All File Changes

v278_base to v279_preview (2013-01-22 to 2013-01-29) v279

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 1, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/gfServer/gfServer.c
  • lines changed 8, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 8, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
  • lines changed 11, context: html, text, full: html, text
    Added detailed description of how paths are handled between gfServer commandline and the various clients that use gfServer.
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 8, context: html, text, full: html, text
    Added new error condition to checkTableCoords, to avoid a segfault whena table looks like BED12 but has blockCount=0 and NULL blockSizes & chromStarts.
    
• src/hg/hgTables/bigBed.c
  • lines changed 7, context: html, text, full: html, text
    Bug #9860 (TB paste IDs button not working for bigBed) - Steve foundthat while one can now get to the paste IDs page for bigBed, one can't
    get out of it -- clicking submit caused another illegal mysql query.
    Added the rest of the missing implementation for pasted/uploaded IDs
    for bigBed.
    
• src/hg/hgTables/identifiers.c
  • lines changed 14, context: html, text, full: html, text
    Bug #9860 (TB paste IDs button not working for bigBed) - Steve foundthat while one can now get to the paste IDs page for bigBed, one can't
    get out of it -- clicking submit caused another illegal mysql query.
    Added the rest of the missing implementation for pasted/uploaded IDs
    for bigBed.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
• src/hg/hgTracks/mainMain.c
  • lines changed 2, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
  • lines changed 1, context: html, text, full: html, text
    removing unneeded include
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    set udc cache location early before cart and doMiddle if possible. Restoring saved sessions with bigDataUrl custom tracks was leaking to /tmp/udcCache instead of correct CGI location under trash.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 20, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): remove an asObj tweak that was causing pgSnp load problem in annoGratorGpVar.Also get the trackDb for the selected subtrack, which is not the behavior of trackDbForTrack -- it returns composite tdb.
    Implement "mustOverlap" grator behavior.
    
• src/hg/hgc/peakClusters.c
  • lines changed 7, context: html, text, full: html, text
    Sorting items in cluster by metadata made more general
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Adding link to new AWG Uniform DNase downloads for ENCODE RM#9850
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 6, context: html, text, full: html, text
    Whitespace changes.
  • lines changed 9, context: html, text, full: html, text
    Reworded slightly and added note about the standalone and graphical versions of blat being different, and included a link to the graphical version.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Added white rhinoceros.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 55, context: html, text, full: html, text
    Added white rhinoceros.
  • lines changed 6, context: html, text, full: html, text
    Added white rhino announcement and credits.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 52, context: html, text, full: html, text
    Added white rhino announcement and credits.
• src/hg/htdocs/indexNews.html
  • lines changed 41, context: html, text, full: html, text
    Added white rhino announcement and credits.
• src/hg/inc/hdb.h
  • lines changed 6, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): remove an asObj tweak that was causing pgSnp load problem in annoGratorGpVar.Also get the trackDb for the selected subtrack, which is not the behavior of trackDbForTrack -- it returns composite tdb.
    Implement "mustOverlap" grator behavior.
    
• src/hg/inc/mdb.h
  • lines changed 5, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    Tricky cart session handling calls custom track parser early, so need to set the udc cache dir here in a CGI-independent way.
• src/hg/lib/cv.c
  • lines changed 2, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/lib/fileUi.c
  • lines changed 18, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/lib/geoMirror.c
  • lines changed 9, context: html, text, full: html, text
    better documentation of geoSuffix and testing
• src/hg/lib/gpFx.c
  • lines changed 2, context: html, text, full: html, text
    take out some errAborts in gpFX.c that were in there just to remind me to write code . Requested by Angie
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): remove an asObj tweak that was causing pgSnp load problem in annoGratorGpVar.Also get the trackDb for the selected subtrack, which is not the behavior of trackDbForTrack -- it returns composite tdb.
    Implement "mustOverlap" grator behavior.
    
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/lib/mdb.c
  • lines changed 9, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/lib/pgSnp.c
  • lines changed 7, context: html, text, full: html, text
    Targeted change to fetchCodons() to avoid seg fault when calculated sequence length is less than or equal to zero.
• src/hg/liftUp/liftUp.c
  • lines changed 1, context: html, text, full: html, text
    during align file lift the sequence ids can become large due to big contig names plus the start stop coordinates as part of the name
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 34, context: html, text, full: html, text
    Add downloads. Rework trackDb organization and track labels to address versioning, with input from Brooke. #9954 ENCODE Regulation: DNase Clusters V2
  • lines changed 12, context: html, text, full: html, text
    Add metaDb for V2 (needed to activate downloads link). Track #9954: ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    Documented the renameing and reload the qPcrPrimer tables for mm1o and hg19 (redmine #9269)
• src/hg/makeDb/doc/mm10.txt
  • lines changed 22, context: html, text, full: html, text
    Documented the renameing and reload the qPcrPrimer tables for mm10 and hg19(redmine #9269)
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added cerSim1 (redmine #8752)
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added cerSim1 (redmine #8752)
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 9, context: html, text, full: html, text
    1. hgFileUi now only prints data restriction warning if the composite has a restricted object. 2. Add -cv option to mdbPrint to allow alternate CV file. 2. 3. A step toward modularizing restriction timestamp handling. #10006 Mute File UI loud warnings when they are not applicable.
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    make ucscGenePfam searchable, add to all.joiner, capitalize D in Domains (#9135)
• src/hg/makeDb/trackDb/README
  • lines changed 52, context: html, text, full: html, text
    added back some loading instructions that I was a little too agressive cutting out with commit f55d1c8d119443325da881dc08428fae21f4adf0
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added appropriate override sections so chain/net track description pages would appear properly (redmine #8752)
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing broken link, http://stemcells.nih.gov/research/registry/BresaGen.asp for cv.ra
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, fixing a broken link, Kate added update to allow mutiple accession numbers
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Copying beta/cv.ra to public/cv.ra to fix link >.../registry/BresaGen.asp
• src/hg/makeDb/trackDb/human/hg19/chainCanFam2.ra
  • lines changed 1, context: html, text, full: html, text
    Added white rhinoceros to hg19 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/human/hg19/chainCanFam3.ra
  • lines changed 1, context: html, text, full: html, text
    Added white rhinoceros to hg19 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/.nfs000000001c22961e000002bd
  • lines changed 43, context: html, text, full: html, text
    Remove bogus file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/acc.out
  • lines changed 2, context: html, text, full: html, text
    Remove bogus files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/new.txt
  • lines changed 127, context: html, text, full: html, text
    Remove bogus files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra
  • lines changed 14, context: html, text, full: html, text
    Comment out multiple accession lists until ENCODE experiment matrix can handle them. MLQ #10028: ENCODE Experiment matrix doesn't load
  • lines changed 15, context: html, text, full: html, text
    Add magic number to metaDb after removing accession lists. MLQ #10028: ENCODE Experiment matrix doesn't load
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegDnaseClustered.ra
  • lines changed 8, context: html, text, full: html, text
    Add metaDb for V2 (needed to activate downloads link). Track #9954: ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgDnaseUniform.ra
  • lines changed 15, context: html, text, full: html, text
    Restaging metaData on beta and public for AWG DNase Uniform RM#9850 Release1, removing double accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegDnaseClustered.ra
  • lines changed 8, context: html, text, full: html, text
    Copied metadata from alpha to beta/public; removed release tags from .ra file; made minor correctiosn to html (redmine #9954)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAwgDnaseUniform.ra
  • lines changed 15, context: html, text, full: html, text
    Restaging metaData on beta and public for AWG DNase Uniform RM#9850 Release1, removing double accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegDnaseClustered.ra
  • lines changed 8, context: html, text, full: html, text
    Copied metadata from alpha to beta/public; removed release tags from .ra file; made minor correctiosn to html (redmine #9954)
• src/hg/makeDb/trackDb/human/hg19/netCanFam2.ra
  • lines changed 1, context: html, text, full: html, text
    Added white rhinoceros to hg19 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/human/hg19/netCanFam3.ra
  • lines changed 1, context: html, text, full: html, text
    Added white rhinoceros to hg19 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 41, context: html, text, full: html, text
    Added white rhinoceros to hg19 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Add downloads. Rework trackDb organization and track labels to address versioning, with input from Brooke. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html
  • lines changed 7, context: html, text, full: html, text
    Adding reference suggested by lab, per Kate email for AWG DNase Uniform
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    ENCODE Regulation release 2 changes. Retiring the .releaseN.ra files. Track #7526: ENCODE Regulation track update
  • lines changed 20, context: html, text, full: html, text
    Retiring the supertrack .releaseN.ra files. Track #7526: ENCODE Regulation track update
  • lines changed 32, context: html, text, full: html, text
    Add DNase Clusters track update (renaming old to V1). Track #7526: ENCODE Regulation track update
  • lines changed 18, context: html, text, full: html, text
    Copied metadata from alpha to beta/public; removed release tags from .ra file; made minor correctiosn to html (redmine #9954)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra
  • lines changed 333, context: html, text, full: html, text
    Retiring the supertrack .releaseN.ra files. Track #7526: ENCODE Regulation track update
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release3.ra
  • lines changed 348, context: html, text, full: html, text
    Retiring the supertrack .releaseN.ra files. Track #7526: ENCODE Regulation track update
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release4.ra
  • lines changed 23, context: html, text, full: html, text
    Add downloads. Rework trackDb organization and track labels to address versioning, with input from Brooke. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html
  • lines changed 30, context: html, text, full: html, text
    Add downloads. Rework trackDb organization and track labels to address versioning, with input from Brooke. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV2.html
  • lines changed 51, context: html, text, full: html, text
    Add downloads. Rework trackDb organization and track labels to address versioning, with input from Brooke. #9954 ENCODE Regulation: DNase Clusters V2
  • lines changed 2, context: html, text, full: html, text
    Add link to ENCODE portal to track description (non-standard ENCODE track so it doesn't show in top menu bar. Track #9954 ENCODE Regulation: DNase Clusters V2
  • lines changed 3, context: html, text, full: html, text
    Copied metadata from alpha to beta/public; removed release tags from .ra file; made minor correctiosn to html (redmine #9954)
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 1, context: html, text, full: html, text
    Replaced quotes with html code per Brooke's code review (redmine #10026)
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to NCBI bioproject page
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 13, context: html, text, full: html, text
    added s to Glire and Euarchontoglire because Glires is a latin word (thaks, Tom Pringle for ointing that out). without the s it is not a word. Also Capitalized both words whereever found
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 41, context: html, text, full: html, text
    Added white rhinoceros to mm10 placental chain/net composite track; had to edit letters of other assemblies as a result of the insertion (redmine #8752)
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 13, context: html, text, full: html, text
    added s to Glire and Euarchontoglire because Glires is a latin word (thaks, Tom Pringle for ointing that out). without the s it is not a word. Also Capitalized both words whereever found
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Added appropriate override sections so chain/net track description pages would appear properly (redmine #8752)
• src/hg/makeDb/trackDb/qPcrPrimers.html
  • lines changed 9, context: html, text, full: html, text
    Fixed typos found in code review. Changed punctuation in naming scheme section.
  • lines changed 1, context: html, text, full: html, text
    Moved a period inside a quotation mark to be consistent with that style later on the page, and because we are American and don't use the more logical British style.
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • lines changed 4, context: html, text, full: html, text
    Added notes to point out that rheMac2 is an Indian macaque and rheMac3 is a Chinese macaque. RM #9802. Wording is taken from links in RM #9777#note-4.
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 5, context: html, text, full: html, text
    Added notes to point out that rheMac2 is an Indian macaque and rheMac3 is a Chinese macaque. RM #9802. Wording is taken from links in RM #9777#note-4.
• src/hg/makeDb/trackDb/rhino/cerSim1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #8752)
• src/hg/makeDb/trackDb/rhino/cerSim1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #8752)
• src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.chainNet.ra
  • lines changed 15, context: html, text, full: html, text
    Added appropriate override sections so chain/net track description pages would appear properly (redmine #8752)
• src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Added appropriate override sections so chain/net track description pages would appear properly (redmine #8752)
  • lines changed 7, context: html, text, full: html, text
    add gold search to find all the fragments
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    make ucscGenePfam searchable, add to all.joiner, capitalize D in Domains (#9135)
• src/hg/pslCDnaFilter/cDnaAligns.c
  • lines changed 32, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/cDnaAligns.h
  • lines changed 8, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 9, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/hapLoci.id-psl
  • lines changed 12, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/tests/expected/hapLocalTest/hapLoci.id-psl
  • lines changed 12, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/tests/expected/hapLocalXenoTest/hapLoci.id-psl
  • lines changed 0, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/pslCDnaFilter/usage.txt
  • lines changed 7, context: html, text, full: html, text
    Added option to pslCDnaFilter to output an indentification of the haplotype locigrouping that were defined when using haplotype map filtering.
    
• src/hg/utils/automation/ensGene/petMar2.ensGene.ra
  • lines changed 6, context: html, text, full: html, text
    redmine #9407: Add petMar2 to Ensembl Genes v69 update.
• src/hg/utils/bedToPsl/bedToPsl.c
  • lines changed 1, context: html, text, full: html, text
    fix bedToPsl to create only one block for bed4 #9135
• src/inc/bits.h
  • lines changed 23, context: html, text, full: html, text
    Added local memeory support for bits and a couple of routines to query lm size.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 3, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/inc/elmTree.h
  • lines changed 122, context: html, text, full: html, text
    Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 1, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/inc/localmem.h
  • lines changed 19, context: html, text, full: html, text
    Added local memeory support for bits and a couple of routines to query lm size.
• src/inc/vcf.h
  • lines changed 147, context: html, text, full: html, text
    Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
• src/jkOwnLib/genoFind.c
  • lines changed 7, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 7, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/lib/annoGrator.c
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): remove an asObj tweak that was causing pgSnp load problem in annoGratorGpVar.Also get the trackDb for the selected subtrack, which is not the behavior of trackDbForTrack -- it returns composite tdb.
    Implement "mustOverlap" grator behavior.
    
• src/lib/bits.c
  • lines changed 69, context: html, text, full: html, text
    Added local memeory support for bits and a couple of routines to query lm size.
• src/lib/common.c
  • lines changed 10, context: html, text, full: html, text
    Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general.
  • lines changed 10, context: html, text, full: html, text
    Revert "Add ability to tolerate paths in .2bit filename with gfServer. Paths are removed leaving only the filename. Clients are on other machines and therefore cannnot use them in general."
    This reverts commit ef98cc65cd9626157087f5ad3dd6eac5012c50d8.
    
    Turns out that on some rare cases the relative paths were useful.
    Instead will add a message to gfServer explaining better how the
    paths in the filenames given will be used.
    
• src/lib/elmTree.c
  • lines changed 275, context: html, text, full: html, text
    Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
• src/lib/localmem.c
  • lines changed 56, context: html, text, full: html, text
    Added local memeory support for bits and a couple of routines to query lm size.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
• src/lib/vcf.c
  • lines changed 571, context: html, text, full: html, text
    Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v279 preview1
• src/webBlat/install.txt
  • lines changed 5, context: html, text, full: html, text
    Fixed incorrect and misleading config lines in documentation for webBlat.

• lines changed: 3218
• files changed: 121