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
  • lines changed 1, context: html, text, full: html, text
    Correcting typo
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 77, context: html, text, full: html, text
    Adding news about new UDR download method
  • lines changed 1, context: html, text, full: html, text
    Correcting typo
• 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
    made correction to links
  • 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 3, context: html, text, full: html, text
    made correction to links
  • 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 39, context: html, text, full: html, text
    new track: ncbi clinvar
  • 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
  • lines changed 38, context: html, text, full: html, text
    new track: ncbi clinvar
• 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 11, context: html, text, full: html, text
    new track: ncbi clinvar
  • 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.
  • lines changed 33, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testIt
  • lines changed 6, context: html, text, full: html, text
    Got output to compile. Added a test script.
  • lines changed 8, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/makefile
  • lines changed 3, context: html, text, full: html, text
    Got output to compile. Added a test script.
  • lines changed 1, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.as
  • lines changed 34, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.expected
  • lines changed 1, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.ra
  • lines changed 27, context: html, text, full: html, text
    Streamlining unit test.
• 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