All File Changes
v289_base to v290_preview (2013-09-09 to 2013-09-16) v290
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
- lines changed 19, context: html, text, full: html, text
Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
- src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
- lines changed 21, context: html, text, full: html, text
Making it so polls for new work every 30 seconds instead of every 60. Removing need for synchronization signals in FIFO to end with new line.
- src/hg/encode3/encodeDataWarehouse/edwRunOnIds/edwRunOnIds.c
- lines changed 59, context: html, text, full: html, text
Seems to work. Best used with edwTempJob.
- src/hg/encode3/encodeDataWarehouse/edwRunOnIds/makefile
- lines changed 4, context: html, text, full: html, text
Seems to work. Best used with edwTempJob.
- src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
- lines changed 1, context: html, text, full: html, text
Coping with new parameter for edwLib routine.
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
- lines changed 8, context: html, text, full: html, text
Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
- lines changed 38, context: html, text, full: html, text
First cut at putting in 'stop upload' button.
- lines changed 5, context: html, text, full: html, text
Doing clean up of temp files after user stops an upload early.
- src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
- lines changed 2, context: html, text, full: html, text
Improving 'enriched in' display in case where it is not set in manifest.
- src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
- lines changed 54, context: html, text, full: html, text
First cut at putting in 'stop upload' button.
- src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
- lines changed 3, context: html, text, full: html, text
First cut at putting in 'stop upload' button.
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
- lines changed 2, context: html, text, full: html, text
Making readSizeMin/Max be integers rather than doubles.
- src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c
- lines changed 142, context: html, text, full: html, text
Redoing with improved parser generator.
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
- lines changed 3, context: html, text, full: html, text
Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
- lines changed 9, context: html, text, full: html, text
First cut at putting in 'stop upload' button.
- lines changed 1, context: html, text, full: html, text
Fixed uninitialized variable warning.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
- lines changed 3, context: html, text, full: html, text
Making readSizeMin/Max be integers rather than doubles.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
- lines changed 7, context: html, text, full: html, text
Making readSizeMin/Max be integers rather than doubles.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
- lines changed 3, context: html, text, full: html, text
Making readSizeMin/Max be integers rather than doubles.
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw
- lines changed 9, context: html, text, full: html, text
Adding another email for Chin, and also some male & female specific assemblies for mouse and human.
- src/hg/hgLogin/hgLogin.c
- lines changed 1, context: html, text, full: html, text
Docs #8293 hgLogin password screen instructionsChange the "Current Password" UI text to "Current or Emailed Password"
- src/hg/hgTracks/snakeTrack.c
- lines changed 11, context: html, text, full: html, text
first pass at making dup bars in snakes into rainhows
- lines changed 2, context: html, text, full: html, text
thicken up the duplication bars in snake tracks
- lines changed 20, context: html, text, full: html, text
use a different palette for duplication bars in snakes
- src/hg/hgVai/hgVai.c
- lines changed 341, context: html, text, full: html, text
Adding 'Artificial Example Variants' as an option for variant track.Since there is now at least one source of variants from which to choose,
we no longer need to hide the rest of the UI until the user provides
some variants.
The variants are generated from genes in the user's cart position if
possible. Variants are cached in trash files unique to database and
cart position.
refs #11110
- src/hg/hgc/hgc.c
- lines changed 118, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/htdocs/ENCODE/FAQ/index.html
- lines changed 1, context: html, text, full: html, text
Correcting typo for ENCODE FAQ page
- lines changed 2, context: html, text, full: html, text
Adding resource link to cv.ra in ENCODE FAQ page refs MLQ #11727
- lines changed 4, context: html, text, full: html, text
On second thought, burrying link to confusing cv.ra resource into FAQ question rather than giving top billing on ENCODE FAQ page MLQ refs #11727
- lines changed 1, context: html, text, full: html, text
Adding a comma to new line refs #11727
- lines changed 14, context: html, text, full: html, text
Updating ENCODE FAQ about new UDR method
- src/hg/htdocs/ENCODE/index.html
- lines changed 15, context: html, text, full: html, text
Adding news about new UDR download method
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 77, context: html, text, full: html, text
Adding news about new UDR download method
- src/hg/htdocs/FAQ/FAQlicense.html
- lines changed 3, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/FAQ/FAQmaillist.html
- lines changed 3, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 1, context: html, text, full: html, text
added info for new alpaca assembly (vicPac2)
- lines changed 6, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- lines changed 3, context: html, text, full: html, text
Adding link to genome-mirror google groups
- src/hg/htdocs/admin/mirror.html
- lines changed 105, context: html, text, full: html, text
added new section for UDR
- lines changed 6, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/contacts.html
- lines changed 7, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/goldenPath/credits.html
- lines changed 3, context: html, text, full: html, text
added info for new alpaca assembly (vicPac2)
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 3, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/goldenPath/help/ftp.html
- lines changed 2, context: html, text, full: html, text
Adding further suggestions about rysnc based on MLQ refs #11703
- lines changed 1, context: html, text, full: html, text
Correcting typo about rysnc MLQ refs #11703
- lines changed 1, context: html, text, full: html, text
Correcting another typo about rysnc MLQ refs #11703
- lines changed 5, context: html, text, full: html, text
Adding commas to ftp.html per Code Review refs #11712
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 14, context: html, text, full: html, text
Adding comments about rsync to downloads section of hgTracksHelp.html page per CR refs #11712
- src/hg/htdocs/goldenPath/help/mysql.html
- lines changed 4, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 29, context: html, text, full: html, text
added info for new alpaca assembly (vicPac2)
- lines changed 3, context: html, text, full: html, text
fixed a few formatting errors
- src/hg/htdocs/images/phylo/hg19_100way.png
- lines changed 0, context: html, text, full: html, text
hg19 100way phylo tree diagram refs #10272
- src/hg/htdocs/indexNews.html
- lines changed 43, context: html, text, full: html, text
added info for new alpaca assembly (vicPac2)
- lines changed 0, context: html, text, full: html, text
fixed a few formatting errors
- src/hg/htdocs/mirror.html
- lines changed 3, context: html, text, full: html, text
Emphasizing public searchable mailing list in red text refs #11597
- src/hg/inc/dgvPlus.h
- lines changed 84, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/inc/encode3/encode3Valid.h
- lines changed 3, context: html, text, full: html, text
Adding encode3IsGzip routine to see if a file starts with gzip signature.
- src/hg/lib/annoFormatVep.c
- lines changed 5, context: html, text, full: html, text
Correcting off-by-one intron number; adding recognition of stop_lost caused by inframe_deletion.
- lines changed 1, context: html, text, full: html, text
Wording change in header comment as suggested by b0b.
- src/hg/lib/customFactory.c
- lines changed 1, context: html, text, full: html, text
showing longer error messages in customfactory to better debug mirror problems, see #11733
- src/hg/lib/dgvPlus.as
- lines changed 26, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/lib/dgvPlus.c
- lines changed 255, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/lib/dgvPlus.sql
- lines changed 34, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/lib/encode3/encode3Valid.c
- lines changed 10, context: html, text, full: html, text
Adding encode3IsGzip routine to see if a file starts with gzip signature.
- src/hg/lib/gpFx.c
- lines changed 7, context: html, text, full: html, text
Correcting off-by-one intron number; adding recognition of stop_lost caused by inframe_deletion.
- src/hg/lib/jksql.c
- lines changed 2, context: html, text, full: html, text
Fixing a problem with Ubuntu and other systems where load data LOCAL infile has been disabled by default for mysql clients
- lines changed 2, context: html, text, full: html, text
adding flag to hg.conf to disable LOCAL in mysql commands entirely
- lines changed 14, context: html, text, full: html, text
because Ubuntu currently has a hard time getting pstack to work, I do not want any dumpStack statements that cannot be turned off by a flag in hg.conf
- lines changed 1, context: html, text, full: html, text
renaming to db.neverLocal to keep in line with the other hg.conf directives
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/makeDb/doc/hg18.txt
- lines changed 73, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/makeDb/doc/hg19.txt
- lines changed 64, context: html, text, full: html, text
running lastz panTig1 Amur tiger refs #10272
- lines changed 19, context: html, text, full: html, text
allSin1 lastz done and swapping panTig1 refs #10272
- lines changed 73, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
added new alpaca assembly (vicPac2)
- src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c
- lines changed 3, context: html, text, full: html, text
gbSanity.c (genbank) properly escaping the mysql where clauses
- src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
- lines changed 6, context: html, text, full: html, text
gbSanity.c (genbank) properly escaping the mysql where clauses
- src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c
- lines changed 3, context: html, text, full: html, text
gbSanity.c (genbank) properly escaping the mysql where clauses
- src/hg/makeDb/trackDb/human/clinvar.html
- src/hg/makeDb/trackDb/human/dgvPlus.html
- lines changed 103, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- lines changed 56, context: html, text, full: html, text
Updated DGV composite track description, borrowing some text fromhttp://dgv.tcag.ca/dgv/docs/201306-DGV_Newsletter.pdf .
I will run this by Jeff MacDonald.
refs #11200
- src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
- lines changed 1, context: html, text, full: html, text
adding vicPac2 to placental group
- src/hg/makeDb/trackDb/human/hg19/cons100way.html
- lines changed 447, context: html, text, full: html, text
initial contents, needs updated species list refs #10272
- src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
- lines changed 239, context: html, text, full: html, text
begin display of 100-way conservation track refs #10272
- lines changed 1, context: html, text, full: html, text
temporary track title refs #10272
- lines changed 1, context: html, text, full: html, text
no frames until they are loaded refs #10272
- lines changed 1, context: html, text, full: html, text
ready to display frames refs #10272
- lines changed 2, context: html, text, full: html, text
forgot a couple of organisms on the 100-way refs #10272
- lines changed 8, context: html, text, full: html, text
adding extra clade divisions in the 100-way display refs #10272
- lines changed 43, context: html, text, full: html, text
turn on phastCons wiggle and most conserved elements refs #10272
- lines changed 2, context: html, text, full: html, text
correctly set default codon species and adding hg19_100way.png image refs #10272
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
begin display of 100-way conservation track refs #10272
- lines changed 24, context: html, text, full: html, text
lifted uc16 and ux16 from hg18 for ultra conserved elements to view in 100-way alignment refs #10272
- lines changed 4, context: html, text, full: html, text
add hg18 lifted note and icon to the ultra conserved tracks;
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 40, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- lines changed 17, context: html, text, full: html, text
Changing label of older DGV track for release=alpha.refs #11200
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
- lines changed 3, context: html, text, full: html, text
added vicPac2 to placental group
- lines changed 3, context: html, text, full: html, text
adding vicPac2 to placental group
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 5, context: html, text, full: html, text
adding extra clade divisions in the 100-way display refs #10272
- src/hg/oneShot/freen/freen.c
- lines changed 6, context: html, text, full: html, text
Adding encode3IsGzip routine to see if a file starts with gzip signature.
- src/hg/utils/automation/translateDgvPlus.pl
- lines changed 59, context: html, text, full: html, text
New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
more columns than the older dgv tables.
The track description needs to be updated to make more clear what
DGV gets from dbVar/DGVa and what it adds.
refs #11200
- src/hg/utils/mysqlSecurityCheck/mysqlSecurityCheck.c
- lines changed 2, context: html, text, full: html, text
removing a condition that is not needed.
- src/hg/utils/phyloTrees/113way.commonNames.nh
- lines changed 113, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/hg/utils/phyloTrees/113way.nh
- lines changed 112, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/hg/utils/phyloTrees/113way.scientificNames.nh
- lines changed 113, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/hg/utils/phyloTrees/commonNames.sh
- lines changed 1, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/hg/utils/phyloTrees/makefile
- lines changed 7, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/hg/utils/phyloTrees/scientificNames.sh
- lines changed 1, context: html, text, full: html, text
adding Amur tiger refs #10272
- src/inc/basicBed.h
- lines changed 9, context: html, text, full: html, text
Adding bed4{New,Free,FreeList}.
- src/inc/paraFetch.h
- lines changed 7, context: html, text, full: html, text
Adding parallelFetchInterruptable, which has a callback that checks for interrupt.
- lines changed 5, context: html, text, full: html, text
Adding parallelFetchRemovePartial clean up function.
- src/inc/raToStruct.h
- lines changed 36, context: html, text, full: html, text
Adding support for arrays, and also extraH option to raToStructGen.
- src/lib/basicBed.c
- lines changed 37, context: html, text, full: html, text
Adding bed4{New,Free,FreeList}.
- src/lib/net.c
- lines changed 15, context: html, text, full: html, text
net.c: Adding read and write timeouts to the tcp open. One site was connecting but then failing to send a response and hanging indefinitely.
- src/lib/paraFetch.c
- lines changed 20, context: html, text, full: html, text
Adding parallelFetchInterruptable, which has a callback that checks for interrupt.
- lines changed 9, context: html, text, full: html, text
Adding parallelFetchRemovePartial clean up function.
- src/lib/raToStruct.c
- lines changed 104, context: html, text, full: html, text
Adding support for arrays, and also extraH option to raToStructGen.
- src/parasol/paraNode/paraNode.c
- lines changed 1, context: html, text, full: html, text
ubuntu needs #include <sys/resource.h>
- src/product/README.mysql.setup
- lines changed 14, context: html, text, full: html, text
noting that users should use myisam instead of innodb
- lines changed 23, context: html, text, full: html, text
updating README.mysql.setup with new configuration information regarding LOAD DATA LOCAL INFILE -- since we learned a better way to do it. This works now because of new support for a client side setting to enable LOCAL at connect time in jksql.c
- src/product/ex.hg.conf
- lines changed 2, context: html, text, full: html, text
fixing typos in ex.hg.conf
- src/utils/git-reports/git-reports.c
- lines changed 15, context: html, text, full: html, text
more problems with white space only diffs refs #11571
- lines changed 2, context: html, text, full: html, text
more problems with white space only diffs refs #11571
- src/utils/makefile
- lines changed 2, context: html, text, full: html, text
people need gitFiles in gitTools/ in order to make in htdocs, so gitTools is moving from the UCSC_APPS list to the UTILS_APPLIST
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
preview 1 day for v290 refs #11650
- src/utils/qa/weeklybld/doNewBranch.csh
- lines changed 1, context: html, text, full: html, text
the email address is ann not zweig refs #11650
- src/utils/qa/weeklybld/unsymtrick.csh
- lines changed 1, context: html, text, full: html, text
oops fixed typo in errmsg
- src/utils/raToStructGen/raToStructGen.c
- lines changed 110, context: html, text, full: html, text
Pretty major reworking. Making an enum with symbolic names for the field offsets. Adding computed field option so not all fields need to be addressed by parser. Generating more functions. The code generated passes visual inspection but has not been compiled and tested.
- lines changed 44, context: html, text, full: html, text
Got output to compile. Added a test script.
- lines changed 18, context: html, text, full: html, text
Adding support for arrays, and also extraH option to raToStructGen.
- src/utils/raToStructGen/test.as
- lines changed 33, context: html, text, full: html, text
Starting to add test cases.
- src/utils/raToStructGen/testIt
- lines changed 6, context: html, text, full: html, text
Got output to compile. Added a test script.
- src/utils/raToStructGen/testOut/makefile
- lines changed 3, context: html, text, full: html, text
Got output to compile. Added a test script.
- src/utils/raToStructGen/testOut/test.as
- src/utils/raToStructGen/testOut/test.expected
- src/utils/raToStructGen/testOut/test.ra
- src/utils/raToStructGen/testOut/testRaToStruct.c
- lines changed 301, context: html, text, full: html, text
Streamlining unit test.
- lines changed 14, context: html, text, full: html, text
Adding support for arrays, and also extraH option to raToStructGen.
- lines changed: 4382
- files changed: 147