All File Changes

v296_preview2 to v296_base (2014-02-17 to 2014-02-24) v296

• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/edwFakeEncode2Submit.c
  • lines changed 208, context: html, text, full: html, text
    ode and necessary data files checked in for encodedcc RM# 1079 EDW updating issue 1 and 2.
    Create edwSubmit row for encode2 files imported into encode3 EDW.
    At the same time, update the edwFile row with the newly created edwSubmit id and real upload time during the encode2 project.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/encode2labs.tsv
  • lines changed 40, context: html, text, full: html, text
    ode and necessary data files checked in for encodedcc RM# 1079 EDW updating issue 1 and 2.
    Create edwSubmit row for encode2 files imported into encode3 EDW.
    At the same time, update the edwFile row with the newly created edwSubmit id and real upload time during the encode2 project.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/hg19_encode2_date.tab
  • lines changed 20834, context: html, text, full: html, text
    ode and necessary data files checked in for encodedcc RM# 1079 EDW updating issue 1 and 2.
    Create edwSubmit row for encode2 files imported into encode3 EDW.
    At the same time, update the edwFile row with the newly created edwSubmit id and real upload time during the encode2 project.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/makefile
  • lines changed 4, context: html, text, full: html, text
    ode and necessary data files checked in for encodedcc RM# 1079 EDW updating issue 1 and 2.
    Create edwSubmit row for encode2 files imported into encode3 EDW.
    At the same time, update the edwFile row with the newly created edwSubmit id and real upload time during the encode2 project.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/mm9_encode2_date.tab
  • lines changed 4696, context: html, text, full: html, text
    ode and necessary data files checked in for encodedcc RM# 1079 EDW updating issue 1 and 2.
    Create edwSubmit row for encode2 files imported into encode3 EDW.
    At the same time, update the edwFile row with the newly created edwSubmit id and real upload time during the encode2 project.
    
• src/hg/hgMirror/hgMirror
  • lines changed 40, context: html, text, full: html, text
    add cancel button to download progress page and refuse to download if adownload is already going on, as to Matt's suggestion, refs #11957
    note 105
    
  • lines changed 61, context: html, text, full: html, text
    adding a DB dropdown box selector to hgMirror, refs #11957
  • lines changed 1, context: html, text, full: html, text
    forgot to pass db through with hidden variable, refs #11957
  • lines changed 2, context: html, text, full: html, text
    fixing a warning message in hgMirror, refs #11957
  • lines changed 1, context: html, text, full: html, text
    adding two more tables to hgMirror, refs #11957
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 17, context: html, text, full: html, text
    Following up on UI suggestion from code review. Move checkbox for cleaner page (motif highligting)
  • lines changed 1, context: html, text, full: html, text
    Fix typo in error message.
• src/hg/hgTracks/hgTracks.c
  • lines changed 27, context: html, text, full: html, text
    Fixes ##12648. This fixes a problem caused by a new glibc malloc policy in which a new heap arena of 64MB is created per thread instead of per cpu. A track hub with many visible will use up to 100 threads, CGI can waste 15GB of RAM and rlimits on RR cause out-of-memory failures. The fix is to explicitly set the maximum number of arenas to 8 using a new malloc option before launching threads.
• src/hg/hgc/wiggleClick.c
  • lines changed 2, context: html, text, full: html, text
    making bigwig hgc page gbib ready, refs #11957 note 105
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 215, context: html, text, full: html, text
    adding gbib install help page, refs #11957
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    Rewording examples for composite tracks to use compositeTrack on, ref #11271
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    made a few corrections per code review #12706
  • lines changed 1, context: html, text, full: html, text
    added missing period, refs #12706
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 6, context: html, text, full: html, text
    Add factorSource filterBy setting description
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 11, context: html, text, full: html, text
    Add factorSource filterBy setting description
  • lines changed 5, context: html, text, full: html, text
    Rewording examples for composite tracks to use compositeTrack on, ref #11271
• src/hg/htdocs/images/gbib-add.png
  • lines changed 0, context: html, text, full: html, text
    adding gbib install help page, refs #11957
• src/hg/htdocs/images/gbib-powerOff.png
  • lines changed 0, context: html, text, full: html, text
    adding gbib install help page, refs #11957
• src/hg/htdocs/images/gbib-shared.png
  • lines changed 0, context: html, text, full: html, text
    adding gbib install help page, refs #11957
• src/hg/htdocs/images/gbib-start.png
  • lines changed 0, context: html, text, full: html, text
    adding gbib install help page, refs #11957
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v296
• src/hg/lib/customFactory.c
  • lines changed 3, context: html, text, full: html, text
    Fix to problem with customtrack bed detail files. refs #12721
  • lines changed 21, context: html, text, full: html, text
    Fixes ##12648. This fixes a problem caused by a new glibc malloc policy in which a new heap arena of 64MB is created per thread instead of per cpu. A track hub with many visible will use up to 100 threads, CGI can waste 15GB of RAM and rlimits on RR cause out-of-memory failures. The fix is to explicitly set the maximum number of arenas to 8 using a new malloc option before launching threads.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    making bigbed hgc pages gbib-ready, refs #11957
• src/hg/lib/lav.c
  • lines changed 3, context: html, text, full: html, text
    fix a bug that caused the first letter of some sequence names to bechopped off.
    
• src/hg/lib/targetDb.c
  • lines changed 22, context: html, text, full: html, text
    making hgPcr target dbs work in the browserbox, refs #11957
• src/hg/lib/trackDbCustom.c
  • lines changed 8, context: html, text, full: html, text
    making hgTables gbib ready, refs #11957
  • lines changed 3, context: html, text, full: html, text
    Matt luckily immediately found the bug in previous commit, refs #11957
• src/hg/lib/web.c
  • lines changed 6, context: html, text, full: html, text
    making phoneHome send a different string for the gbib, refs #11957
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 75, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 581, context: html, text, full: html, text
    Add Factorbook motif tables, used in TF ChIP clusters track
• src/hg/makeDb/doc/hg18.txt
  • lines changed 19, context: html, text, full: html, text
    added hg18 to hg38 liftOver refs #12722
• src/hg/makeDb/doc/hg38.txt
  • lines changed 19, context: html, text, full: html, text
    add trackDb entries and doc for the lifted over version of wgEncodeGencodeV19
  • lines changed 10, context: html, text, full: html, text
    tweak lifted GENCODE track on hg38 to have pennant icon and propercontents
    
  • lines changed 12, context: html, text, full: html, text
    add preliminary version of the tRNA track for UCSC genes build on hg38
  • lines changed 1, context: html, text, full: html, text
    correct table name for the hg38ContigDiff track on hg19 browser refs #11681
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 13, context: html, text, full: html, text
    Fix to problem with customtrack bed detail files. refs #12721
• src/hg/makeDb/hgLoadBed/tests/RunTest.sh
  • lines changed 2, context: html, text, full: html, text
    Fix to problem with customtrack bed detail files. refs #12721
• src/hg/makeDb/hgLoadBed/tests/bed6Detail.txt.gz
  • lines changed 0, context: html, text, full: html, text
    Fix to problem with customtrack bed detail files. refs #12721
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgSegmentation.ra
  • lines changed 168, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 185, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
  • lines changed 8, context: html, text, full: html, text
    Add Display Conventions to describe filter control. refs #12259
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.ra
  • lines changed 169, context: html, text, full: html, text
    First cut of ENCODE Segmentation track (from analysis hub). res #12259
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 22, context: html, text, full: html, text
    Staging ENCODE Txn ChIPV4 Motif on beta, and making small changes to track html Refs #12551
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 13, context: html, text, full: html, text
    Staging ENCODE Txn ChIPV4 Motif on beta, and making small changes to track html Refs #12551
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    add trackDb entries and doc for the lifted over version of wgEncodeGencodeV19
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    add trackDb entries and doc for the lifted over version of wgEncodeGencodeV19
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.ra
  • lines changed 262, context: html, text, full: html, text
    add trackDb entries and doc for the lifted over version of wgEncodeGencodeV19
  • lines changed 1, context: html, text, full: html, text
    tweak lifted GENCODE track on hg38 to have pennant icon and propercontents
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Making mm10 snp137 hidden by default, and snp138 on dense by default, refs #12490
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 6, context: html, text, full: html, text
    Revoke SYDH MEL H3K27ac ChIP experiment (EM003324). Lab says it was performed with incorrect antibody. refs #10465
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html
  • lines changed 7, context: html, text, full: html, text
    Revoke SYDH MEL H3K27ac ChIP experiment (EM003324). Lab says it was performed with incorrect antibody. refs #10465
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
  • lines changed 19, context: html, text, full: html, text
    Revoke SYDH MEL H3K27ac ChIP experiment (EM003324). Lab says it was performed with incorrect antibody. refs #10465
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 163, context: html, text, full: html, text
    removing haussler wetlab specific data from repeats2 browser and addinga track so one can search for "chromosome" names
    
• src/lib/gff3.c
  • lines changed 4, context: html, text, full: html, text
    Fixed bug in validating GFF3 attribute tag names.
  • lines changed 1, context: html, text, full: html, text
    added check the GFF3 Derives_from attributes is only specified once per record
• src/lib/twoBit.c
  • lines changed 6, context: html, text, full: html, text
    changed incorrectly inline functions to static, this confuses clang on OS/X
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v295 final build refs #12535

• lines changed: 28022
• files changed: 65