All File Changes
v437_preview2 to v437_base (2022-09-12 to 2022-09-19) v437
Show details
- src/hg/gar/gar.cgi.pl
- lines changed 5, context: html, text, full: html, text
a0b5687117ecc4f594719d5bd97fcf6ee3f51921 Fri Sep 16 12:02:02 2022 -0700
more strict acceptance of the five required arguments refs #30003
- src/hg/hgPhyloPlace/hgPhyloPlace.c
- lines changed 1, context: html, text, full: html, text
2d0f1f1f85b147f9176abe594f56106b364229e8 Mon Sep 12 14:09:52 2022 -0700
trackHubOpen doesn't actually connect the hub; use hubConnectLoadHubs so if/when the user selects the hub, it is connected.
- lines changed 2, context: html, text, full: html, text
bd83334864d00974729eac73a1411f0b583c6c87 Mon Sep 12 15:15:41 2022 -0700
Add hidden input to set db correctly when only one db is supported.
- src/hg/hgPhyloPlace/parsimonyProto.c
- lines changed 3, context: html, text, full: html, text
9b1292002a4ede647cfea3d0a357c184d6fe557a Wed Sep 14 08:31:30 2022 -0700
SARS-CoV-2 protobuf size is now larger than BIGNUM; use BIGLONGLONG to avoid cryptic error. refs #29994
- src/hg/hgPhyloPlace/phyloPlace.c
- lines changed 17, context: html, text, full: html, text
2d0f1f1f85b147f9176abe594f56106b364229e8 Mon Sep 12 14:09:52 2022 -0700
trackHubOpen doesn't actually connect the hub; use hubConnectLoadHubs so if/when the user selects the hub, it is connected.
- src/hg/hgPhyloPlace/phyloPlace.h
- lines changed 2, context: html, text, full: html, text
2d0f1f1f85b147f9176abe594f56106b364229e8 Mon Sep 12 14:09:52 2022 -0700
trackHubOpen doesn't actually connect the hub; use hubConnectLoadHubs so if/when the user selects the hub, it is connected.
- src/hg/hgTracks/bigRmskTrack.c
- lines changed 1, context: html, text, full: html, text
abb65703416720e75367ebcb234cb3337095f7de Tue Sep 13 18:34:11 2022 -0700
don't bother with generating bigRmsk lables in dense mode
- src/hg/hgc/togaClick.c
- lines changed 1, context: html, text, full: html, text
cf5c80a95a2776705958e59a5a7d36361c0af876 Tue Sep 13 16:46:09 2022 -0700
close a div so that the HTML for toga tracks appear
- src/hg/htdocs/goldenPath/help/bigRmsk.html
- lines changed 1, context: html, text, full: html, text
e19b35681f137d5bcc141f968112bf77476fac28 Tue Sep 13 17:09:32 2022 -0700
added maxWindowToDraw to bigRmsk example
- src/hg/htdocs/indexNews.html
- lines changed 2, context: html, text, full: html, text
46e4518bd5fed298eaa31a1405745a3e0a4a1a7b Mon Sep 12 15:42:35 2022 -0700
fixed date
- src/hg/inc/versionInfo.h
- lines changed 1, context: html, text, full: html, text
8eb698a50a97e1da02a8df3ebbc26379273dafc8 Mon Sep 19 10:22:28 2022 -0700
New version number v437
- src/hg/makeDb/doc/chm13v2.0userData/trackDb/t2tRepeatMasker.trackDb.txt
- lines changed 4, context: html, text, full: html, text
66dc4a7ff27cb4b452b51e554c7591c824f8438d Mon Sep 19 10:18:09 2022 -0700
set max window to draw at 5Mb to avoid timeout on large views refs #29995
- src/hg/makeDb/doc/danRer11/lastzRuns.txt
- lines changed 83, context: html, text, full: html, text
92bbe798bc4650f7f91cf6cd0fa4b5294ca7553b Tue Sep 13 10:41:59 2022 -0700
per user request danRer11 vs dm6 lastz/chain/net refs #29981
- src/hg/makeDb/doc/dm6/lastzRuns.txt
- lines changed 87, context: html, text, full: html, text
92bbe798bc4650f7f91cf6cd0fa4b5294ca7553b Tue Sep 13 10:41:59 2022 -0700
per user request danRer11 vs dm6 lastz/chain/net refs #29981
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
db68c943281694d716659cfc7ea7ccd2a8f5a14f Thu Sep 15 18:11:38 2022 -0700
adding GCA_019973935.1_Tncv_1.0 golden silk orb-weaver (2021) per user request refs #30015
- src/hg/makeDb/doc/mpxvRivers/initialBuild.txt
- lines changed 42, context: html, text, full: html, text
0fe15208a5b0fcf50da228078fe3f4a332f2fc37 Mon Sep 12 16:49:09 2022 -0700
a quick and dirty monkeypox browser for the Rivers strain
- src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt
- lines changed 19, context: html, text, full: html, text
3f76453673b9825c8057d3f16f2c4dd12800daab Tue Sep 13 14:25:13 2022 -0700
added PCR amplicon track to mpxvRivers
- src/hg/makeDb/trackDb/TOGAannotation.html
- lines changed 53, context: html, text, full: html, text
d2ac08231c388dcae68ce7031d5a7dddb91beb97 Mon Sep 12 10:55:19 2022 -0700
expanded documentation from Michael refs #29982
- src/hg/makeDb/trackDb/human/hs1/clinVar20220313.trackDb.ra
- lines changed 1, context: html, text, full: html, text
6a5eeafa42f878d8cc03d1cd468f092f945f63db Tue Sep 13 17:25:31 2022 -0700
update chm13 clinVar20220313 and gwasSNPs2022-03-08 tracks to use the UCSC names
- src/hg/makeDb/trackDb/human/hs1/dbSNP155.trackDb.ra
- lines changed 1, context: html, text, full: html, text
5a7760ebf2c5157a406606abeb20629db087d3d4 Mon Sep 12 16:27:07 2022 -0700
use UCSC named VCF on CHM13
- src/hg/makeDb/trackDb/human/hs1/encode.trackDb.ra
- lines changed 10, context: html, text, full: html, text
0f04531cb987d811394aabf6602228bdc7a4e760 Wed Sep 14 17:26:52 2022 -0700
made 22Rv1 tag a valid tag name
- src/hg/makeDb/trackDb/human/hs1/gwasSNPs2022-03-08.trackDb.ra
- lines changed 1, context: html, text, full: html, text
6a5eeafa42f878d8cc03d1cd468f092f945f63db Tue Sep 13 17:25:31 2022 -0700
update chm13 clinVar20220313 and gwasSNPs2022-03-08 tracks to use the UCSC names
- src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
- lines changed 32, context: html, text, full: html, text
b316b7748a5e2352e1e56392fbc7df9c23b65483 Tue Sep 13 15:44:36 2022 -0700
make summary and linkDataUrl have absolute addresses in them
- src/hg/makeDb/trackDb/human/hs1/t2tRepeatMasker.trackDb.ra
- lines changed 1, context: html, text, full: html, text
ce0c582d58d72ec112484932ff9b933aa4663ded Tue Sep 13 16:58:34 2022 -0700
limit chm13 repeat masker maxWindowToDraw to 10000000
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
30d97725dc1081e029f6577d12ccef896e7d10b9 Fri Sep 16 10:01:05 2022 -0700
need bigGenePred on colorByStrand no redmine
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 2, context: html, text, full: html, text
8c4eff5f7832be1b022735416a2bb1d4c7ad42be Wed Sep 14 13:17:02 2022 -0700
Releasing the UniProt bugs update to the RR, refs #28560
- src/hg/makeDb/trackDb/trackDb.uniprot.ra
- lines changed 226, context: html, text, full: html, text
8c4eff5f7832be1b022735416a2bb1d4c7ad42be Wed Sep 14 13:17:02 2022 -0700
Releasing the UniProt bugs update to the RR, refs #28560
- src/hg/makeDb/trackDb/uniprot.html
- lines changed 124, context: html, text, full: html, text
8c4eff5f7832be1b022735416a2bb1d4c7ad42be Wed Sep 14 13:17:02 2022 -0700
Releasing the UniProt bugs update to the RR, refs #28560
- src/hg/makeDb/trackDb/uniprot.ra
- lines changed 1, context: html, text, full: html, text
8c4eff5f7832be1b022735416a2bb1d4c7ad42be Wed Sep 14 13:17:02 2022 -0700
Releasing the UniProt bugs update to the RR, refs #28560
- src/hg/makeDb/trackDb/uniprotAlpha.html
- lines changed 302, context: html, text, full: html, text
8c4eff5f7832be1b022735416a2bb1d4c7ad42be Wed Sep 14 13:17:02 2022 -0700
Releasing the UniProt bugs update to the RR, refs #28560
- src/hg/makeDb/trackDb/virus/mpxv2022/assembly.html
- lines changed 33, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/chainNet.html
- lines changed 148, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/cpgIslands.html
- lines changed 78, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/description.html
- lines changed 123, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/gc5Base.html
- lines changed 21, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/ncbiGene.html
- lines changed 16, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.html
- lines changed 57, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.ra
- lines changed 8, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/repeatMasker.html
- lines changed 261, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/simpleRepeat.html
- lines changed 48, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/tanDups.html
- lines changed 101, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/trackDb.ra
- lines changed 204, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- src/hg/makeDb/trackDb/virus/mpxv2022/windowMasker.html
- lines changed 38, context: html, text, full: html, text
5f59c0ab7d2d5ef41d98349402d22d221b0b55e0 Wed Sep 14 13:55:48 2022 -0700
initial set of docs for mpxv2022 refs #30012
- lines changed 3, context: html, text, full: html, text
84e11afc2e82703669b4da2481ea2072bb9f2f8b Fri Sep 16 09:33:46 2022 -0700
can not have $ signs in trackDb html refs #30012
- src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.html
- lines changed 57, context: html, text, full: html, text
4ad0b7aa482bb5b9d41cc3558239613fe8efe233 Wed Sep 14 03:41:12 2022 -0700
adding docs page for monkeypox primers, refs #30012
- src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.ra
- lines changed 8, context: html, text, full: html, text
3f76453673b9825c8057d3f16f2c4dd12800daab Tue Sep 13 14:25:13 2022 -0700
added PCR amplicon track to mpxvRivers
- lines changed 4, context: html, text, full: html, text
4ad0b7aa482bb5b9d41cc3558239613fe8efe233 Wed Sep 14 03:41:12 2022 -0700
adding docs page for monkeypox primers, refs #30012
- src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra
- lines changed 127, context: html, text, full: html, text
0fe15208a5b0fcf50da228078fe3f4a332f2fc37 Mon Sep 12 16:49:09 2022 -0700
a quick and dirty monkeypox browser for the Rivers strain
- lines changed 11, context: html, text, full: html, text
e1a439736248e92bd41cd38f53b003192d53fa9f Mon Sep 12 17:00:17 2022 -0700
oops, take out a test track
- lines changed 2, context: html, text, full: html, text
3f76453673b9825c8057d3f16f2c4dd12800daab Tue Sep 13 14:25:13 2022 -0700
added PCR amplicon track to mpxvRivers
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
- lines changed 1, context: html, text, full: html, text
66d28199bb0698ae1c041e04736065712f014394 Mon Sep 12 20:30:23 2022 -0700
Spell Anna Niewiadomska's name correctly
- src/hg/utils/automation/asmHubChainNet.pl
- lines changed 4, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/asmHubChainNetComposite.pl
- lines changed 4, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/asmHubChainNetTrackDb.pl
- lines changed 11, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/asmHubChainNetTrackDb.sh
- lines changed 19, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/asmHubChromAlias.pl
- lines changed 19, context: html, text, full: html, text
f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 13, context: html, text, full: html, text
5308f161d60d310ffe5a80e7755e835ff7ea7a9f Tue Sep 13 12:47:32 2022 -0700
OK to allow duplicate names no redmine
- lines changed 4, context: html, text, full: html, text
0f9627d32b1a95d56c1078595924d387375e487d Tue Sep 13 14:37:39 2022 -0700
the chromAlias needs to know about the NCBI asmId refs #29811
- src/hg/utils/automation/asmHubGatewayPage.pl
- lines changed 4, context: html, text, full: html, text
ad8d6746d5d68ff4e893262d2ff28d9b2a71ac26 Mon Sep 12 11:45:58 2022 -0700
no longer any need for asmHubName argument to gateway page no redmine
- lines changed 7, context: html, text, full: html, text
2248d4012416d220927d54ea0c47295560792625 Mon Sep 12 22:06:58 2022 -0700
now working through gatewayPage although it needs to have URLs for downloads adjusted refs #29811
- src/hg/utils/automation/asmHubNcbiGene.pl
- lines changed 10, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 23, context: html, text, full: html, text
9595301c34b8e4818baa37a72eff7e5cbfcfcb4e Tue Sep 13 13:20:15 2022 -0700
now working thru trackDb although the generated html needs to be fixed up refs #29811
- lines changed 21, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- lines changed 2, context: html, text, full: html, text
729ef3108c56a032423a2a3d47f454d671d1a89c Thu Sep 15 18:31:43 2022 -0700
remove debug statement not needed no redmine
- src/hg/utils/automation/asmHubWindowMasker.pl
- lines changed 3, context: html, text, full: html, text
4d29ce62c5c76ed62d132f9e2ed05cfa61f7fc1a Fri Sep 16 10:04:48 2022 -0700
can not use bare dollar sign in html text causes confusion for trackDb make refs #30012
- src/hg/utils/automation/doAssemblyHub.pl
- lines changed 12, context: html, text, full: html, text
ad8d6746d5d68ff4e893262d2ff28d9b2a71ac26 Mon Sep 12 11:45:58 2022 -0700
no longer any need for asmHubName argument to gateway page no redmine
- lines changed 38, context: html, text, full: html, text
03886581a00e4d626316a657c170287b1f266e35 Mon Sep 12 15:55:14 2022 -0700
beginning a oneAndDone browser build script and therefore adding a new argument to the assembly build for a concise UCSC style dbName refs #29811
- lines changed 14, context: html, text, full: html, text
f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 9, context: html, text, full: html, text
2248d4012416d220927d54ea0c47295560792625 Mon Sep 12 22:06:58 2022 -0700
now working through gatewayPage although it needs to have URLs for downloads adjusted refs #29811
- lines changed 4, context: html, text, full: html, text
8fcf6d7d3fd31a5f0ff9d1793ab00eec67c7b04d Mon Sep 12 22:12:21 2022 -0700
now working thru gc5Base refs #29811
- lines changed 51, context: html, text, full: html, text
7f813719b7ad2dde53149de49c2ec989b9630ea7 Tue Sep 13 12:09:58 2022 -0700
now working through augustus step refs #29811
- lines changed 3, context: html, text, full: html, text
9595301c34b8e4818baa37a72eff7e5cbfcfcb4e Tue Sep 13 13:20:15 2022 -0700
now working thru trackDb although the generated html needs to be fixed up refs #29811
- lines changed 1, context: html, text, full: html, text
0f9627d32b1a95d56c1078595924d387375e487d Tue Sep 13 14:37:39 2022 -0700
the chromAlias needs to know about the NCBI asmId refs #29811
- lines changed 9, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/automation/oneAndDoneBrowser.sh
- lines changed 175, context: html, text, full: html, text
03886581a00e4d626316a657c170287b1f266e35 Mon Sep 12 15:55:14 2022 -0700
beginning a oneAndDone browser build script and therefore adding a new argument to the assembly build for a concise UCSC style dbName refs #29811
- lines changed 18, context: html, text, full: html, text
f9ce722d011fb87c9f61a4d892b9140ef7fa9047 Mon Sep 12 20:38:56 2022 -0700
now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811
- lines changed 11, context: html, text, full: html, text
7f813719b7ad2dde53149de49c2ec989b9630ea7 Tue Sep 13 12:09:58 2022 -0700
now working through augustus step refs #29811
- lines changed 40, context: html, text, full: html, text
92509db0231e9b1ae83aa0c85182883dd8eabc9b Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811
- src/hg/utils/otto/omim/makefile
- lines changed 1, context: html, text, full: html, text
806ffeed2a266ddda82a124a90ce365095d66bd2 Thu Sep 15 11:02:44 2022 -0700
oops, broke validateOmim.sh with an earlier change
- src/hg/utils/otto/omim/validateOmim.sh
- lines changed 3, context: html, text, full: html, text
806ffeed2a266ddda82a124a90ce365095d66bd2 Thu Sep 15 11:02:44 2022 -0700
oops, broke validateOmim.sh with an earlier change
- src/inc/srcVersion.h
- lines changed 1, context: html, text, full: html, text
8eb698a50a97e1da02a8df3ebbc26379273dafc8 Mon Sep 19 10:22:28 2022 -0700
New version number v437
- src/index/makefile
- lines changed 2, context: html, text, full: html, text
90cfcb6d83cbbc97519069d0f5175c258f9a059c Sun Sep 11 20:38:12 2022 -0700
added command to do multiple trix index searches from a file
- src/index/trixMultiSearch/makefile
- lines changed 4, context: html, text, full: html, text
90cfcb6d83cbbc97519069d0f5175c258f9a059c Sun Sep 11 20:38:12 2022 -0700
added command to do multiple trix index searches from a file
- src/index/trixMultiSearch/trixMultiSearch.c
- lines changed 88, context: html, text, full: html, text
90cfcb6d83cbbc97519069d0f5175c258f9a059c Sun Sep 11 20:38:12 2022 -0700
added command to do multiple trix index searches from a file
- src/lib/obscure.c
- lines changed 2, context: html, text, full: html, text
ef238f93d0c9ff7ce3debc79bbb880ff5ee1a2be Mon Sep 12 14:41:09 2022 -0700
readInGulp only works on regular files, reading from a pipe returns an empty result. Generate an error if one attempts to read from a pipe. Perhaps this should be recoded to read to EOF if it is not a regular file
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
ca58c1d2be568d10dcc04244f29c54a1783d7ccf Mon Sep 19 10:20:28 2022 -0700
v437 final build, refs #29979
- lines changed: 3009
- files changed: 86