All File Changes

v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248

• python/ucscgenomics/rafile/filter.ra
  • lines changed 25, context: html, text, full: html, text
    Updated raFile suite, added raInspect which can verify cv.ra as well as perform filtering tasks on any ra file
• python/ucscgenomics/rafile/filterEntry.py
  • lines changed 49, context: html, text, full: html, text
    Updated raFile suite, added raInspect which can verify cv.ra as well as perform filtering tasks on any ra file
• python/ucscgenomics/rafile/filterFile.py
  • lines changed 27, context: html, text, full: html, text
    Updated raFile suite, added raInspect which can verify cv.ra as well as perform filtering tasks on any ra file
• python/ucscgenomics/rafile/raFile.py
  • lines changed 18, context: html, text, full: html, text
    Updated raFile suite, added raInspect which can verify cv.ra as well as perform filtering tasks on any ra file
• python/ucscgenomics/rafile/raInspect.py
  • lines changed 63, context: html, text, full: html, text
    Updated raFile suite, added raInspect which can verify cv.ra as well as perform filtering tasks on any ra file
• python/ucscgenomics/style.txt
  • lines changed 5, context: html, text, full: html, text
    Add doc convention
• src/ai/paraFlow/compiler/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/ai/paraFlow/runAsm/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/ai/paraFlow/runtime/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/aladdin/aladdin/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cbAli/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/ali2alx/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/aliGlue/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/binGood/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/cdnaOff/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/cluster/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/exonAli/makefile
  • lines changed 3, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/introns/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/pairClo/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/patCount/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/patSpace/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/refineAli/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/sortFilt/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/cdnaAli/stitchea/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/dnaDust/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/fuzzyFind/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/getgene/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/affyGnf/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/affyTransciptome/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/altSplice/affySplice/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/altSplice/axtCountBeds/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/altSplice/exonWalk/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/altSplice/filterEdges/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/altSplice/spliceWalk/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/autoXml/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/blastToPsl/pslBuild.c
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):This is a total mystery to me, but for some reason when tabix.h is included via linefile.h, the compiler complains about the redefinition of pslBuildScoresOpen when bool is used... fortunately boolean is OK. I have no idea why using bool would be OK in the rest of the tree but not here. ??? Anyway, since using boolean allows it to compile, I'll just go with that.
• src/hg/blastToPsl/pslBuild.h
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):This is a total mystery to me, but for some reason when tabix.h is included via linefile.h, the compiler complains about the redefinition of pslBuildScoresOpen when bool is used... fortunately boolean is OK. I have no idea why using bool would be OK in the rest of the tree but not here. ??? Anyway, since using boolean allows it to compile, I'll just go with that.
• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 5, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Fixed error is script when trying to find gbdb links for bam files that are download only.
  • lines changed 1, context: html, text, full: html, text
    missspelled str
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 4, context: html, text, full: html, text
    Added wgEncodeUncBsuProt
• src/hg/fakeOut/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/gigAssembler/conJobs/patJobs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/gigAssembler/conJobs/repMaskJobs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/hgApi/hgApi.c
  • lines changed 27, context: html, text, full: html, text
    Another step towards supporting multi-selects in track search and file search
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 750, context: html, text, full: html, text
    Working on file search as a stand alone CGI. Not ready yet, but it does work.
  • lines changed 1, context: html, text, full: html, text
    Brooke suggests 'is amung' instead of 'is (any of)'.
  • lines changed 1, context: html, text, full: html, text
    Mdb vars for files, not tables
• src/hg/hgFileSearch/makefile
  • lines changed 15, context: html, text, full: html, text
    Working on file search as a stand alone CGI. Not ready yet, but it does work.
• src/hg/hgTracks/bamTrack.c
  • lines changed 7, context: html, text, full: html, text
    a comment from Angie's code review that I'll implement when I move to get BAM's to display as wigs automagically. Also, a change to the bamWig predraw array that is still not right. :(
  • lines changed 7, context: html, text, full: html, text
    bamWigMethods was used but undefined in the absence of USE_BAM=1.
  • lines changed 18, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 34, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/bigWarn.c
  • lines changed 114, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/bigWarn.h
  • lines changed 23, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 50, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/container.c
  • lines changed 9, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/container.h
  • lines changed 3, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/hgTracks.c
  • lines changed 0, context: html, text, full: html, text
    Making it so that the blue bar on the top doesn't get fat when you make the window narrow.
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/multiWig.c
  • lines changed 21, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/hgTracks/searchTracks.c
  • lines changed 15, context: html, text, full: html, text
    Fixed redmine 2911. 'No tracks found' message was lost but now is found.
  • lines changed 91, context: html, text, full: html, text
    Support for multi-selects for mdb searches on advanced tab. Requires cv.ra change to be active.
  • lines changed 1, context: html, text, full: html, text
    Brooke suggests 'is amung' instead of 'is (any of)'.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 70, context: html, text, full: html, text
    Added functions for omimLocation.
  • lines changed 28, context: html, text, full: html, text
    Updated functions for new OMIM tracks.
  • lines changed 69, context: html, text, full: html, text
    Added function for omimLocation to set color for its entries of different classes.
  • lines changed 2, context: html, text, full: html, text
    Added description for mouse over omimAvSnp entries.
  • lines changed 27, context: html, text, full: html, text
    backing out pointing things on decipher blocks #1953
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    Fine tuned omimAvSnp details page.
  • lines changed 19, context: html, text, full: html, text
    Fine tuned details page for OMIM new tracks.
  • lines changed 5, context: html, text, full: html, text
    Fix mismatch problem of NumtS track
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 3, context: html, text, full: html, text
    Corrected spelling for 'commercial'
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    Added panTro3.
• src/hg/htdocs/images/Nomascus_leucogenys.jpg
  • lines changed 0, context: html, text, full: html, text
    Add Gibbon Picture
  • lines changed 0, context: html, text, full: html, text
    touch up description.html
• src/hg/htdocs/inc/FAQ.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
  • lines changed 0, context: html, text, full: html, text
    fixed 755 mode
• src/hg/htdocs/inc/download.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/encode.custTracks.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/encode.home.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/encode.terms.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/encode.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/encode.topbar_pilot.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/help.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/home.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/neandertal.topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/inc/topbar.html
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    per Mark's advice, move html printout from hdb to hui
• src/hg/inc/hgFindSpec.h
  • lines changed 11, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/inc/hui.h
  • lines changed 8, context: html, text, full: html, text
    per Mark's advice, move html printout from hdb to hui
• src/hg/inc/knetUdc.h
  • lines changed 10, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/hg/inc/mdb.h
  • lines changed 33, context: html, text, full: html, text
    Added mdbObjsEncodeExperimentify() which will organize objects into experiments and allow the expId to be updated into the mdb
• src/hg/js/hgTracks.js
  • lines changed 446, context: html, text, full: html, text
    Moved code from 'hgTracks.js' to common 'utils.js' and added support for multi-selects in file and track search
• src/hg/js/utils.js
  • lines changed 466, context: html, text, full: html, text
    Moved code from 'hgTracks.js' to common 'utils.js' and added support for multi-selects in file and track search
  • lines changed 1, context: html, text, full: html, text
    Brooke suggests 'is amung' instead of 'is (any of)'.
• src/hg/lib/bamFile.c
  • lines changed 2, context: html, text, full: html, text
    squashed my dev branch bigNetErrDisplay to test making code review easier; this code helps hgTracks display big network warnings and errors with a yellow background; it supports bigWig, bigBed, bam, and multiWig; In the case of multiWig, it can only draw the yellow background once at the beginning, and is limited to only drawing the first track that has a network error since overlapping multiple error messages would be unreadable
• src/hg/lib/customFactory.c
  • lines changed 8, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/lib/fileUi.c
  • lines changed 15, context: html, text, full: html, text
    File search can get terribly slow with too many files. Limit to 1000.
• src/hg/lib/genbank.c
  • lines changed 1, context: html, text, full: html, text
    When recording a selenocysteine exception, save the specific information on the exception in the hash. This will be useful later in txCdsPick.c
• src/hg/lib/hdb.c
  • lines changed 59, context: html, text, full: html, text
    per Mark's advice, move html printout from hdb to hui
• src/hg/lib/hgFind.c
  • lines changed 12, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/lib/hgFindSpecCustom.c
  • lines changed 66, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/lib/hui.c
  • lines changed 59, context: html, text, full: html, text
    per Mark's advice, move html printout from hdb to hui
• src/hg/lib/knetUdc.c
  • lines changed 87, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/hg/lib/mdb.c
  • lines changed 789, context: html, text, full: html, text
    Added mdbObjsEncodeExperimentify() which will organize objects into experiments and allow the expId to be updated into the mdb
  • lines changed 2, context: html, text, full: html, text
    Always print composite summary msg in mdbObjsEncodeExperimentify()
  • lines changed 23, context: html, text, full: html, text
    Beginning to support mutiSelects for cv.ra searchables
  • lines changed 1, context: html, text, full: html, text
    Need to change cv.ra white list to include multiSelects.
  • lines changed 16, context: html, text, full: html, text
    Cleaned up a little code to make track search not dependent upon var=tableName being set.
• src/hg/lib/pgSnp.c
  • lines changed 4, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    removing debugging output
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    add white-space: nowrap in a bunch of places to fix topbar wrapping on narrow displays. Should be done in style sheet, however couldnt find a good way to do it give the current html
  • lines changed 1, context: html, text, full: html, text
    redid change to prevent topbar word wrap to work through separate CCS
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 44, context: html, text, full: html, text
    Re-do multiz13way.maf
  • lines changed 1, context: html, text, full: html, text
    construct download files for panTro3 and running cpgIsland
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethyl27.release1.notes
  • lines changed 190, context: html, text, full: html, text
    New notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release2.notes
  • lines changed 321, context: html, text, full: html, text
    Added release 2 of UW DGF and UW DNaseI HS tracks.
  • lines changed 76, context: html, text, full: html, text
    Updated paths of files.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release2.notes
  • lines changed 1588, context: html, text, full: html, text
    Added release 2 of UW DGF and UW DNaseI HS tracks.
  • lines changed 430, context: html, text, full: html, text
    Updated paths of files.
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 45, context: html, text, full: html, text
    re-do the multiz6way.maf
• src/hg/makeDb/doc/hg17.txt
  • lines changed 11, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): following DGV's swap to newcoloring convention decided at ISCA, we're swapping red <-> blue. While we're at it, since DGV now uses brown for 'both gain and loss', switch green to brown.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 12, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): following DGV's swap to newcoloring convention decided at ISCA, we're swapping red <-> blue. While we're at it, since DGV now uses brown for 'both gain and loss', switch green to brown.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 73, context: html, text, full: html, text
    Rebuilt uniGene_3 track.
  • lines changed 11, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): following DGV's swap to newcoloring convention decided at ISCA, we're swapping red <-> blue. While we're at it, since DGV now uses brown for 'both gain and loss', switch green to brown.
  • lines changed 59, context: html, text, full: html, text
    running panTro3 lastz
  • lines changed 7, context: html, text, full: html, text
    continuing lastz run on panTro3
  • lines changed 10, context: html, text, full: html, text
    finished with hg19 panTro3 lastz
  • lines changed 64, context: html, text, full: html, text
    resolve merge conflict
  • lines changed 73, context: html, text, full: html, text
    hg19 UNIGENE/SAGE
  • lines changed 2, context: html, text, full: html, text
    remove temporary comment
• src/hg/makeDb/doc/panTro2.txt
  • lines changed 13, context: html, text, full: html, text
    have rn blat liftOver panTro2 to panTro3
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 64, context: html, text, full: html, text
    done with RM and TRF repeats
  • lines changed 37, context: html, text, full: html, text
    ctgPos2 done and all 'other' gaps are marked
  • lines changed 261, context: html, text, full: html, text
    blat server setup, genbank running lastz with calJac3 and rheMac2 running
  • lines changed 48, context: html, text, full: html, text
    running lastz rn4
  • lines changed 167, context: html, text, full: html, text
    start human proteins track
  • lines changed 352, context: html, text, full: html, text
    lastz running for mm9 ponAbe2 rheMac2 calJac3 equCab2 canFam2 monDom5 galGal3
  • lines changed 6, context: html, text, full: html, text
    finished exon blast
  • lines changed 97, context: html, text, full: html, text
    construct download files for panTro3 and running cpgIsland
  • lines changed 23, context: html, text, full: html, text
    cpgIsland track done
  • lines changed 16, context: html, text, full: html, text
    genbank done
  • lines changed 2, context: html, text, full: html, text
    no perChrom tables needed for genbank
  • lines changed 1, context: html, text, full: html, text
    genbank reloaded
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    adding panTro3 to the daily update cycle
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding panTro3
  • lines changed 1, context: html, text, full: html, text
    add panTro3.lift file
  • lines changed 1, context: html, text, full: html, text
    turn off perChromTables for panTro3
  • lines changed 1, context: html, text, full: html, text
    switch mm9 to new mouse ccds
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    adding panTro3 to the daily update cycle
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 14, context: html, text, full: html, text
    added debug facility to collect profiling info on gbAlignGet
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • lines changed 2, context: html, text, full: html, text
    exclude widtra reviewed, withdrawl pending from tracks
• src/hg/makeDb/genbank/src/lib/gbRelease.c
  • lines changed 2, context: html, text, full: html, text
    decreased size of unnecessarly large hash tables to decreased signficanit amount of time used initializing them
• src/hg/makeDb/genbank/src/lib/seqTbl.c
  • lines changed 1, context: html, text, full: html, text
    decreased size of unnecessarly large hash tables to decreased signficanit amount of time used initializing them
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 16, context: html, text, full: html, text
    Added -encodeExp options to mdbPrint and mdbUpdate allowing organizing objects into experiments and possibly updating the expId
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 46, context: html, text, full: html, text
    Added -encodeExp options to mdbPrint and mdbUpdate allowing organizing objects into experiments and possibly updating the expId
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding panTro3
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPS 132 (dbSNP)): Added snp132ExceptionDesc to tablesIgnored (thanks Brooke).
  • lines changed 1, context: html, text, full: html, text
    add chain net PanTro3
• src/hg/makeDb/trackDb/chimp/panTro3/ctgPos2.html
  • lines changed 10, context: html, text, full: html, text
    adding ctgPos2 track
• src/hg/makeDb/trackDb/chimp/panTro3/gap.html
  • lines changed 4, context: html, text, full: html, text
    update numbers and types
• src/hg/makeDb/trackDb/chimp/panTro3/gold.html
  • lines changed 4, context: html, text, full: html, text
    update numbers and types
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding ctgPos2 track
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Accepted a couple provisional stanzas. Drafted a validation regex for md5sums
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in vendor id, extra 1 present.
  • lines changed 0, context: html, text, full: html, text
    Updated unit spacing to be consistent with rest of browswer. Issue 59, note 16.
  • lines changed 27, context: html, text, full: html, text
    Now that multiSelect is supported in track search and file search, turn in on in cv.
  • lines changed 1, context: html, text, full: html, text
    Changed the comment for submittedDataVersion validation to be more clear (I hope).
  • lines changed 2, context: html, text, full: html, text
    Accepted provisional changes, cleaned up one comment
  • lines changed 58, context: html, text, full: html, text
    Renamed several antibodies, in response to Redmine Bug # 2965
  • lines changed 3, context: html, text, full: html, text
    Fixed a broken link introduced wen addressing Redmine bug 2965
  • lines changed 56, context: html, text, full: html, text
    (1) Clarified the comments on expected values, especially concerning the interrelations between stanzas. (2) Added a couple stanzas to document expected values for familiar types (e.g. organism, tier). (3) Added data for one Farnham lab cell type that had been registered provisionally. (4) Fixed the antibody validation line convention of <antibody>_(<validationType>):<filename> as opposed to <antibody>_(<validationType>)_<PI>:<filename>. The reason: adding the name of the lab that validated the antibody adds no information, since it's the same as the lab that first entered the antibody. Having the name displayed in the validation column just adds clutter to the column
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 51, context: html, text, full: html, text
    Copied a bunch of changes from alpha to beta
  • lines changed 29, context: html, text, full: html, text
    Copying a bunch of changes from alpha to beta
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 41, context: html, text, full: html, text
    touch up description.html
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 6, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): following DGV's swap to newcoloring convention decided at ISCA, we're swapping red <-> blue. While we're at it, since DGV now uses brown for 'both gain and loss', switch green to brown.
  • lines changed 1, context: html, text, full: html, text
    clarified color description a bit
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDnaseSeq.ra
  • lines changed 175, context: html, text, full: html, text
    staging release 4 of UW DNase I HS on beta, Redmine Issue #1842
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDnaseSeq.ra
  • lines changed 175, context: html, text, full: html, text
    releasing release 4 of UW DNaseI HS, Redmine issue #1842
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    converting to release tags in the include statements
  • lines changed 2, context: html, text, full: html, text
    staging release 4 of UW DNase I HS on beta, Redmine Issue #1842
  • lines changed 2, context: html, text, full: html, text
    releasing release 4 of UW DNaseI HS, Redmine issue #1842
  • lines changed 9, context: html, text, full: html, text
    grammar tweak: An repressor to A repressor
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • lines changed 7, context: html, text, full: html, text
    releasing release 4 of UW DNaseI HS, Redmine issue #1842
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
  • lines changed 6, context: html, text, full: html, text
    editing the Release Notes section for clarity, Redmine Issue #1842
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 226, context: html, text, full: html, text
    converting to release tags in the include statements
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 235, context: html, text, full: html, text
    converting to release tags in the include statements
  • lines changed 57, context: html, text, full: html, text
    releasing release 4 of UW DNaseI HS, Redmine issue #1842
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Kate missed this step - shame
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 89, context: html, text, full: html, text
    add the combined replicates to download only
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 64, context: html, text, full: html, text
    Ran mdbUpdate and print to composite.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl27.ra
  • lines changed 133, context: html, text, full: html, text
    Fixed links for data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 183, context: html, text, full: html, text
    Added submission 3246, which was missing.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    Removed Antibodies
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 137, context: html, text, full: html, text
    Kate wrangles
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    Made a change in capitalization to make this data consistent with the files in the downloads directory
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging UW Affy Exon, redmine# 59
  • lines changed 1, context: html, text, full: html, text
    staging metadata for UW TFBS on beta, Redmine Issue #1604
  • lines changed 1, context: html, text, full: html, text
    staging UTA TFBS on hgwbeta: adding 'title' to include statment, adding release tags to include statements, removing release tags from trackDb blocks, staging metaData, Redmine Isse #62
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 5897, context: html, text, full: html, text
    staging UTA TFBS on hgwbeta: adding 'title' to include statment, adding release tags to include statements, removing release tags from trackDb blocks, staging metaData, Redmine Isse #62
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 2636, context: html, text, full: html, text
    staging UW Affy Exon, redmine# 59
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 11504, context: html, text, full: html, text
    staging metadata for UW TFBS on beta, Redmine Issue #1604
• src/hg/makeDb/trackDb/human/hg19/omimAvSnp.html
  • lines changed 74, context: html, text, full: html, text
    Added description html for omimAvSnp.
  • lines changed 1, context: html, text, full: html, text
    Added Robert Kuhn to Credit section.
• src/hg/makeDb/trackDb/human/hg19/omimGeneClass3.html
  • lines changed 88, context: html, text, full: html, text
    Added description html for omimGeneClass3.
  • lines changed 1, context: html, text, full: html, text
    Added Robert Kuhn to Credit section.
• src/hg/makeDb/trackDb/human/hg19/omimLocation.html
  • lines changed 82, context: html, text, full: html, text
    Added description html for omimLocation.
  • lines changed 17, context: html, text, full: html, text
    modified description based on conversation with Joanna Amberger some time ago
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 5, context: html, text, full: html, text
    Trying to fix the Tiling going into a supertrack on public, I changed the release tags in trackDb.wgEncode.ra, I added wgEncodeSunyAlbanyTiling.new.ra
  • lines changed 1, context: html, text, full: html, text
    changed wgEncodeSunyAlbanyTiling.ra to wgEncodeSunyAlbanyTiling.new.ra so that it will be in a super track on hgwdev, redmine# 460
  • lines changed 4, context: html, text, full: html, text
    putting include statement for UW TFBS under its own heading so it is easier to find; adding release tags because it is in a supertrack
  • lines changed 4, context: html, text, full: html, text
    staging UTA TFBS on hgwbeta: adding 'title' to include statment, adding release tags to include statements, removing release tags from trackDb blocks, staging metaData, Redmine Isse #62
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra
  • lines changed 6415, context: html, text, full: html, text
    New submissions added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 66, context: html, text, full: html, text
    Changed Rep View to 1 and 3; Rep 0 to Gen 0
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
  • lines changed 1, context: html, text, full: html, text
    added a missing word, redmine issues# 144 & 59
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 8, context: html, text, full: html, text
    fix up default tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 6, context: html, text, full: html, text
    Fixed release tags and types for newly added tracks
  • lines changed 6, context: html, text, full: html, text
    Removed release tags and added new submissions
  • lines changed 1, context: html, text, full: html, text
    Fixed Labels on description page by removing <br>s
  • lines changed 6, context: html, text, full: html, text
    remove color lines and origAssembly lines
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 1, context: html, text, full: html, text
    Commented out the maxWindowToDraw
  • lines changed 1, context: html, text, full: html, text
    Added Description Page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 40, context: html, text, full: html, text
    Added submission 3246, which was missing.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 25, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 56, context: html, text, full: html, text
    Further fine-tuning as per QA
  • lines changed 18, context: html, text, full: html, text
    minor edits and some formatting changes
  • lines changed 1, context: html, text, full: html, text
    fixed convert to converted per Vanessa's code review, thanks Vanessa! Redmine Issue #2932
  • lines changed 11, context: html, text, full: html, text
    Removed erroneous text from the methods section
  • lines changed 5, context: html, text, full: html, text
    Oops. Added paragraph back in.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 196, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 1, context: html, text, full: html, text
    Minor changes to composite long label to further identify lab
  • lines changed 1, context: html, text, full: html, text
    Further fine-tuning as per QA
  • lines changed 1, context: html, text, full: html, text
    Base Overlap is not 'raw'
  • lines changed 1, context: html, text, full: html, text
    Standardizing tier 1 and 2 labels
  • lines changed 177, context: html, text, full: html, text
    Back to the new style 'Dnesity Signal' and 'Overlap Signal' labelling
  • lines changed 1, context: html, text, full: html, text
    Back and forth 'Density Signal' and 'Overlap Signal' labelling
  • lines changed 8, context: html, text, full: html, text
    unabbreviating treatments for UTA TFBS (Open Chrom)
  • lines changed 115, context: html, text, full: html, text
    staging UTA TFBS on hgwbeta: adding 'title' to include statment, adding release tags to include statements, removing release tags from trackDb blocks, staging metaData, Redmine Isse #62
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 24, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 52, context: html, text, full: html, text
    Further fine-tuning as per QA
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 230, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 1, context: html, text, full: html, text
    Base Overlap is not 'raw'
  • lines changed 219, context: html, text, full: html, text
    Back to the new style 'Dnesity Signal' and 'Overlap Signal' labelling
  • lines changed 1, context: html, text, full: html, text
    Back and forth 'Density Signal' and 'Overlap Signal' labelling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 24, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 49, context: html, text, full: html, text
    Further fine-tuning as per QA
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 126, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 1, context: html, text, full: html, text
    Minor changes to composite long label to further identify lab
  • lines changed 1, context: html, text, full: html, text
    Further fine-tuning as per QA
  • lines changed 1, context: html, text, full: html, text
    Base Overlap is not 'raw'
  • lines changed 128, context: html, text, full: html, text
    Back to the new style 'Dnesity Signal' and 'Overlap Signal' labelling
  • lines changed 1, context: html, text, full: html, text
    Back and forth 'Density Signal' and 'Overlap Signal' labelling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 53, context: html, text, full: html, text
    Further fine-tuning as per QA
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 22, context: html, text, full: html, text
    Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • lines changed 1, context: html, text, full: html, text
    Further fine-tuning as per QA
  • lines changed 1, context: html, text, full: html, text
    Standardizing tier 1 and 2 labels
  • lines changed 2, context: html, text, full: html, text
    Back to the new style 'Dnesity Signal' and 'Overlap Signal' labelling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRIPSuper.html
  • lines changed 88, context: html, text, full: html, text
    Copied a bunch of changes from alpha to beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
  • lines changed 1, context: html, text, full: html, text
    Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 117, context: html, text, full: html, text
    In long labels rep->Rep, and Total->total
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 5, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 3, context: html, text, full: html, text
    Updated Tenenbaum link
  • lines changed 10, context: html, text, full: html, text
    Added Scotts Contact Details
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 1, context: html, text, full: html, text
    Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
  • lines changed 50, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 1, context: html, text, full: html, text
    Trying to fix the Tiling going into a supertrack on public, I changed the release tags in trackDb.wgEncode.ra, I added wgEncodeSunyAlbanyTiling.new.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
  • lines changed 12, context: html, text, full: html, text
    Added Scotts Contact details
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.new.ra
  • lines changed 104, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 1, context: html, text, full: html, text
    Trying to fix the Tiling going into a supertrack on public, I changed the release tags in trackDb.wgEncode.ra, I added wgEncodeSunyAlbanyTiling.new.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 1, context: html, text, full: html, text
    Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
  • lines changed 8, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 1, context: html, text, full: html, text
    Trying to fix the Tiling going into a supertrack on public, I changed the release tags in trackDb.wgEncode.ra, I added wgEncodeSunyAlbanyTiling.new.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 72, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 1, context: html, text, full: html, text
    Added this track into the ENCODE RBP supertrack
  • lines changed 1, context: html, text, full: html, text
    Removed duplicate line for super track designation.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
  • lines changed 11, context: html, text, full: html, text
    Added Scotts Contact Details
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 1, context: html, text, full: html, text
    Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
  • lines changed 8, context: html, text, full: html, text
    Added many changes from the approval call for SUNY, lots of label changes, default settings, putting in superTrack
  • lines changed 1, context: html, text, full: html, text
    Trying to fix the Tiling going into a supertrack on public, I changed the release tags in trackDb.wgEncode.ra, I added wgEncodeSunyAlbanyTiling.new.ra
  • lines changed 1, context: html, text, full: html, text
    Changed longLabel, added fileSortOrder
  • lines changed 1, context: html, text, full: html, text
    Actually added fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
  • lines changed 7, context: html, text, full: html, text
    Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 3, context: html, text, full: html, text
    minor edits
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 28, context: html, text, full: html, text
    Minor HTML text editing, for clarity
  • lines changed 59, context: html, text, full: html, text
    Incorporated some feedback from the Giddings lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    Added the localization to the long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 7, context: html, text, full: html, text
    fixed some grammar issues and formatted the html so it was more readable, redmine# 59
  • lines changed 1, context: html, text, full: html, text
    fixed link so that it is relative, redmine #59
  • lines changed 0, context: html, text, full: html, text
    added space before the unit, redmine #59
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Affy Gene 1.0
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 137, context: html, text, full: html, text
    staging UW Affy Exon, redmine# 59
  • lines changed 1, context: html, text, full: html, text
    Changed the downloads page to have file sort order
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in Cell AoAF as AOAF.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.html
  • lines changed 5, context: html, text, full: html, text
    editing for clarity, Redmine issue #1604
  • lines changed 1, context: html, text, full: html, text
    minor edit, Redmine Issue #1604
  • lines changed 1, context: html, text, full: html, text
    minor edit, Redmine issue #1604
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 72, context: html, text, full: html, text
    Added 7 missing trackDb enteries listed in Issue: 1604 Note: 13.
  • lines changed 253, context: html, text, full: html, text
    removing release tags from trackDb blocks since I added them to the include statement instead, Redmine Issue #1604
  • lines changed 252, context: html, text, full: html, text
    Removed origAssembly from trackDb lines. Addressed redmine issue: 1604, note: 17.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Fine tuned new OMIM tracks.
  • lines changed 57, context: html, text, full: html, text
    Added search terms for the 3 new OMIM tracks.
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    making the old calJac3 conservation track that was never pushed (8-way) on hide by default since I am starting to QA the new 13-way conservation track
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 201, context: html, text, full: html, text
    Added sub 3052.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 245, context: html, text, full: html, text
    Added track description to get ready for release 1.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 263, context: html, text, full: html, text
    Added track Description in preperation for release 1.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 21, context: html, text, full: html, text
    Added sub 3052.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 81, context: html, text, full: html, text
    Added track description to make it one step closer to release.
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 21, context: html, text, full: html, text
    Mostly tiny tweaks to wording and punctuation, but substantial change to the class MNP and function locus descriptions, gleaned from http://www.ncbi.nlm.nih.gov/snp. Discussed in Redmine #1684.
  • lines changed 1, context: html, text, full: html, text
    Fixed tiny typo.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 50, context: html, text, full: html, text
    adding chain net PanTro3 business
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    add matrix to chain and net composites
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Go ahead and make the new hgFileSearch cgi
• src/hg/nci60/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 2, context: html, text, full: html, text
    Fixing a seg-fault in hgMapToGene that was apparent creating knownToEnsembl on mm9. Just a missing NULL check.
• src/hg/splitFa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/txCds/txCdsPick/txCdsPick.c
  • lines changed 3, context: html, text, full: html, text
    When transferring information on a selenocysteine exception, grab the specific information on the exception now stored in the selenocysteine hash
• src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh
  • lines changed 16, context: html, text, full: html, text
    Simplified the argument list. Now this script takes only three arguments: the old directory (required), the new directory (required), and an optional argument for ctime
  • lines changed 1, context: html, text, full: html, text
    Added one more critical step: removing the temporary directory just created
  • lines changed 3, context: html, text, full: html, text
    Reversed the order of the first two arguments to make them consistent with the documentation
• src/hg/utils/gtfToGenePred/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 2, context: html, text, full: html, text
    Improved usage message
• src/idbQuery/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/inc/common.mk
  • lines changed 31, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):added common.mk variables analogous to those for samtools: TABIXDIR, USE_TABIX, TABIXINC, TABIXLIB. When compiling with tabix, also set KNETFILE_HOOKS so tabix will use udc like samtools.
• src/inc/knetUdc.h
  • lines changed 10, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/inc/linefile.h
  • lines changed 26, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/inc/regexHelper.h
  • lines changed 29, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/index/fofFa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/index/indexRa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/index/ixxenost/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/lib/knetUdc.c
  • lines changed 87, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/lib/linefile.c
  • lines changed 122, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/lib/regexHelper.c
  • lines changed 80, context: html, text, full: html, text
    New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c. The primary motivation for this is so I can use regex functions in the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope this will make it easier in general to use regexes in any new code.
• src/lib/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/checkLayout/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/chkGlue/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/cntGlue/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/coverage/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/deEns/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/dynAlign/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/fixInfo/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/grokGff/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/invert/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/m22dirs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/ooRev/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/passHi/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/patJobs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/shorten/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/sources/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/splitSql/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/tabixFetch/makefile
  • lines changed 18, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/oneShot/tabixFetch/tabixFetch.c
  • lines changed 114, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then lineFileNext and its derivatives work as usual. lineFileSetTabixRegion seeks to the given position range, and subsequent lineFileNext's return lines in that position range. lineFileSeek is not supported -- tabix doesn't have linear offsets but rather a block number and offset which are packed into 64 bits. Line numbers are not known after calls to lineFileSetTabixRegion.
• src/oneShot/uniqSize/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/unmasked/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/oneShot/unwrap/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/netC/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/netS/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/para/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/paraHubStop/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/paraNode/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/paraNodeStart/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/paraNodeStatus/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/paraNodeStop/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/parasol/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/simpleC/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/parasol/simpleS/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/primeMate/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/product/scripts/browserEnvironment.txt
  • lines changed 18, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Updated src/product's sample environment config script with new variables USE_TABIX etc.
• src/protDust/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/fa4blast/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/fatont4/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/fsg/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/gb2cdi/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/gbToFaRa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/gbtofa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/geniegff/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/gffgenes/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/makeOrf2gene/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/makec2c/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/moresyn/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/reformat/wabToSt/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/scanIntrons/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/test/makefile
  • lines changed 4, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/addCols/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/aveCols/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
  • lines changed 26, context: html, text, full: html, text
    output a more efficient bedgraph
  • lines changed 2, context: html, text, full: html, text
    Added initial values of a few new vars, to satisfy ubuntu's extra-Wall check. Due to the use of boolean firstTime, the values would not be used uninitialized, this is just to satisfy gcc.
• src/utils/cCp/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/catUncomment/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/ccCp/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/ccCpLock/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/colCount/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/countChars/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faGapLocs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faGapSizes/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faNoise/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faOneRecord/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faRandomize/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/faSplit/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/fixCr/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/htmlPics/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/jkUniq/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/newProg/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/nibCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/nibFrag/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/nibSize/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v248 preview
• src/utils/rmFaDups/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/scaffoldFaToAgp/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/scrambleFa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/sortFa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/subChar/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/subs/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/tailLines/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/toLower/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/toUpper/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/undupFa/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/upper/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/utils/wordLine/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/webBlat/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/weblet/bottleneck/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/weblet/hitreport/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/wormAli/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/aliStats/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/blastStats/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/bwana/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/cbAli/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/dynAlign/makefile
  • lines changed 0, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/newIntron/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/smithWat/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/stitcher/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/waba/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/xaShow/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.
• src/xenoAli/xenWorm/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact that many makefiles did not include ${L} properly.

• lines changed: 41266
• files changed: 451