All File Changes

v249_base to v250_preview (2011-03-29 to 2011-04-05) v250

• src/hg/dbTrash/dbTrash.c
  • lines changed 173, context: html, text, full: html, text
    moved show table status into an option to improve performance
• src/hg/encode/DAFs/2.0/gisChiaPet.daf
  • lines changed 2, context: html, text, full: html, text
    added fastq required, at suggestion of Brian
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 2, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 4, context: html, text, full: html, text
    Depersonalize comments
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 19, context: html, text, full: html, text
    Added logic to ignore objType=composite in files
• src/hg/gbOneAcc/gbOneAcc.c
  • lines changed 1, context: html, text, full: html, text
    allow for longer than 20 line descriptions in genbank entries
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    make sure that appropriate track is visible when user selects something via gene suggest box (see redmine #3484)
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 115, context: html, text, full: html, text
    fixing hgLiftOver: grouping and slightly re-ordering options; adding a new section to show what parameters were actually used to display the results, since code currently resets most options to the values in the chain liftOverChains record; also renamed minSizeT to minChainT since that is what it really is, everywhere except liftOverChain.as and the actual db tables and liftOverChain.sql
• src/hg/hgTables/usage.c
  • lines changed 2, context: html, text, full: html, text
    With my previous commit, I removed the section about ENCODE regions,but Brooke pointd out in code review that there are still ENCODE regions in previous human assemblies.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Nav linlks should not depend upon dimensions alone
• src/hg/hgTracks/bamTrack.c
  • lines changed 2, context: html, text, full: html, text
    Code Review #3440 (Jim): removing calls to udcSetCacheTimeout withhardwired time -- hgTracks.c now sets it with cart var + default.
• src/hg/hgTracks/bedTrack.c
  • lines changed 6, context: html, text, full: html, text
    Bugs #3475, #3476 (hgTracks map links messed up for SNPs, omimGene):These were side-effects of my commit a8d97808 Mar. 11, in which I enabled next-prev-exon for all simple beds (which, because they don't have exons/blocks, just means zap-to-edge), instead of only for dbVar where it was requested. It turns out that way too many bed-based tracks with custom drawItems and/or drawItemAt methods are missing something necessary for the nextItem stuff to work. In this fix, instead of hooking up zap-to-edge for all simple bed, I hook it up only to GVF (dbVar/ISCA).
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 7, context: html, text, full: html, text
    restore winStart and winEnd values in hgc links (see redmine 2456)
• src/hg/hgTracks/gvfTrack.c
  • lines changed 1, context: html, text, full: html, text
    Bugs #3475, #3476 (hgTracks map links messed up for SNPs, omimGene):These were side-effects of my commit a8d97808 Mar. 11, in which I enabled next-prev-exon for all simple beds (which, because they don't have exons/blocks, just means zap-to-edge), instead of only for dbVar where it was requested. It turns out that way too many bed-based tracks with custom drawItems and/or drawItemAt methods are missing something necessary for the nextItem stuff to work. In this fix, instead of hooking up zap-to-edge for all simple bed, I hook it up only to GVF (dbVar/ISCA).
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Remvoed obsolete assert. The build will have to be patched with this.
  • lines changed 4, context: html, text, full: html, text
    make sure that appropriate track is visible when user selects something via gene suggest box (see redmine #3484)
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    Bugs #3475, #3476 (hgTracks map links messed up for SNPs, omimGene):These were side-effects of my commit a8d97808 Mar. 11, in which I enabled next-prev-exon for all simple beds (which, because they don't have exons/blocks, just means zap-to-edge), instead of only for dbVar where it was requested. It turns out that way too many bed-based tracks with custom drawItems and/or drawItemAt methods are missing something necessary for the nextItem stuff to work. In this fix, instead of hooking up zap-to-edge for all simple bed, I hook it up only to GVF (dbVar/ISCA).
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    make sure that appropriate track is visible when user selects something via gene suggest box (see redmine #3484)
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    Code Review #3440 (Jim): removing calls to udcSetCacheTimeout withhardwired time -- hgTracks.c now sets it with cart var + default.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Letting there be another clustered DNAse track with a special details page.
  • lines changed 4, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): De-emphasizing dbSNP's "clinically-associated" flag as suggested by Brooke.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    Added UW Affy Exon and fixed css syntax quotes, redmine# 59
  • lines changed 29, context: html, text, full: html, text
    fixing one last css class syntax change
• src/hg/htdocs/goldenPath/help/fileSearch.html
  • lines changed 88, context: html, text, full: html, text
    first draft of file search documentaion
• src/hg/inc/cv.h
  • lines changed 1, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 1, context: html, text, full: html, text
    Cleaned up fileSortOrderGet's discovery of sortable vars to use cv.ra searchable with a couple of exceptions
• src/hg/inc/liftOverChain.h
  • lines changed 1, context: html, text, full: html, text
    fixing hgLiftOver: grouping and slightly re-ordering options; adding a new section to show what parameters were actually used to display the results, since code currently resets most options to the values in the chain liftOverChains record; also renamed minSizeT to minChainT since that is what it really is, everywhere except liftOverChain.as and the actual db tables and liftOverChain.sql
• src/hg/inc/mdb.h
  • lines changed 8, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 8, context: html, text, full: html, text
    Cleaned up fileSortOrderGet's discovery of sortable vars to use cv.ra searchable with a couple of exceptions
• src/hg/inc/suggest.h
  • lines changed 8, context: html, text, full: html, text
    add assemblyGeneSuggestTrack (used in fixing redmine #3483)
• src/hg/js/hgGateway.js
  • lines changed 33, context: html, text, full: html, text
    make sure that appropriate track is visible when user selects something via gene suggest box (see redmine #3484)
• src/hg/js/hgTracks.js
  • lines changed 27, context: html, text, full: html, text
    make sure that appropriate track is visible when user selects something via gene suggest box (see redmine #3484)
• src/hg/lib/cv.c
  • lines changed 4, context: html, text, full: html, text
    Cleaned up fileSortOrderGet's discovery of sortable vars to use cv.ra searchable with a couple of exceptions
• src/hg/lib/encode/encodeExp.c
  • lines changed 3, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
• src/hg/lib/fileUi.c
  • lines changed 27, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 27, context: html, text, full: html, text
    Cleaned up fileSortOrderGet's discovery of sortable vars to use cv.ra searchable with a couple of exceptions
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 2, context: html, text, full: html, text
    Get allButtonPairs working again.
• src/hg/lib/liftOverChain.as
  • lines changed 1, context: html, text, full: html, text
    fixing hgLiftOver: grouping and slightly re-ordering options; adding a new section to show what parameters were actually used to display the results, since code currently resets most options to the values in the chain liftOverChains record; also renamed minSizeT to minChainT since that is what it really is, everywhere except liftOverChain.as and the actual db tables and liftOverChain.sql
• src/hg/lib/liftOverChain.c
  • lines changed 6, context: html, text, full: html, text
    fixing hgLiftOver: grouping and slightly re-ordering options; adding a new section to show what parameters were actually used to display the results, since code currently resets most options to the values in the chain liftOverChains record; also renamed minSizeT to minChainT since that is what it really is, everywhere except liftOverChain.as and the actual db tables and liftOverChain.sql
• src/hg/lib/mdb.c
  • lines changed 46, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 33, context: html, text, full: html, text
    Cleaned up fileSortOrderGet's discovery of sortable vars to use cv.ra searchable with a couple of exceptions
  • lines changed 1, context: html, text, full: html, text
    Replaced another couple of literals
• src/hg/lib/pseudoYale60.sql
  • lines changed 15, context: html, text, full: html, text
    Created pseudoYale60.sql.
• src/hg/lib/pseudoYale60Class.sql
  • lines changed 6, context: html, text, full: html, text
    Created pseudoYale60Class.sql.
• src/hg/lib/suggest.c
  • lines changed 28, context: html, text, full: html, text
    add assemblyGeneSuggestTrack (used in fixing redmine #3483)
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    oops %% not to be used with puts(), its not like printf
  • lines changed 2, context: html, text, full: html, text
    fixing with Marks help swapped lines bug
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 53, context: html, text, full: html, text
    lastz with Turkey melGal1
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeDukeAffyExonArray.release2.notes.txt
  • lines changed 174, context: html, text, full: html, text
    4 Lhsr experiments are being removed
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaCnv.release2.notes
  • lines changed 76, context: html, text, full: html, text
    Release notes for Color Change for CNV
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release1.notes
  • lines changed 74, context: html, text, full: html, text
    Removed 4 experiments due to suspect files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibRnaSeq.release1.notes
  • lines changed 493, context: html, text, full: html, text
    New notes file
• src/hg/makeDb/doc/galGal3.txt
  • lines changed 20, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 46, context: html, text, full: html, text
    lastz with Turkey melGal1
• src/hg/makeDb/doc/hg18.txt
  • lines changed 22, context: html, text, full: html, text
    Added B CELL RNA-SEQ TRACKS.
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 52, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 189, context: html, text, full: html, text
    Documented pseudoYale60 track build.
  • lines changed 6, context: html, text, full: html, text
    Lastz with Turkey melGal1
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 141, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 28, context: html, text, full: html, text
    Lastz with Turkey melGal1
  • lines changed 147, context: html, text, full: html, text
    lastz with Turkey melGal1
  • lines changed 22, context: html, text, full: html, text
    Rat and Turkey Lastz
• src/hg/makeDb/doc/mm9.txt
  • lines changed 53, context: html, text, full: html, text
    Lastz with Turkey melGal1
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 52, context: html, text, full: html, text
    Lastz with Turkey melGal1
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 656, context: html, text, full: html, text
    done with phastCons and now running phyloP
  • lines changed 60, context: html, text, full: html, text
    done with phastCons and phyloP tracks for 12-way
  • lines changed 2, context: html, text, full: html, text
    loaded phastConsElements12wayPrimate
• src/hg/makeDb/doc/rn4.txt
  • lines changed 53, context: html, text, full: html, text
    Rat and Turkey Lastz
• src/hg/makeDb/doc/taeGut1.txt
  • lines changed 20, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 2, context: html, text, full: html, text
    Lastz with Turkey melGal1
• src/hg/makeDb/doc/xenTro2.txt
  • lines changed 23, context: html, text, full: html, text
    lastz with Turkey melGal1
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    added Sheep assemblyto list, oviAri1, to start Genbank updates
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • lines changed 1, context: html, text, full: html, text
    fixed stupid check for fork failure (bad mark, no donut)
• src/hg/makeDb/hgAddLiftOverChain/hgAddLiftOverChain.c
  • lines changed 7, context: html, text, full: html, text
    renamed minSizeT to minChainT since that is what it really is. Note that the actual database field in liftOverChains table is still has the old name minSizeT.
• src/hg/makeDb/trackDb/README
  • lines changed 8, context: html, text, full: html, text
    Added extraFields description since Brian is already using it and Angie is interested.
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 6, context: html, text, full: html, text
    remove Turkey melGal1 form trackDb.chainNet
• src/hg/makeDb/trackDb/chimp/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for NCBI Clone Registry website
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 425, context: html, text, full: html, text
    initial contents may be complete
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    setting limits on phyloP 12-way tracks
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 11, context: html, text, full: html, text
    Accepting several provisional stanzas from Venkat
  • lines changed 2, context: html, text, full: html, text
    Addressing code review feedback from Katrina
  • lines changed 257, context: html, text, full: html, text
    First draft at adding views to the CV
  • lines changed 12, context: html, text, full: html, text
    Changed the dataType to Genotype. This will make it consistent with other tracks that all data in the same composite has the same dataType
  • lines changed 4, context: html, text, full: html, text
    The IRF4 antibody had a typo in the vendor id. Used SC-6509 instead of SC-6059.
  • lines changed 49, context: html, text, full: html, text
    Accepting several provisional stanzas
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 11, context: html, text, full: html, text
    Moving some changes from alpha to beta after code review
  • lines changed 278, context: html, text, full: html, text
    Copying several changes from alpha
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 38, context: html, text, full: html, text
    releasing changes to public after reviewing
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 70, context: html, text, full: html, text
    Moved the track details file for the affy exon array to hg19, where it is actually used
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeq.html
  • lines changed 45, context: html, text, full: html, text
    Created ceuBcellRNASeq.html.
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeqBW.html
  • lines changed 1, context: html, text, full: html, text
    Created ceuBcellRNASeqBW.html.
• src/hg/makeDb/trackDb/human/hg18/ceuBcellSuper.html
  • lines changed 1, context: html, text, full: html, text
    Created ceuBcellSuper.html (a symlink).
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 52, context: html, text, full: html, text
    Changed the colors in the tables, changed the table names to V2, changed the html to reflect the new colors of red, blue, orange
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    Added B Cell RNA-Seq tracks.
  • lines changed 16, context: html, text, full: html, text
    Added ceuBcellSuper and refined titles of B-Cell tracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 302, context: html, text, full: html, text
    Split out mapability from trackDb.wgEncode.ra into separate ra files
  • lines changed 1, context: html, text, full: html, text
    add release alpha to view to fix tdbQuery complaints
  • lines changed 14, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.new.ra
  • lines changed 109, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 109, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
  • lines changed 104, context: html, text, full: html, text
    Added back metadata lines I accidentally removed from beta,public verion.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 49, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 49, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra
  • lines changed 59, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
  • lines changed 58, context: html, text, full: html, text
    Fixing the beta,public versions of two composites that I screwed up by dropping metadata lines too early
  • lines changed 59, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.new.ra
  • lines changed 8, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 8, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.new.ra
  • lines changed 24, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 24, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.new.ra
  • lines changed 5, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing the beta,public versions of two composites that I screwed up by dropping metadata lines too early
  • lines changed 5, context: html, text, full: html, text
    In my last commit I added release tags to Affy RNA Loc, Duke Affy Exon, and Helicos RNA-seq because I thought they didn't have any since there was no metadata showing on the RR, however, when i tried to do a make, I noticed that there was a release tag conflict. There already were release tags within the .ra and .new.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html
  • lines changed 95, context: html, text, full: html, text
    Changed the colors in the tables, changed the table names to V2, changed the html to reflect the new colors of red, blue, orange
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.ra
  • lines changed 9, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
  • lines changed 4, context: html, text, full: html, text
    Changed the colors in the tables, changed the table names to V2, changed the html to reflect the new colors of red, blue, orange
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
  • lines changed 9, context: html, text, full: html, text
    adding missing release tags for Affy RNA Loc, Helicos RNA-seq, Duke Affy Exon; changing release tags from in .ra to in include statement for HudsonalphaCnv, CshlShortRnaSeq, GisRNASeq and GisDNAPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • lines changed 2, context: html, text, full: html, text
    Made a new verion of hg19 wgEncodeMapability.html describing Duke Uniqueness/Excluded Regions. Also emphasized which assembly the nearly identical tracks are for.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.new.ra
  • lines changed 177, context: html, text, full: html, text
    Split out mapability from trackDb.wgEncode.ra into separate ra files
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra
  • lines changed 189, context: html, text, full: html, text
    Split out mapability from trackDb.wgEncode.ra into separate ra files
• src/hg/makeDb/trackDb/human/hg19/affyExonArray.html
  • lines changed 70, context: html, text, full: html, text
    Moved the track details file for the affy exon array to hg19, where it is actually used
  • lines changed 1, context: html, text, full: html, text
    adding italics to affy exon track html
  • lines changed 1, context: html, text, full: html, text
    removing '#1_1' from affy exon html per redmine issue http://redmine.soe.ucsc.edu/issues/3181#note-28
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 35, context: html, text, full: html, text
    Recovered lost data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 2575, context: html, text, full: html, text
    Removed errant Na in the file names of the fastqs
  • lines changed 84, context: html, text, full: html, text
    Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal
  • lines changed 1, context: html, text, full: html, text
    Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal, THIS TIME WITH MAGIC NUMBER
  • lines changed 40, context: html, text, full: html, text
    Consolidate ExonsGene and ExonGen and remove Aligns as views
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1003, context: html, text, full: html, text
    Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal
  • lines changed 1, context: html, text, full: html, text
    Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal, THIS TIME WITH MAGIC NUMBER
  • lines changed 57, context: html, text, full: html, text
    Consolidate ExonsGene and ExonGen and remove Aligns as views
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 53, context: html, text, full: html, text
    added mean+whiskers, fileSortOrder, changed release tags to new method, fixed subgroup labels, added missing information in the mdb
  • lines changed 45, context: html, text, full: html, text
    Trying to commit again to deal with the fact that hgwdev hung on my previous git commit
  • lines changed 519, context: html, text, full: html, text
    Removed 4 experiments due to suspect files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 36, context: html, text, full: html, text
    Standardized obtainedBy to lab names from PI names
  • lines changed 91, context: html, text, full: html, text
    Changed the dataType to Genotype. This will make it consistent with other tracks that all data in the same composite has the same dataType
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 405, context: html, text, full: html, text
    More re-shuffling of metadata terms and filetypes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 31, context: html, text, full: html, text
    continuing to consolidate views TranscriptGencV3 -> V3c, Fastq -> RawData
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 302, context: html, text, full: html, text
    Removed 13 files and meta-data on advisment from lab. Redmine 3057.
  • lines changed 101, context: html, text, full: html, text
    Updated 40 files with meta-data problems. Redmine 3057.
  • lines changed 633, context: html, text, full: html, text
    Updated 11 experiment set to have correct metaDb of protocols embedded in the file name. Redmine 2731.
  • lines changed 114, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 51, context: html, text, full: html, text
    Get Duke Uniqueness and Excluded Regions metadata in
  • lines changed 3, context: html, text, full: html, text
    Removed dateUnrestricted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 5, context: html, text, full: html, text
    Trying to commit again to deal with the fact that hgwdev hung on my previous git commit
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    changed the target protien to be under antibody even though there is no antibody in this experiment so that the links would work
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 115, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed error in meta-data for obj wgEncodeUwHistoneK562InputStdRawRep1 to have correct view name RawSignal instead of RawSigna.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging UW DNase DGF on beta, redmine# 2398
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 972, context: html, text, full: html, text
    staging UW DNase DGF on beta, redmine# 2398
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing for release of UW Affy Exon, redmine# 59
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
  • lines changed 42, context: html, text, full: html, text
    Created pseudoYale60.html, an edit of mm9 pseudoYale60.html.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 55, context: html, text, full: html, text
    Reordered the Affy Exon subtracks so that the order of the subtracks in the matrix would be consistent with the order of their descriptions in the track description page
  • lines changed 16, context: html, text, full: html, text
    Adding back in Mary's modifications to standardize the Affy Exon shortlabels
  • lines changed 45, context: html, text, full: html, text
    Re-fixed the Affy Exon track to provide separate view display controls for probe and probeset
  • lines changed 18, context: html, text, full: html, text
    lastz with Turkey melGal1
  • lines changed 1, context: html, text, full: html, text
    Checking in some finishing (?) touches for affy exon
  • lines changed 1, context: html, text, full: html, text
    Changing the sort parameters for affy exon
  • lines changed 1, context: html, text, full: html, text
    Removed an extraneous blank line in affy exon core
  • lines changed 2, context: html, text, full: html, text
    changing the view setting for affy exon
  • lines changed 1, context: html, text, full: html, text
    Rearranged the sort order for the Affy Exon array to put the probe(set) type first
  • lines changed 17, context: html, text, full: html, text
    remove Turkey from hg19's multiz track
  • lines changed 97, context: html, text, full: html, text
    Redid some of Anns changes from last week that due to a weird git conflict got erased by my commit on the same file. Ann's comments: Changes to the multiz46way Chain/Net Composite track species ordering. This isto accommodate David's request that species are ordered phylogenetically by default. As it was, they were ordered alphabetically. I added the alpha-prefix to the labels in the subGroup lists for all three composites. For the actual phylo order I followed the listing in the 46way Conservation track's Multiz Alignments Configuration page (even if it clashed slightly with the hg19_46way.gif image). Hiram says that it was in phylo order when it was released but that somehow it must have been reverted (to alpha order).
  • lines changed 1, context: html, text, full: html, text
    Missed one change that was supposed to be made in my previous edit, for a total of 98 lines changed to match Anns previous changes. For details, see my other change to this file.
  • lines changed 10, context: html, text, full: html, text
    found a couple other changes that Ann had made and that I missed. For details see my other comment on this file from today.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Putting in commented out line to stuff I'm working on. Trying to be inobtrusive is why it's commented out.
  • lines changed 1, context: html, text, full: html, text
    added mean+whiskers, fileSortOrder, changed release tags to new method, fixed subgroup labels, added missing information in the mdb
  • lines changed 2, context: html, text, full: html, text
    Removed alpha tags in trackDb and put alpha tag at composite level in trackDb.wgEncode.ra file. This should fix errors on make beta/public.
  • lines changed 57, context: html, text, full: html, text
    Split out mapability from the trackDb.wgEncode.ra file and added Duke Uniquness and Excluded Regions
  • lines changed 1, context: html, text, full: html, text
    removed a comment so that RIKEN track display's on hgwdev per katrinas code review, redmine #3428
  • lines changed 2, context: html, text, full: html, text
    staging UW DNase DGF on beta, redmine# 2398
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 126, context: html, text, full: html, text
    Changed the long labels for the Contigs, uncertain if we will display the Junctions
  • lines changed 238, context: html, text, full: html, text
    Fixed display issue and shortLabels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 230, context: html, text, full: html, text
    Added new submissions
  • lines changed 50, context: html, text, full: html, text
    Fixed bed 9 display issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 4, context: html, text, full: html, text
    Changed label format
  • lines changed 12, context: html, text, full: html, text
    Sort the Tier 1 to the top
  • lines changed 13, context: html, text, full: html, text
    Changed Tier 2 to sort to the top
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
  • lines changed 26, context: html, text, full: html, text
    fixed links, fix references to the affy exon track, fixed html, and reordered references, redmine#s59 & 3082
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 104, context: html, text, full: html, text
    added mean+whiskers, fileSortOrder, changed release tags to new method, fixed subgroup labels, added missing information in the mdb
  • lines changed 18, context: html, text, full: html, text
    Removed 4 experiments due to suspect files
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 3, context: html, text, full: html, text
    Changed colors of insertions/deletions to conform to the red/blue standard.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the dataType to Genotype. This will make it consistent with other tracks that all data in the same composite has the same dataType
  • lines changed 5, context: html, text, full: html, text
    Added origAssembly for the lifted tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 52, context: html, text, full: html, text
    More re-shuffling of metadata terms and filetypes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Changed label for A549 to be correct from A459
  • lines changed 271, context: html, text, full: html, text
    Added new data
  • lines changed 30, context: html, text, full: html, text
    Fixed Long Labels
  • lines changed 27, context: html, text, full: html, text
    New Submission 3868 Added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 705, context: html, text, full: html, text
    Removed alpha tags in trackDb and put alpha tag at composite level in trackDb.wgEncode.ra file. This should fix errors on make beta/public.
  • lines changed 60, context: html, text, full: html, text
    Removed 13 files and meta-data on advisment from lab. Redmine 3057.
  • lines changed 18, context: html, text, full: html, text
    Updated 40 files with meta-data problems. Redmine 3057.
  • lines changed 39, context: html, text, full: html, text
    Updated 11 experiment set to have correct metaDb of protocols embedded in the file name. Redmine 2731.
  • lines changed 151, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
  • lines changed 24, context: html, text, full: html, text
    Forgot to change labels for YY1_(C-20) to new YY1_(SC-281). Redmine 2897.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 2, context: html, text, full: html, text
    Made a new verion of hg19 wgEncodeMapability.html describing Duke Uniqueness/Excluded Regions. Also emphasized which assembly the nearly identical tracks are for.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
  • lines changed 83, context: html, text, full: html, text
    Made a new verion of hg19 wgEncodeMapability.html describing Duke Uniqueness/Excluded Regions. Also emphasized which assembly the nearly identical tracks are for.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 123, context: html, text, full: html, text
    Split out mapability from the trackDb.wgEncode.ra file and added Duke Uniquness and Excluded Regions
  • lines changed 16, context: html, text, full: html, text
    Fine tuning
  • lines changed 6, context: html, text, full: html, text
    Made a new verion of hg19 wgEncodeMapability.html describing Duke Uniqueness/Excluded Regions. Also emphasized which assembly the nearly identical tracks are for.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.ra
  • lines changed 62, context: html, text, full: html, text
    Split out mapability from the trackDb.wgEncode.ra file and added Duke Uniquness and Excluded Regions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 1, context: html, text, full: html, text
    Fixed problem with missing <DL> tags
  • lines changed 5, context: html, text, full: html, text
    Still or <DL> <DT> errors.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 3, context: html, text, full: html, text
    Fixed problem with missing <DL> tags
  • lines changed 4, context: html, text, full: html, text
    Still or <DL> <DT> errors.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 3, context: html, text, full: html, text
    Fixed problem with missing <DL> tags
  • lines changed 4, context: html, text, full: html, text
    Still or <DL> <DT> errors.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 29, context: html, text, full: html, text
    Fixed problem with missing <DL> tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 26, context: html, text, full: html, text
    changed long labels to have RIP-chip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    changed the target protien to be under antibody even though there is no antibody in this experiment so that the links would work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 7, context: html, text, full: html, text
    Added line to state that Signal and Peaks are pooled samples and provided link to download site to get raw data and alignments.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 27, context: html, text, full: html, text
    Removed alpha tags in trackDb and put alpha tag at composite level in trackDb.wgEncode.ra file. This should fix errors on make beta/public.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 116, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 3, context: html, text, full: html, text
    fixed links, fix references to the affy exon track, fixed html, and reordered references, redmine#s59 & 3082
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 137, context: html, text, full: html, text
    preparing for release of UW Affy Exon, redmine# 59
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
  • lines changed 17, context: html, text, full: html, text
    Updated RawSignal windowingFunction from maximum -> mean+whiskers. Removed deafult subtracks on for HotSpots,Peaks and RawSignal so that tracks were not grayed-out with checkboxes selected since views are hidden by default. Also added release 2 notes into html page. All changes address QA changes for redmine issue: #2398, notes: #17.#18.#19.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 6, context: html, text, full: html, text
    Updated RawSignal windowingFunction from maximum -> mean+whiskers. Removed deafult subtracks on for HotSpots,Peaks and RawSignal so that tracks were not grayed-out with checkboxes selected since views are hidden by default. Also added release 2 notes into html page. All changes address QA changes for redmine issue: #2398, notes: #17.#18.#19.
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 6, context: html, text, full: html, text
    remove Turkey from hg19's multiz track
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Added hg19 pseudoYale60 track.
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made organutan, human, chimp, gorilla, mouse and opossum on by default in the multiz track
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 31, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 13, context: html, text, full: html, text
    Changed meta-data antibody names and tags to match updated antibody naming schema. Redmine #2897
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 2, context: html, text, full: html, text
    Changed these->those; made wording consistent between tracks.
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 1, context: html, text, full: html, text
    Track #1684: suggestions from b0b for description html.
• src/hg/makeDb/trackDb/snp132Common.html
  • lines changed 3, context: html, text, full: html, text
    Track #1684: suggestions from b0b for description html.
• src/hg/makeDb/trackDb/snp132NonUnique.html
  • lines changed 2, context: html, text, full: html, text
    Track #1684: suggestions from b0b for description html.
  • lines changed 1, context: html, text, full: html, text
    Changed these->those; made wording consistent between tracks.
• src/hg/makeDb/trackDb/snp132Patient.html
  • lines changed 2, context: html, text, full: html, text
    Track #1684: suggestions from b0b for description html.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 53, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 106, context: html, text, full: html, text
    setting turkey defaults to be good for primates
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 4, context: html, text, full: html, text
    Add link to assemble details page
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 18, context: html, text, full: html, text
    lastz for Turkey melGal1
• src/hg/makeDb/trackDb/turkey/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    lastz for Turkey melGal1
• src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    lastz for Turkey melGal1
  • lines changed 4, context: html, text, full: html, text
    remove Turkey melGal1 form trackDb.chainNet
• src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
  • lines changed 13, context: html, text, full: html, text
    Generating trackDb.ra for more histone marks, and correcting color on K562 which before was too dark.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding utility to correlate enahancers and promoters with similar activities.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
  • lines changed 234, context: html, text, full: html, text
    Adding utility to correlate enahancers and promoters with similar activities.
  • lines changed 137, context: html, text, full: html, text
    Making it have three types of BED outputs. I think I like the third the best.
  • lines changed 19, context: html, text, full: html, text
    Adding a new output type and a new column to existing output.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/test.csh
  • lines changed 2, context: html, text, full: html, text
    Making it have three types of BED outputs. I think I like the third the best.
• src/hg/regulate/companion/regCompanionEntropy/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding utility to calculate entropy of expression vectors.
• src/hg/regulate/companion/regCompanionEntropy/regCompanionEntropy.c
  • lines changed 92, context: html, text, full: html, text
    Adding utility to calculate entropy of expression vectors.
• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/long.lst
  • lines changed 44, context: html, text, full: html, text
    Adding some stuff to query neighborhood around promoters producing averages across all genes.
• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding some stuff to query neighborhood around promoters producing averages across all genes.
  • lines changed 1, context: html, text, full: html, text
    Making it take an input table with clamping values, how-to-handle-missing-zeroes on a file-by-file basis.
• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c
  • lines changed 189, context: html, text, full: html, text
    Adding some stuff to query neighborhood around promoters producing averages across all genes.
  • lines changed 58, context: html, text, full: html, text
    Adding -missingZero and -maxVal flags to improve Caltech RNA results. Reworking plus/minus strand logic so there's less duplication of code.
  • lines changed 35, context: html, text, full: html, text
    Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
  • lines changed 102, context: html, text, full: html, text
    Making it take an input table with clamping values, how-to-handle-missing-zeroes on a file-by-file basis.
• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/toWig.awk
  • lines changed 27, context: html, text, full: html, text
    Adding some stuff to query neighborhood around promoters producing averages across all genes.
  • lines changed 16, context: html, text, full: html, text
    Adding -missingZero and -maxVal flags to improve Caltech RNA results. Reworking plus/minus strand logic so there's less duplication of code.
  • lines changed 14, context: html, text, full: html, text
    Adding viewLimits to track generator.
• src/hg/regulate/companion/regCompanionPickEnhancers/makefile
  • lines changed 18, context: html, text, full: html, text
    Program to pick enhancers is starting to go. Still a ways left though.
• src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
  • lines changed 170, context: html, text, full: html, text
    Program to pick enhancers is starting to go. Still a ways left though.
  • lines changed 256, context: html, text, full: html, text
    Seems to be picking an interesting set. Some browsing suggests that the number of calls are a little conservative, but that's ok.
  • lines changed 83, context: html, text, full: html, text
    Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
  • lines changed 1, context: html, text, full: html, text
    Updating a comment.
  • lines changed 20, context: html, text, full: html, text
    Some debugging added.
• src/hg/regulate/companion/regCompanionPickEnhancers/test.csh
  • lines changed 2, context: html, text, full: html, text
    Program to pick enhancers is starting to go. Still a ways left though.
• src/hg/regulate/companion/regCompanionPickGeneSet/makefile
  • lines changed 18, context: html, text, full: html, text
    Committing a half-abandoned attempt at a gene picker for the companion paper in C to replace scripts I was using. May come back to it later.
• src/hg/regulate/companion/regCompanionPickGeneSet/regCompanionPickGeneSet.c
  • lines changed 189, context: html, text, full: html, text
    Committing a half-abandoned attempt at a gene picker for the companion paper in C to replace scripts I was using. May come back to it later.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • lines changed 10, context: html, text, full: html, text
    Adding another input variant format
• src/hg/regulate/regStartSampleEmbl/makefile
  • lines changed 18, context: html, text, full: html, text
    A little utility to make a template EMBL file for annotating regulatory regions by hand.
• src/hg/regulate/regStartSampleEmbl/regStartSampleEmbl.c
  • lines changed 129, context: html, text, full: html, text
    A little utility to make a template EMBL file for annotating regulatory regions by hand.
• src/hg/utils/bedWeedOverlapping/bedWeedOverlapping.c
  • lines changed 8, context: html, text, full: html, text
    Added -invert flag.
• src/hg/utils/phyloTrees/50way.dissect.txt
  • lines changed 693, context: html, text, full: html, text
    adding turkey to the mix
• src/hg/utils/phyloTrees/50way.nh
  • lines changed 24, context: html, text, full: html, text
    adding turkey to the mix
• src/hg/utils/phyloTrees/README
  • lines changed 26, context: html, text, full: html, text
    adding turkey to the mix
• src/hg/utils/phyloTrees/chainNet.pl
  • lines changed 7, context: html, text, full: html, text
    adding turkey to the mix
• src/hg/utils/phyloTrees/findScores.pl
  • lines changed 4, context: html, text, full: html, text
    adding turkey to the mix
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 2, context: html, text, full: html, text
    adding turkey to the mix
• src/inc/bigWig.h
  • lines changed 27, context: html, text, full: html, text
    Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
  • lines changed 11, context: html, text, full: html, text
    Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
• src/inc/bwgInternal.h
  • lines changed 16, context: html, text, full: html, text
    Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
• src/inc/chain.h
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    add compare routine for cBlocks based on query position
• src/inc/common.h
  • lines changed 19, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
• src/inc/net.h
  • lines changed 1, context: html, text, full: html, text
    updating paraFetch and paraSync to support -newer option which only downloads newer files, very useful now that the dates are being preserved
  • lines changed 1, context: html, text, full: html, text
    adding progress bar showing filesize, progress, total time, and avg download rate in MB/sec.
• src/lib/bwgQuery.c
  • lines changed 13, context: html, text, full: html, text
    Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
• src/lib/bwgValsOnChrom.c
  • lines changed 72, context: html, text, full: html, text
    Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
  • lines changed 142, context: html, text, full: html, text
    Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
• src/lib/chain.c
  • lines changed 8, context: html, text, full: html, text
    add compare routine for cBlocks based on query position
• src/lib/common.c
  • lines changed 159, context: html, text, full: html, text
    Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used.
  • lines changed 5, context: html, text, full: html, text
    Bullet proof slNameListOfUniqueWords() fixing bug that Kate found.
  • lines changed 2, context: html, text, full: html, text
    Fixed bug in slPairListFromString caused by leading white-space
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
• src/lib/net.c
  • lines changed 39, context: html, text, full: html, text
    updating paraFetch and paraSync to support -newer option which only downloads newer files, very useful now that the dates are being preserved
  • lines changed 46, context: html, text, full: html, text
    adding progress bar showing filesize, progress, total time, and avg download rate in MB/sec.
• src/product/README.building.source
  • lines changed 9, context: html, text, full: html, text
    add note about PNGINCL
• src/utils/bedGeneParts/test.in
  • lines changed 9, context: html, text, full: html, text
    Adding test case.
• src/utils/bedRemoveOverlap/bedRemoveOverlap.c
  • lines changed 1, context: html, text, full: html, text
    add cast to resolve problems building on 32-bit machines
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 49, context: html, text, full: html, text
    Making bigWigAverageOverBed use the bigWigValsOnChrom interface.
• src/utils/correlate/correlate.c
  • lines changed 12, context: html, text, full: html, text
    Making it so that for this command line utility '1' rather than '0' refers to the first column, which is more consistent with other command line utilities.
• src/utils/cvsTools/cvsFiles
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    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
• src/utils/cvsTools/cvsStatusFilter
  • lines changed 105, context: html, text, full: html, text
    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
• src/utils/cvsTools/cvscheck
  • lines changed 2, context: html, text, full: html, text
    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
• src/utils/cvsTools/cvsup
  • lines changed 195, context: html, text, full: html, text
    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
• src/utils/cvsTools/makefile
  • lines changed 21, context: html, text, full: html, text
    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
• src/utils/linesInAllFiles/linesInAllFiles.c
  • lines changed 105, context: html, text, full: html, text
    Utility to print out lines shared by all files (or from a column in all files) seems to work.
• src/utils/linesInAllFiles/makefile
  • lines changed 18, context: html, text, full: html, text
    Utility to print out lines shared by all files (or from a column in all files) seems to work.
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    removed no longer needed cvs tools, which are mistakenly being run by some stray crontabs
  • lines changed 6, context: html, text, full: html, text
    Adding new utilities to makefile.
• src/utils/paraFetch/paraFetch.c
  • lines changed 6, context: html, text, full: html, text
    updating paraFetch and paraSync to support -newer option which only downloads newer files, very useful now that the dates are being preserved
  • lines changed 23, context: html, text, full: html, text
    allowing last parameter to be optional, i.e. derived from url if unspecified, as requested by a user
  • lines changed 5, context: html, text, full: html, text
    adding progress bar showing filesize, progress, total time, and avg download rate in MB/sec.
• src/utils/paraSync/paraSync.c
  • lines changed 21, context: html, text, full: html, text
    updating paraFetch and paraSync to support -newer option which only downloads newer files, very useful now that the dates are being preserved
  • lines changed 6, context: html, text, full: html, text
    adding progress bar showing filesize, progress, total time, and avg download rate in MB/sec.
• src/utils/qa/weeklybld/buildBeta.csh
  • lines changed 2, context: html, text, full: html, text
    don't get fooled by bigWarn in hgTracks
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v250 preview

• lines changed: 20865
• files changed: 315