All File Changes

v280_base to v281_preview (2013-03-05 to 2013-03-12) v281

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    Improved label of submit button.
• src/hg/hgTables/bam.c
  • lines changed 4, context: html, text, full: html, text
    more assembly hub changes to prevent database connections (#8072)
• src/hg/hgTables/bigBed.c
  • lines changed 4, context: html, text, full: html, text
    another fix to avoid opening an SQL connection on assembly hub (#8072)
• src/hg/hgTracks/container.c
  • lines changed 1, context: html, text, full: html, text
    Removing commented out debugging statement.
• src/hg/hgTracks/hgTracks.c
  • lines changed 26, context: html, text, full: html, text
    text changes to pdf/ps page, redmine #10317 and #1077
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/hgTracks/imageV2.c
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    Changing 'ugly' in comment to 'unsightly' since like to use ugly as a keyword for debugging code.
• src/hg/hgTracks/multiWig.c
  • lines changed 158, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
  • lines changed 16, context: html, text, full: html, text
    Making reverse work with new transparency code.
• src/hg/hgTracks/wigCommon.h
  • lines changed 24, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/hgTracks/wigTrack.c
  • lines changed 94, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 49, context: html, text, full: html, text
    Feature #6152 (varAnnogrator): fixing bugs uncovered by switching todifferent organisms and assemblies when the cart has a queryConfig
    that includes sources available in some assemblies but not others.
    Tests for NULLs, propagate changes to default from group to track,
    etc. Also found that mouse's Phenotype group has a slightly different
    name from human's, so check for both.
    
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    Removing extra </a> from title bar, accidentally added by bad cut and paste of other title bar, for downloads.html
  • lines changed 1, context: html, text, full: html, text
    Adding back style line accidentally removed,.undecoratedLink { text-decoration: none; }, is used in downloads.html page
  • lines changed 10, context: html, text, full: html, text
    Changes from Brian L. code review (clean-up remaining in-line style directives)
  • lines changed 4, context: html, text, full: html, text
    Add link to cv.ra file. ENCODE Docs #10346: Making cv.ra accessible
  • lines changed 1, context: html, text, full: html, text
    Adjust description of segmentation track, responding to request by Michael Hoffman of AWG. ENCODE Docs #10047: Portal - Add section to downloads for analysis fiels on EBI track hub
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 1, context: html, text, full: html, text
    Changing dates for ENCODE/downloadsMouse.html , CR:10328
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 1, context: html, text, full: html, text
    corrected, code review redmine #10330
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Fixed typo: visiblity -> visibility.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    added announcement for mm10 dbSNP 137 tracks
  • lines changed 1, context: html, text, full: html, text
    added missing </p> tag
  • lines changed 2, context: html, text, full: html, text
    adjusted spacing and added missing html tags
  • lines changed 1, context: html, text, full: html, text
    removed extra <hr> tag
• src/hg/htdocs/images/Mustela_putorius_furo.png
  • lines changed 0, context: html, text, full: html, text
    photograph from Alfredo Gutiérrez and Wikimedia Commons
• src/hg/htdocs/indexNews.html
  • lines changed 50, context: html, text, full: html, text
    added dbSNP 137 mm10 announcement
  • lines changed 1, context: html, text, full: html, text
    added missing ':' to denisova announcement
• src/hg/inc/annoFormatVep.h
  • lines changed 43, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 4, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/inc/gpFx.h
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/inc/soTerm.h
  • lines changed 82, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/inc/soterm.h
  • lines changed 74, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/annoFormatVep.c
  • lines changed 405, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
  • lines changed 1, context: html, text, full: html, text
    Fixing strict-gcc warning: non-literal format argument.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 127, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/annoStreamDb.c
  • lines changed 12, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/hg/lib/gpFx.c
  • lines changed 174, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/soTerm.c
  • lines changed 43, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 56, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 6, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 46, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 17, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/tests/input/annoGrator/vepSample.pgSnp.tab
  • lines changed 2, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/variant.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
    with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.
    
• src/hg/lib/wiggleCart.c
  • lines changed 1, context: html, text, full: html, text
    Changing default value of aggregate to NONE rather than transparent.
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 51, context: html, text, full: html, text
    add quality track redmine 10350
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 108, context: html, text, full: html, text
    Add metadata generation
  • lines changed 23, context: html, text, full: html, text
    Add track description. Add target to metadata. ENCODE Track #10042: Uniform TFBS
  • lines changed 32, context: html, text, full: html, text
    Add accessions to metadata. Rename files for downloads. ENCODE Track #10042: Uniform TFBS
  • lines changed 32, context: html, text, full: html, text
    Massage labels. Start downloads. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/doc/hg19.txt
  • lines changed 68, context: html, text, full: html, text
    Started nomLeu3 lastz refs#9812
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 3, context: html, text, full: html, text
    redmine Bug #10358 rebuild rn4.knownToEnsembl using rgdGene2 instead of knownGene.
• src/hg/makeDb/doc/musFur1.txt
  • lines changed 74, context: html, text, full: html, text
    running repeat masker simple repeats and window masker
  • lines changed 92, context: html, text, full: html, text
    done with masking, running genscan and cpgIslands getting ready for genbank
  • lines changed 1509, context: html, text, full: html, text
    done and in the pushQ redmine 6352 pushQ 06988
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 120, context: html, text, full: html, text
    Updating makedoc with more progress.
  • lines changed 56, context: html, text, full: html, text
    Adding more updates to makedoc. refs #9812
  • lines changed 10, context: html, text, full: html, text
    Completed loading of genbank tracks. refs #9812
  • lines changed 10, context: html, text, full: html, text
    Finalizing makedoc...assembly is done! refs #9812
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 46, context: html, text, full: html, text
    Finished doRepeatMasker
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added musFur1/ferret to the daily build
  • lines changed 1, context: html, text, full: html, text
    Added nomLeu3. refs #9812
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding musFur1 ferret redmine 6352
  • lines changed 19, context: html, text, full: html, text
    adding nomLeu3 Gibbon refs #9812
  • lines changed 15, context: html, text, full: html, text
    adding panPan1 bonobo
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added musFur1/ferret to the daily build
  • lines changed 1, context: html, text, full: html, text
    Added nomLeu3. refs #9812
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for musFurNames redmine 6352
  • lines changed 2, context: html, text, full: html, text
    adding definition for panPanNames Pan paniscus
  • lines changed 1, context: html, text, full: html, text
    adding definition for panPanNames Pan paniscus
• src/hg/makeDb/schema/all.joiner
  • lines changed 7, context: html, text, full: html, text
    adding musFur1 redmine 6342
  • lines changed 10, context: html, text, full: html, text
    Ignore all numt* tables for all assemblies.
  • lines changed 1, context: html, text, full: html, text
    Adjusted the threshold of dm1.bdgpToRefSeq.value from 0.94 to 0.91 which eliminated a joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the threshold of dm2.flyBaseToRefSeq.value from 0.96 to 0.94 which eliminated a joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the threshold of hg16,hg17.knownToRefSeq.value from 0.94 to 0.93 which eliminated an hg16 joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted the threshold of hg18,hg19,mm9,mm10.kgXref.geneSymbol from 0.85 to 0.84 which eliminated an mm10 joinerCheck error
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 338, context: html, text, full: html, text
    Comments revision of cv.ra, removing comments to make cv.ra downloadable RM#10346
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 338, context: html, text, full: html, text
    Comments revision of cv.ra copying to beta, removing comments to make cv.ra downloadable RM#10346
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 338, context: html, text, full: html, text
    Comments revision of cv.ra copying to public/cv.ra, removing comments to make cv.ra downloadable RM#10346
• src/hg/makeDb/trackDb/ferret/musFur1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.ra
• src/hg/makeDb/trackDb/ferret/musFur1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.ra
• src/hg/makeDb/trackDb/ferret/musFur1/gold.html
  • lines changed 33, context: html, text, full: html, text
    initial files from makeGenomeDb.ra
• src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra
  • lines changed 11799, context: html, text, full: html, text
    Metadata for ENCODE Uniform TFBS track. RM 10042
  • lines changed 1884, context: html, text, full: html, text
    Add target metadata. Remove dummy dccAccessions. ENCODE Track #10042: Uniform TFBS
  • lines changed 695, context: html, text, full: html, text
    Add DCC accessions. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 108, context: html, text, full: html, text
    Add track description. #10042 - ENCODE Uniform Tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 2, context: html, text, full: html, text
    temporary joke image (ref Grauer et al)
  • lines changed 1391, context: html, text, full: html, text
    Add labs. Reformat long labels using ideas from analysis hub
  • lines changed 107, context: html, text, full: html, text
    Trim long labels to proper length. ENCODE Track #10042: Uniform TFBS
  • lines changed 112, context: html, text, full: html, text
    Trim short labels. ENCODE Track #10042: Uniform TFBS
  • lines changed 141, context: html, text, full: html, text
    Add lab identifier to short labels to distinguish same experiment from different labs. h=HudsonAlpha, s=Stanford, t=UTexas-Austin, w=UWashington, c=USC, v=Harvard, y=Yale, b=Broad. ENCODE Track #10042: Uniform TFBS
  • lines changed 109, context: html, text, full: html, text
    Tweak default on subtracks. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    renamed kap1 and znf486 tracks as requested by wetlab
  • lines changed 3, context: html, text, full: html, text
    change button type for repeats2 browser to give understandable descriptions
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Change the short lable 'NumtS on mitochondrion' to 'NumtS on chrM'.
• src/hg/oneShot/freen/freen.c
  • lines changed 14, context: html, text, full: html, text
    Testing loadAndValidateBed.
  • lines changed 17, context: html, text, full: html, text
    Testing some C 1999 extensions.
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 1, context: html, text, full: html, text
    Should use .allGenes.gp.gz instead of .all.genes.gp.gz.
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 2, context: html, text, full: html, text
    avoid the *.ori.out files with a custom library
• src/hg/utils/automation/ensGene/rn4.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    redmine Bug #10358 rebuild rn4.knownToEnsembl using rgdGene2 instead of knownGene.
• src/hg/utils/automation/ensGene/rn5.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    redmine Bug #10358 rebuild rn4.knownToEnsembl using rgdGene2 instead of knownGene.
• src/hg/utils/decipher/checkDecipher.sh
  • lines changed 1, context: html, text, full: html, text
    DECIPHER changed this directory to include a bed file that we end up grabbing. Make sure we get the txt file. #5172
• src/hg/utils/phyloTrees/62way.nh
  • lines changed 1, context: html, text, full: html, text
    fixup name for allMis1 in 62way and update petMar1 to petMar2 in 65way, redmine 7482
• src/hg/utils/phyloTrees/65way.nh
  • lines changed 2, context: html, text, full: html, text
    fixup name for allMis1 in 62way and update petMar1 to petMar2 in 65way, redmine 7482
• src/hg/utils/phyloTrees/70way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    common names for 70-way, redmine 10272
• src/hg/utils/phyloTrees/70way.nh
  • lines changed 70, context: html, text, full: html, text
    working up the larger tree
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 27, context: html, text, full: html, text
    adding new assemblies redmine 7482
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 5, context: html, text, full: html, text
    adding new assemblies redmine 7482
• src/hg/utils/pslMap/pslMap.c
  • lines changed 16, context: html, text, full: html, text
    convert pslmap to from binKeeper to genomeRangeTree to reduce memory use by two orders of magintude
• src/inc/asParse.h
  • lines changed 4, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/inc/bPlusTree.h
  • lines changed 9, context: html, text, full: html, text
    Adding bptKeyAtPos and bptStringKeyAtPos methods so can go from a chromosome index back to a chromosome name quickly without loading all the chromosomes.
  • lines changed 4, context: html, text, full: html, text
    Adding support for multiple values with same key to bPlusTree.
• src/inc/bbiFile.h
  • lines changed 7, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 8, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 18, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
  • lines changed 23, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 6, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 5, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
  • lines changed 10, context: html, text, full: html, text
    Polishing code a little with no functional change.
• src/inc/bigBed.h
  • lines changed 11, context: html, text, full: html, text
    Adding chromId to bigBedInterval structure for item name based queries. Removing unused ppBed structure.
  • lines changed 30, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 4, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 6, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 7, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 7, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/inc/bigWig.h
  • lines changed 5, context: html, text, full: html, text
    Exposing bwgCreate() function at Diane Trout at Caltech's request.
  • lines changed 5, context: html, text, full: html, text
    Moving bwgCreate prototype to bwgInternal to fix compiler warning.
• src/inc/bwgInternal.h
  • lines changed 5, context: html, text, full: html, text
    Moving bwgCreate prototype to bwgInternal to fix compiler warning.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Adding slRefFreeListAndVals utility routine.
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    Added -Wformat-security to hgwdev's HG_WARN so that a common stricter-gcc warning is detected during development.
• src/inc/memgfx.h
  • lines changed 9, context: html, text, full: html, text
    Adding functions to extract a color component from a 32 bit color.
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 59, context: html, text, full: html, text
    Rearranging logging levels so verbose(2) prints a handful of status messages one for each major phase. Some of the logging leaks memory, so put in a test to avoid this unless logging level is high.
  • lines changed 68, context: html, text, full: html, text
    Some refactoring in anticipation of expanding output if need be to accommodate full monomer diversity.
  • lines changed 68, context: html, text, full: html, text
    Adding maxToMiss and maxOutSize parameters to let program expand output size if need be to get in all monomers, or to miss a few monomers.
  • lines changed 1, context: html, text, full: html, text
    Fixed bug where the empty string was always making it look like one monomer was missing.
• src/lib/annoFormatTab.c
  • lines changed 1, context: html, text, full: html, text
    bugfix: if some word is NULL, print out empty string.
• src/lib/annoGrator.c
  • lines changed 1, context: html, text, full: html, text
    When freeing annoRows created by internal source, pass in internal source not self. (#6152)
• src/lib/annoRow.c
  • lines changed 1, context: html, text, full: html, text
    bugfix: forgot to null out *pList in a FreeList function.
• src/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    Removed outdated comment.
• src/lib/asParse.c
  • lines changed 12, context: html, text, full: html, text
    Libified asColumnFindIx. (#6152)
• src/lib/bPlusTree.c
  • lines changed 68, context: html, text, full: html, text
    Adding bptKeyAtPos and bptStringKeyAtPos methods so can go from a chromosome index back to a chromosome name quickly without loading all the chromosomes.
  • lines changed 94, context: html, text, full: html, text
    Adding support for multiple values with same key to bPlusTree.
  • lines changed 4, context: html, text, full: html, text
    Fixing bug in rFindMulti that was making bigBed name index crash on uc021tvv.1 in ucscGenes.bb
  • lines changed 16, context: html, text, full: html, text
    Making a lot of the arithmetic 64-bit so that it doesn't overflow on files with lots of items.
  • lines changed 2, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/lib/basicBed.c
  • lines changed 14, context: html, text, full: html, text
    Fixing a bug that caused crashes and error messages on beds with lots of blocks.
  • lines changed 14, context: html, text, full: html, text
    Renaming a local variable to be a bit more descriptive.
• src/lib/bbiRead.c
  • lines changed 2, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 14, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 13, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
• src/lib/bbiWrite.c
  • lines changed 16, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 42, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Adding chromId to bigBedInterval structure for item name based queries. Removing unused ppBed structure.
  • lines changed 164, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 122, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 69, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 78, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 79, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/lib/bwgCreate.c
  • lines changed 1, context: html, text, full: html, text
    Exposing bwgCreate() function at Diane Trout at Caltech's request.
  • lines changed 2, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/lib/common.c
  • lines changed 14, context: html, text, full: html, text
    Adding slRefFreeListAndVals utility routine.
• src/lib/errabort.c
  • lines changed 27, context: html, text, full: html, text
    Deal with out of memory issue in errAbort::getThreadVars() since errAbort thread data is being stored in a hash whose functions can themselves errAbort when out of memory. This issue was reported by Max H. and Mark D.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 3, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 2, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 94, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 1, context: html, text, full: html, text
    Reducing verbosity a bit.
  • lines changed 305, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
  • lines changed 35, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 10, context: html, text, full: html, text
    Polishing code a little with no functional change.
• src/utils/bedToBigBed/itemRgb.bed
  • lines changed 1, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 1, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 11, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
• src/utils/bigBedNamedItems/bigBedNamedItems.c
  • lines changed 120, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 47, context: html, text, full: html, text
    First cut at read side of named index seems to work. Still needs testing and polishing.
  • lines changed 9, context: html, text, full: html, text
    Fixing bug where it only finds item if it's in first part of block.
  • lines changed 2, context: html, text, full: html, text
    Removing some debugging uglyfs
  • lines changed 59, context: html, text, full: html, text
    Making it so that multiple items can have same name, and all such items are found.
  • lines changed 31, context: html, text, full: html, text
    Refactoring in preparation for moving much of this to library.
  • lines changed 151, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 16, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 8, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 4, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/utils/bigBedNamedItems/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding bigBedNamedItems to utilities compilation.
• src/utils/qa/makeCytoBandIdeo.csh
  • lines changed 1, context: html, text, full: html, text
    at hiram's suggestion, adding -ef flag to first line. he says it'll hard-quit on an error, but I haven't found any difference in what it does.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v281 preview1
• src/utils/qa/weeklybld/summaryEmail.sh
  • lines changed 2, context: html, text, full: html, text
    Added --stat to the git log command that reminds us what we changed inthe branch, so it will also remind us which files changed with each commit.
    

• lines changed: 23774
• files changed: 189