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
- lines changed 1, context: html, text, full: html, text
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 2, context: html, text, full: html, text
adjusted spacing and added missing html tags
- 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
- 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
- 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
- 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.
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- files changed: 189