, context: html, text, full: html, text
1c97569bf82e2552afd965837460817e10b5dff2 Fri Aug 12 15:10:25 2016 -0700
Removing human-specific snp track settings from mouse/trackDb.ra.
- src/hg/makeDb/trackDb/mrna.html
- lines changed 9, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/refGene.html
- lines changed 10, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 6, context: html, text, full: html, text
bf995164e069593e3b8e6042699a9d089838cb1c Tue Aug 9 15:44:35 2016 -0700
adding ucscToRefSeq search rule refs #17168
- lines changed 18, context: html, text, full: html, text
3a5e1d8ad7ed20fc507e9a0b2db1b4de3cda09e8 Thu Aug 11 11:34:03 2016 -0700
first commit of crispr trackDb entries
- lines changed 16, context: html, text, full: html, text
3eb9499bc5e5dd021458340d4ede7002ae7a82ac Fri Aug 12 22:51:06 2016 -0700
updates to crispr track
- lines changed 1, context: html, text, full: html, text
146e6f0079284fa8beb7715029f59c44682227d2 Mon Aug 15 09:10:33 2016 -0700
fixing trackDb error found by QA script
- src/hg/makeDb/trackDb/ucscToRefSeq.html
- lines changed 1, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/xenoEst.html
- lines changed 8, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/xenoMrna.html
- lines changed 8, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/makeDb/trackDb/xenoRefGene.html
- lines changed 20, context: html, text, full: html, text
f000e9ed56621ca612980e35c935747e18317a72 Tue Aug 9 12:49:58 2016 -0700
Updating Refernces on various pages, changing link text on ucscToRefSeq page, refs #17168
- src/hg/utils/automation/EnsGeneAutomate.pm
- lines changed 220, context: html, text, full: html, text
901c127a150f87964448da51b90f21ed6cb7a1d2 Mon Aug 8 15:52:20 2016 -0700
adding in v85 definitions refs #17863
- lines changed 1, context: html, text, full: html, text
b96579b4afedef6bd053c08ef65ba4a33cdff496 Mon Aug 8 15:57:25 2016 -0700
correct one name refs #17863
- lines changed 1, context: html, text, full: html, text
c74ee0fa21d22224fa560229559c6a9ff972a23c Mon Aug 8 16:02:15 2016 -0700
correcting lists refs #17863
- src/hg/utils/automation/configFiles/colAng1.config.ra
- lines changed 26, context: html, text, full: html, text
7272b86c19f04618bc40ac45ecce31bee910e43d Mon Aug 8 14:41:21 2016 -0700
config files up to date refs #17817
- src/hg/utils/automation/configFiles/equCab1.config.ra
- lines changed 15, context: html, text, full: html, text
7272b86c19f04618bc40ac45ecce31bee910e43d Mon Aug 8 14:41:21 2016 -0700
config files up to date refs #17817
- src/hg/utils/automation/configFiles/gorGor5.config.ra
- lines changed 31, context: html, text, full: html, text
7272b86c19f04618bc40ac45ecce31bee910e43d Mon Aug 8 14:41:21 2016 -0700
config files up to date refs #17817
- src/hg/utils/automation/configFiles/panTro5.config.ra
- lines changed 26, context: html, text, full: html, text
7272b86c19f04618bc40ac45ecce31bee910e43d Mon Aug 8 14:41:21 2016 -0700
config files up to date refs #17817
- src/inc/htmshell.h
- lines changed 3, context: html, text, full: html, text
2160baec63f853659980b53f4cda17cd56ac31e7 Thu Aug 11 14:08:42 2016 -0700
Revert "Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan"
This reverts commit 4cfc3d3eb5486c004765de17570c548ea6c388d5.
- src/lib/htmshell.c
- lines changed 1, context: html, text, full: html, text
7c23357a1a7352445e138c74cc19931a70722761 Thu Aug 11 14:08:04 2016 -0700
Revert "Finishing touches on html-encoding of errors for warn/abort when using html output."
This reverts commit 4aa7141dedea619f3bc7d42316f886bcfd554349.
- lines changed 1, context: html, text, full: html, text
20f2023e247107b60531978989c912942d5aac65 Thu Aug 11 14:08:28 2016 -0700
Revert "Reverting this line because it seems to cause unnecessary double-encoding of the error message."
This reverts commit f52636fabd76fcf998604f16d815cf606d52c758.
- lines changed 13, context: html, text, full: html, text
2160baec63f853659980b53f4cda17cd56ac31e7 Thu Aug 11 14:08:42 2016 -0700
Revert "Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan"
This reverts commit 4cfc3d3eb5486c004765de17570c548ea6c388d5.
- src/product/installer/README.md
- lines changed 6, context: html, text, full: html, text
879a9e8f572d91aed8a1186d002e3ec49f24b8f6 Thu Aug 11 16:11:47 2016 -0700
Changes to gbic.html based on code review, refs #17860
- src/product/installer/makefile
- lines changed 4, context: html, text, full: html, text
c3749852d1b0c0b74ce90ce2779bc66c3e000d29 Tue Aug 9 13:35:42 2016 -0700
Suppressing extra echo call as per code review, refs #17860
- src/utils/makefile
- lines changed 2, context: html, text, full: html, text
cd79064dde5eff6904e314e21df8baa54aafc889 Mon Aug 8 13:23:10 2016 -0700
adding a command to merge two gene expression matrices, currently useful
for CIRM CDW, but probably useful for other projects that deal with
RNA-seq. No redmine.
- src/utils/matrixMerge
- lines changed 115, context: html, text, full: html, text
cd79064dde5eff6904e314e21df8baa54aafc889 Mon Aug 8 13:23:10 2016 -0700
adding a command to merge two gene expression matrices, currently useful
for CIRM CDW, but probably useful for other projects that deal with
RNA-seq. No redmine.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 4, context: html, text, full: html, text
3d9152108f2483d381c6da36d25bcb6f892148a5 Mon Aug 15 10:30:35 2016 -0700
v337 final build refs #17833
- lines changed: 1349
- files changed: 84