All File Changes

v310_base to v311_preview (2015-01-05 to 2015-01-12) v311

• src/hg/encode3/eap/eapMetaSync/eapMetaSync.c
  • lines changed 5, context: html, text, full: html, text
    Extended jsonWriteObjectStart to support an optional preceding tag;added jsonWriteStringf, jsonWriteBoolean, jsonWriteValueLabelList, and
    jsonWriteSlNameList. To be used by cartJson and hgAi.
    
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    support '=' and 'X' in BAM cigars #14593
• src/hg/hgTables/bigBed.c
  • lines changed 4, context: html, text, full: html, text
    Added a 'data last updated' tag to table display after 'Row Count' and before 'Format description'
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    Added a 'data last updated' tag to table display after 'Row Count' and before 'Format description'
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    support '=' and 'X' in BAM cigars #14593
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 150, context: html, text, full: html, text
    bring up to date with Robert's latest code to help fix bugs refs #9741
• src/hg/hgTracks/simpleTracks.c
  • lines changed 16, context: html, text, full: html, text
    fixed scaling problem when zoomed way into very long features (#14505note 33)
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 35, context: html, text, full: html, text
    stop putting stuff in the cart when displaying wigMaf tracks. #14622
• src/hg/hgVai/hgVai.c
  • lines changed 13, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/hg/hgVai/libifyMe.c
  • lines changed 232, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/hg/hgVai/libifyMe.h
  • lines changed 21, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 172, context: html, text, full: html, text
    Fixing up links on the credits page. refs #14395
  • lines changed 3, context: html, text, full: html, text
    Fixing link I missed in last commit, refs #14395
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 11, context: html, text, full: html, text
    fixed some things per code review. refs #14611
  • lines changed 5, context: html, text, full: html, text
    adding link to YouTube channel and adding pointer to training page
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 40, context: html, text, full: html, text
    Added some new entries, updated some existing entries.
• src/hg/htdocs/images/Macaca_fascicularis.jpg
  • lines changed 0, context: html, text, full: html, text
    photo from Rhett A. Butler mongabay.com refs #11174
• src/hg/htdocs/images/training/titleInformatics.gif
  • lines changed 0, context: html, text, full: html, text
    Adding bob's modified logo image. refs #14408
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Fixing link to training page in top bar. refs #14525
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    fixed some things per code review. refs #14611
  • lines changed 6, context: html, text, full: html, text
    adding link to YouTube channel and adding pointer to training page
• src/hg/htdocs/mirror.html
  • lines changed 13, context: html, text, full: html, text
    Milwaukee mirror is no longer available
• src/hg/htdocs/training/vids/index.html
  • lines changed 25, context: html, text, full: html, text
    Fixing target=_blank for transcript links. refs #14542
• src/hg/inc/cart.h
  • lines changed 7, context: html, text, full: html, text
    Adding cartEmptyShellNoContent so a CGI can postpone the Content-Type decision to doMiddle.
• src/hg/inc/cartJson.h
  • lines changed 58, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/inc/customTrack.h
  • lines changed 3, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/inc/hAnno.h
  • lines changed 31, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/hg/inc/hdb.h
  • lines changed 13, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/lib/cart.c
  • lines changed 27, context: html, text, full: html, text
    Adding cartEmptyShellNoContent so a CGI can postpone the Content-Type decision to doMiddle.
• src/hg/lib/cartJson.c
  • lines changed 731, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/lib/customTrack.c
  • lines changed 9, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/lib/hAnno.c
  • lines changed 303, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/hg/lib/hdb.c
  • lines changed 81, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/lib/hui.c
  • lines changed 9, context: html, text, full: html, text
    handling case that user loads the whole page, refs #14561
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
  • lines changed 1, context: html, text, full: html, text
    Adding cartJson lib module (to be used by hgAi). It parses JSON commands andreturns information in JSON to support moving more UI actions into Javascript.
    The lib supports basic queries and actions like getting a list of the groups,
    tracks and tables (incl. hubs & CTs) and changing the clade/genome/db. Apps/CGIs
    can extend it to handle new commands by registering handler functions.
    
• src/hg/makeDb/doc/hg38/scanAssemblyReport.pl
  • lines changed 87, context: html, text, full: html, text
    finding equivalent names in GCA_000001405.17_GRCh38.p2_assembly_report.txt refs #14167
• src/hg/makeDb/doc/macFas5/initialBuild.txt
  • lines changed 480, context: html, text, full: html, text
    ready for pushQ after genbank is loaded refs #11174
• src/hg/makeDb/doc/macFas5/ucscCompositeAgp.pl
  • lines changed 44, context: html, text, full: html, text
    ready for pushQ after genbank is loaded refs #11174
• src/hg/makeDb/doc/macFas5/unlocalized.pl
  • lines changed 66, context: html, text, full: html, text
    ready for pushQ after genbank is loaded refs #11174
• src/hg/makeDb/doc/macFas5/unplaced.pl
  • lines changed 34, context: html, text, full: html, text
    ready for pushQ after genbank is loaded refs #11174
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 22, context: html, text, full: html, text
    Added nasLar1; refs #14437
  • lines changed 22, context: html, text, full: html, text
    Added macFas5; refs #11174
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added nasLar1; refs #14437
  • lines changed 2, context: html, text, full: html, text
    Added macFas5; refs #11174
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    adding panPan1 refs #8231
  • lines changed 7, context: html, text, full: html, text
    tweaking panPan1 to be clean joinerCheck refs #8231
  • lines changed 16, context: html, text, full: html, text
    adding macFas5 rules refs #11174
• src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
  • lines changed 19, context: html, text, full: html, text
    adding new sequences KP260799.1 KP260800.1 KP260801.1 KP260802.1 KP271018.1 KP271019.1 KP271020.1 refs #14278
  • lines changed 2, context: html, text, full: html, text
    fixup isolate description for two refs #14278
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 1, context: html, text, full: html, text
    adding new sequences KP260799.1 KP260800.1 KP260801.1 KP260802.1 KP271018.1 KP271019.1 KP271020.1 refs #14278
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding new sequences KP260799.1 KP260800.1 KP260801.1 KP260802.1 KP271018.1 KP271019.1 KP271020.1 refs #14278
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 1, context: html, text, full: html, text
    Adding link to bigBed description on clinvar and hgmd track description pages, refs #14411 #14045
• src/hg/makeDb/trackDb/human/hg19/peptideAtlas.html
  • lines changed 1, context: html, text, full: html, text
    Fix URL in track description. refs #14054
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adjusting release tags for peptideAtlas track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 4, context: html, text, full: html, text
    Update email for Michael Hoffman
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 448, context: html, text, full: html, text
    documentation for 17-way primates refs #14560
  • lines changed 19, context: html, text, full: html, text
    description page for 17-way conservation refs #14560
• src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html
  • lines changed 2, context: html, text, full: html, text
    description page for 17-way conservation refs #14560
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
  • lines changed 2, context: html, text, full: html, text
    description page for 17-way conservation refs #14560
• src/hg/makeDb/trackDb/human/hgmd.html
  • lines changed 2, context: html, text, full: html, text
    Adding link to bigBed description on clinvar and hgmd track description pages, refs #14411 #14045
• src/hg/makeDb/trackDb/joinedRmsk.ra
  • lines changed 1, context: html, text, full: html, text
    allow pack squish modes refs #9741
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
  • lines changed 2, context: html, text, full: html, text
    allow pack squish modes refs #9741
• src/hg/makeDb/trackDb/macaca/macFas5/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.ra refs #11174
• src/hg/makeDb/trackDb/macaca/macFas5/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files from makeGenomeDb.ra refs #11174
• src/hg/makeDb/trackDb/macaca/macFas5/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.ra refs #11174
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.ra refs #11174
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding macFas5 to the build refs #11174
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 5, context: html, text, full: html, text
    documentation for 17-way primates refs #14560
  • lines changed 18, context: html, text, full: html, text
    description page for 17-way conservation refs #14560
• src/hg/mouseStuff/axtChain/axtChain.c
  • lines changed 2, context: html, text, full: html, text
    have axtChain error on PSLs with explicty target, which it does not support
• src/hg/oneShot/ga4ghToBed/ga4ghToBed.c
  • lines changed 1, context: html, text, full: html, text
    Extended jsonWriteObjectStart to support an optional preceding tag;added jsonWriteStringf, jsonWriteBoolean, jsonWriteValueLabelList, and
    jsonWriteSlNameList. To be used by cartJson and hgAi.
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 33, context: html, text, full: html, text
    GFF3 allows CDS as a child of transcript as well as mRNA, support create genePred with CDS annotation from such GFF3 files
• src/hg/utils/gff3ToGenePred/tests/expected/transcriptCdsParentTest.gp
  • lines changed 1, context: html, text, full: html, text
    GFF3 allows CDS as a child of transcript as well as mRNA, support create genePred with CDS annotation from such GFF3 files
• src/hg/utils/gff3ToGenePred/tests/input/transcriptCdsParent.gff3
  • lines changed 7, context: html, text, full: html, text
    GFF3 allows CDS as a child of transcript as well as mRNA, support create genePred with CDS annotation from such GFF3 files
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    GFF3 allows CDS as a child of transcript as well as mRNA, support create genePred with CDS annotation from such GFF3 files
• src/hg/utils/liftList/liftList.c
  • lines changed 106, context: html, text, full: html, text
    A utility designed to lift files from one build to another, was used for lifting wgEncode tracks from hg19 to hg38
• src/hg/utils/liftList/liftingScript
  • lines changed 6, context: html, text, full: html, text
    A utility designed to lift files from one build to another, was used for lifting wgEncode tracks from hg19 to hg38
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 39, context: html, text, full: html, text
    clinvar replace -1 and - with empty string, refs #14045. Also fix the broken go-one-month-back function
  • lines changed 11, context: html, text, full: html, text
    one more bugfix to clinvar otto updates, they must have changed the fieldsagain, plus colon fix after refs #14045, plus moving files to archive/
    
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 1, context: html, text, full: html, text
    one more bugfix to clinvar otto updates, they must have changed the fieldsagain, plus colon fix after refs #14045, plus moving files to archive/
    
• src/inc/annoFormatTab.h
  • lines changed 5, context: html, text, full: html, text
    Added annoFormatTabSetColumnVis so that columns can be selectively included in output.
• src/inc/annoStreamBigWig.h
  • lines changed 3, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/inc/annoStreamer.h
  • lines changed 10, context: html, text, full: html, text
    Added annoStreamer{Get,Set}Name so that we're not stuck with awfully long filenames etc.
• src/inc/jsonParse.h
  • lines changed 3, context: html, text, full: html, text
    Fixed the behavior of jsonStringEscape for \n, \r and \t. Previously,it was inserting a \ followed by the actual \n / \r / \t character, which
    was not actually escaping it. A \n needs to be replaced by a \ followed by
    an n not \n. Also added jsonOptionalBooleanField.
    
• src/inc/jsonWrite.h
  • lines changed 15, context: html, text, full: html, text
    Extended jsonWriteObjectStart to support an optional preceding tag;added jsonWriteStringf, jsonWriteBoolean, jsonWriteValueLabelList, and
    jsonWriteSlNameList. To be used by cartJson and hgAi.
    
• src/lib/annoFormatTab.c
  • lines changed 77, context: html, text, full: html, text
    Added annoFormatTabSetColumnVis so that columns can be selectively included in output.
• src/lib/annoStreamBigWig.c
  • lines changed 7, context: html, text, full: html, text
    Libified code from hgVai/libifyMe.c to lib/hAnno.c in anticipationof sharing code with hgAi. Also added hAnnoGetAutoSqlForTdb for hgAi.
    
• src/lib/annoStreamer.c
  • lines changed 13, context: html, text, full: html, text
    Added annoStreamer{Get,Set}Name so that we're not stuck with awfully long filenames etc.
• src/lib/jsonParse.c
  • lines changed 25, context: html, text, full: html, text
    Fixed the behavior of jsonStringEscape for \n, \r and \t. Previously,it was inserting a \ followed by the actual \n / \r / \t character, which
    was not actually escaping it. A \n needs to be replaced by a \ followed by
    an n not \n. Also added jsonOptionalBooleanField.
    
• src/lib/jsonWrite.c
  • lines changed 83, context: html, text, full: html, text
    Extended jsonWriteObjectStart to support an optional preceding tag;added jsonWriteStringf, jsonWriteBoolean, jsonWriteValueLabelList, and
    jsonWriteSlNameList. To be used by cartJson and hgAi.
    
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    build pslPosTarget as a standard tool
• src/utils/pslPosTarget/pslPosTarget.c
  • lines changed 21, context: html, text, full: html, text
    build pslPosTarget as a standard tool
• src/utils/qa/makeCytoBandIdeo.csh
  • lines changed 2, context: html, text, full: html, text
    can not use commands that fail in a csh -fe script since any command that fails stops the script immediately refs #11174
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v311 preview1 refs #14648

• lines changed: 3978
• files changed: 95