All File Changes

v279_base to v280_preview (2013-02-12 to 2013-02-19) v280

• src/hg/altSplice/altSplice/makefile
  • lines changed 4, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgBlat/makefile
  • lines changed 2, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgGateway/hgGateway.c
  • lines changed 6, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
  • lines changed 1, context: html, text, full: html, text
    oops, left out an include #8072
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgKnownGeneList/makefile
  • lines changed 1, context: html, text, full: html, text
    Fixing a few makefiles that were ignoring or overwriting the HG_WARN from inc/common.mk .
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTables/filterFields.c
  • lines changed 12, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTables/hgTables.c
  • lines changed 52, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTables/joining.c
  • lines changed 10, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTables/mainPage.c
  • lines changed 8, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTracks/hgTracks.c
  • lines changed 23, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgTracks/wigCommon.h
  • lines changed 1, context: html, text, full: html, text
    Adding transparency setting to wigCart.
• src/hg/hgTracks/wigTrack.c
  • lines changed 5, context: html, text, full: html, text
    Adding transparency setting to wigCart.
  • lines changed 36, context: html, text, full: html, text
    Some refactoring to make it easier to do normalized transparency.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 4, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/hgc/bamClick.c
  • lines changed 3, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 19, context: html, text, full: html, text
    Some reorg of layout of Downloads page for ENCODE. #10047: Portal: Add section to downloads for analysis files on EBI track hub
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 88, context: html, text, full: html, text
    Making changes to ENCODE/downloads.html page RM#10047 adding Analysis Working Group Files
  • lines changed 127, context: html, text, full: html, text
    Some reorg of layout of Downloads page for ENCODE. #10047: Portal: Add section to downloads for analysis files on EBI track hub
  • lines changed 2, context: html, text, full: html, text
    Fix problematic table header. #10047: Portal: Add section to downloads for analysis files on EBI track hub
  • lines changed 9, context: html, text, full: html, text
    Removing double quotes at end of href= quote-address-quote-quote -> quote-address-quote RM#10047
  • lines changed 10, context: html, text, full: html, text
    Moved GIS ChIA-PET from Chromatin Accessibility section to Chromatin Interactions section (redmine #10225)
• src/hg/htdocs/goldenPath/help/customTrackManage.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link to help doc.
• src/hg/htdocs/images/Xiphophorus_Maculatus.jpg
  • lines changed 0, context: html, text, full: html, text
    Photo of southern platyfish - Xiphophorus maculatus from Xiphophorus Genetic Stock Center
  • lines changed 0, context: html, text, full: html, text
    rename Xiphophorus_Maculatus.jpg -> Xiphophorus_maculatus.jpg
• src/hg/htdocs/images/Xiphophorus_maculatus.jpg
  • lines changed 0, context: html, text, full: html, text
    rename Xiphophorus_Maculatus.jpg -> Xiphophorus_maculatus.jpg
• src/hg/htdocs/indexNews.html
  • lines changed 0, context: html, text, full: html, text
    Minor edit as per code review #10184
• src/hg/inc/annoGratorGpVar.h
  • lines changed 4, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/inc/gpFx.h
  • lines changed 5, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/inc/hubConnect.h
  • lines changed 8, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/inc/jksql.h
  • lines changed 1, context: html, text, full: html, text
    time should be time_t or long but not int, so that the 2030 overflow problem is avoided on 64-bit machines
• src/hg/inc/trackHub.h
  • lines changed 59, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/annoGratorGpVar.c
  • lines changed 66, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/cart.c
  • lines changed 8, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/hdb.c
  • lines changed 91, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/hgFind.c
  • lines changed 14, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/hubConnect.c
  • lines changed 41, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    time should be time_t or long but not int, so that the 2030 overflow problem is avoided on 64-bit machines
• src/hg/lib/mdb.c
  • lines changed 3, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/targetDb.c
  • lines changed 4, context: html, text, full: html, text
    time should be time_t or long but not int, so that the 2030 overflow problem is avoided on 64-bit machines
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 3, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 47, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/hg/lib/trackDbCustom.c
  • lines changed 3, context: html, text, full: html, text
    Handle supertrack names in hub consistently; the hub_ prefix is stripped before adding to trackDb settings. Bug #9751: Error when superTrack children use 'parent' setting superTrack doesnt render for Hubs
• src/hg/lib/trackHub.c
  • lines changed 368, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/trackVersion.c
  • lines changed 2, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/lib/web.c
  • lines changed 16, context: html, text, full: html, text
    changes necessary to support assembly hubs (#8072)
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 14, context: html, text, full: html, text
    Construct lift file Ensembl names to UCSC names.
  • lines changed 4, context: html, text, full: html, text
    Finished ensGene V70 for felCat5 and rn5.
• src/hg/makeDb/doc/rn5.txt
  • lines changed 13, context: html, text, full: html, text
    Finished ensGene V70 for felCat5 and rn5.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Updating CV URL's that were broken, adding info on Attic files as for download only. MLQ# 10203
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 8, context: html, text, full: html, text
    Updating dgv.html links to new site, new black color for unknown items, for release DGV hg17 hg18 hg19 RM#9401
  • lines changed 1, context: html, text, full: html, text
    Updating dgv.html, a unknown -> an unknown, for release DGV hg17 hg18 hg19 RM#9401
  • lines changed 2, context: html, text, full: html, text
    Updating dgv.html, added PMID reference numbers, for release DGV hg17 hg18 hg19 RM#9401
  • lines changed 3, context: html, text, full: html, text
    Correcting accidental typo, and PMID punctuation RM#9401
  • lines changed 27, context: html, text, full: html, text
    Adding paragraph to dgv.html based on user feedback ML#10208from release RM#9401
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 1, context: html, text, full: html, text
    Add next item feature to track. #100042. ENCODE Uniform TFBS
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Staging DGV track on beta, changing release tags for hgFindSpec searchTable dgv and for dgv tables. RM#9401
  • lines changed 3, context: html, text, full: html, text
    Track #9401 (DGV): Fixed a couple issues found by Brian L. (shortLabel, termRegex)
  • lines changed 18, context: html, text, full: html, text
    Releasing DGV to public, removing previous trackDb.ra dgv stanza, updating hgFindSpec DGV search stanza, RM#9401
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed publications track visibility to dense
• src/hg/oneShot/freen/freen.c
  • lines changed 48, context: html, text, full: html, text
    Testing out some log/exponential math for color transparencies.
• src/hg/oneShot/transparentTriangleTest/transparentTriangleTest.c
  • lines changed 188, context: html, text, full: html, text
    New transparency idea tester starting to work.
  • lines changed 60, context: html, text, full: html, text
    Working out some image normalization stuff.
  • lines changed 39, context: html, text, full: html, text
    Making test program produce 10 shades at once.
  • lines changed 23, context: html, text, full: html, text
    Further experiments on color transparency.
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 26, context: html, text, full: html, text
    Add process MT to chrMliftover to process step
• src/hg/utils/automation/ensGene/felCat5.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    Construct lift file Ensembl names to UCSC names.
  • lines changed 9, context: html, text, full: html, text
    Finished ensGene V70 for felCat5 and rn5.
• src/hg/utils/automation/ensGene/hg19.ensGene.ra
  • lines changed 4, context: html, text, full: html, text
    redmine 9407 ensGene V70: add chainOver file for hg19.
• src/hg/utils/automation/ensGene/rn5.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    Finished ensGene V70 for felCat5 and rn5.
• src/inc/annoGrator.h
  • lines changed 24, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/inc/annoStreamer.h
  • lines changed 5, context: html, text, full: html, text
    Added setAutoSqlObject method to annoStreamer, to update both asObj andinternal state derived from it. (for #6152)
    
• src/inc/hex.h
  • lines changed 15, context: html, text, full: html, text
    adding capability to run md5sum against an entire file
  • lines changed 8, context: html, text, full: html, text
    adding functions to decode hexstring to byte
• src/inc/localmem.h
  • lines changed 3, context: html, text, full: html, text
    fix problem with lmCloneString not handling a NULL input correctly (#10199)
• src/inc/md5.h
  • lines changed 11, context: html, text, full: html, text
    adding capability to run md5sum against an entire file
• src/inc/rainbow.h
  • lines changed 4, context: html, text, full: html, text
    Exposing veryLightRainbowAtPos to rest of code.
• src/inc/twoBit.h
  • lines changed 15, context: html, text, full: html, text
    change twoBit library to use either UDC or stdio. #8072
• src/inc/udc.h
  • lines changed 10, context: html, text, full: html, text
    changes to UDC to support twoBit library using it #8072
• src/kehayden/reverseCenReads/makefile
  • lines changed 18, context: html, text, full: html, text
    A little program to massage Karen's centromeric data which looks maybe like it's reversed in some cases.
• src/kehayden/reverseCenReads/reverseCenReads.c
  • lines changed 56, context: html, text, full: html, text
    A little program to massage Karen's centromeric data which looks maybe like it's reversed in some cases.
  • lines changed 1, context: html, text, full: html, text
    Fixed off by one bug.
• src/lib/annoGrator.c
  • lines changed 41, context: html, text, full: html, text
    annoGrator:- Added annoGratorInit so annoGrator can be subclassed and extended;
    - Added enum annoGratorOverlap and setOverlapRule method to specify
    how to treat overlap between primary and internal rows: ignore it,
    require it, or forbid it, via integrate method's retRJFilterFailed.
    - Added setAutoSqlObject method to update both the outward-facing
    (streamer interface) asObj and internal state derived from it.
    annoGratorGpVar:
    - Added cdsOnly property to keep only variants that change CDS
    (via retRJFilterFailed).
    - The language of aggvGenRows implies that multiple effect rows may
    arise from one {variant x gene}. In case that happens, use slCat
    instead of slAddHead to keep all effect rows.
    - Added slReverse to make sure output rows are ordered by position.
    That required shuffling some lines in an expected-results file.
    - Renamed some variables because there are now 3 types of "self":
    streamer, grator, gpVar.
    
• src/lib/annoStreamer.c
  • lines changed 16, context: html, text, full: html, text
    Added setAutoSqlObject method to annoStreamer, to update both asObj andinternal state derived from it. (for #6152)
    
• src/lib/hex.c
  • lines changed 28, context: html, text, full: html, text
    adding capability to run md5sum against an entire file
  • lines changed 3, context: html, text, full: html, text
    oops bug fixes
  • lines changed 19, context: html, text, full: html, text
    adding functions to decode hexstring to byte
• src/lib/localmem.c
  • lines changed 9, context: html, text, full: html, text
    fix problem with lmCloneString not handling a NULL input correctly (#10199)
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    adding capability to run md5sum against an entire file
• src/lib/md5.c
  • lines changed 44, context: html, text, full: html, text
    adding capability to run md5sum against an entire file
• src/lib/memgfx.c
  • lines changed 13, context: html, text, full: html, text
    Making horizontal line setter work with transparent mode. Doing a microoptimization in transparent put dot.
• src/lib/twoBit.c
  • lines changed 195, context: html, text, full: html, text
    change twoBit library to use either UDC or stdio. #8072
• src/lib/udc.c
  • lines changed 22, context: html, text, full: html, text
    changes to UDC to support twoBit library using it #8072
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v280 preview1
• src/utils/reverseLineOrder/reverseLineOrder.c
  • lines changed 44, context: html, text, full: html, text
    LIttle utility to reverse order of lines in file.
• src/utils/wordsInEachLine/makefile
  • lines changed 18, context: html, text, full: html, text
    A little utility I needed to debug some input to centromere maker - counts words in each line of a file separately.
• src/utils/wordsInEachLine/wordsInEachLine.c
  • lines changed 45, context: html, text, full: html, text
    A little utility I needed to debug some input to centromere maker - counts words in each line of a file separately.

• lines changed: 2372
• files changed: 103