All File Changes

v293_base to v294_preview (2013-12-09 to 2013-12-16) v294

• src/hg/encode3/encodeDataWarehouse/lib/makefile
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    correctly avoiding problems during parallel make and remove useless (sub shell) operations
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 20, context: html, text, full: html, text
    correctly avoiding problems during parallel make and remove useless (sub shell) operations
• src/hg/hgTables/gffOut.c
  • lines changed 19, context: html, text, full: html, text
    fixes 12318. for assemblies like rheMac3 that have many thousands of chroms, it is faster to find out a distinct list of chroms that are actually used by the e.g. refGene table and hash them, and then can quickly skip thousands of regions not in the hash. now it goes from timing out over 3 minutes to returning a good result in a few seconds.
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    In MLQ #12327, user reported that BAM track colored by tag was turningblue as we zoomed out, even though most items are red. Unbeknownst to
    me, if a linkedFeatures track has non-NULL colorShades, items are sorted
    by their color, and in this case it favored blue over other colors.
    Only the gray-scale coloring modes need colorShades. So don't add colorShades
    unless the coloring mode is gray-scale. refs #12327
    
• src/hg/hgTracks/pubsTracks.c
  • lines changed 34, context: html, text, full: html, text
    fixing a bug due to a global variable, just checking track name for table version now, rm #12308
• src/hg/hgVai/hgVai.c
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    Thanks Jonathan for noticing I forgot to mention that by 'Variant Identifiers' we mean 'dbSNP rs# ids' for now... refs #11460
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    Fixing bad assumption that htcCdnaAli's aliTable is a track. It may be "all_mrna". Fixes #12322
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 106, context: html, text, full: html, text
    Combined some mostly redundant sections of the Problem/Solution section. Lightly edited a few other sections. Fixed formatting problems in both files.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    Added Raney et al. reference.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    Combined some mostly redundant sections of the Problem/Solution section. Lightly edited a few other sections. Fixed formatting problems in both files.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 9, context: html, text, full: html, text
    Add factorSource motif tables settings to help trackDb help doc. refs #9092
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 23, context: html, text, full: html, text
    Add factorSource motif tables settings to help trackDb help doc. refs #9092
• src/hg/htdocs/images/pubs_bing.png
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    adding transparent image rm #12212
• src/hg/htdocs/mirror.html
  • lines changed 3, context: html, text, full: html, text
    Changing link for Denmark mirror per Code Review, refs #12302
• src/hg/js/hgTracks.js
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    Fix for assembly changing between back-button calls. Redmine #7473 note41-43.
• src/hg/lib/trackHub.c
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    fixes #12337. better way to allow colons in urls by splitting htmlExpandUrl into two functions. the new one is called expandUrlOnBase and includes ftp support as well as http(s).
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 16, context: html, text, full: html, text
    Starting work on liftunder felcat5->4 refs #12163
  • lines changed 1, context: html, text, full: html, text
    Updating cluster reference. refs #12163
• src/hg/makeDb/doc/hg19.txt
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    Starting work on cooper dev delay track refs #9391
• src/hg/makeDb/doc/makeEnsembl.txt
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    record procedures from v74 update refs #12288
• src/hg/makeDb/schema/all.joiner
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    clean up note/using messages for all ensGene v74 db releases refs #12288
  • lines changed 6, context: html, text, full: html, text
    clean up note/using messages for all ensGene v74 db releases refs #12288
• src/hg/makeDb/trackDb/apis/all_est.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/apis/all_mrna.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/apis/chainDm1.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/apis/rmsk.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/blastDm1FB.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/blatFr1.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chainDm2.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chainDm3.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chainNet.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chimp/panTro1/axtNetHg16.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chimp/panTro1/ctgPos.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chimp/panTro1/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/chimp/panTro1/humanDels.html
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• src/hg/makeDb/trackDb/dog/canFam3/description.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/dog/canFam3/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/drosophila/droAna2/gap.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/drosophila/droAna2/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/drosophila/rmsk.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/est.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/geneid.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu2/gap.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu2/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/horse/equCab2/description.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/human/hg19/msr1.html
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    adding the msr interaction track docs
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    Changing release tags to alpha,beta for human brain methyl tracks on hg19, refs #2540
  • lines changed 6, context: html, text, full: html, text
    Changing release tags to alpha,beta,public for human brain methyl tracks on hg19, refs #2540
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    added GENCODE V18 (not to be pushed public)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.html
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    added GENCODE V18 (not to be pushed public)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
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    added GENCODE V18 (not to be pushed public)
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
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• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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• src/hg/makeDb/trackDb/marmoset/calJac1/nscanGene.html
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• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
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• src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
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• src/hg/makeDb/trackDb/moleRat/hetGla2/gap.html
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• src/hg/makeDb/trackDb/moleRat/hetGla2/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    Mouse trackDb changes based on code review, refs #12302
• src/hg/makeDb/trackDb/mrna.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/netDm2.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/netDm3.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/nscanGene.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/phastConsElements.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/pubsBingBlat.html
  • lines changed 4, context: html, text, full: html, text
    Adding PMIDs/PMCIDs to Bing pubs page for those publications that have them, refs #12212
• src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
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• src/hg/makeDb/trackDb/saiBol/saiBol1/gap.html
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• src/hg/makeDb/trackDb/saiBol/saiBol1/gold.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/sgpGene.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/shrew/sorAra1/gap.html
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• src/hg/makeDb/trackDb/shrew/sorAra1/gold.html
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• src/hg/makeDb/trackDb/squirrel/speTri2/gap.html
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• src/hg/makeDb/trackDb/squirrel/speTri2/gold.html
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• src/hg/makeDb/trackDb/squirt/ci1/description.html
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• src/hg/makeDb/trackDb/squirt/ci2/description.html
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• src/hg/makeDb/trackDb/squirt/gap.html
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• src/hg/makeDb/trackDb/squirt/rmsk.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/tRNAs.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/twinscan.html
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• src/hg/makeDb/trackDb/worm/caeJap1/description.html
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• src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html
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• src/hg/makeDb/trackDb/worm/caeRem3/description.html
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• src/hg/makeDb/trackDb/worm/caeRem3/gap.html
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• src/hg/makeDb/trackDb/worm/caeRem3/gold.html
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• src/hg/makeDb/trackDb/worm/cb1/blastzCe1.html
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• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
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• src/hg/makeDb/trackDb/worm/cb1/ce1Chain.html
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• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
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    Track description page changes related to my Code Review, refs #12302
• src/hg/makeDb/trackDb/worm/cb3/description.html
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• src/hg/makeDb/trackDb/worm/cb3/gap.html
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• src/hg/makeDb/trackDb/worm/cb3/gold.html
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• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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• src/hg/makeDb/trackDb/worm/ce10/description.html
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• src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html
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• src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html
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• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
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• src/hg/makeDb/trackDb/worm/ce2/netCb1.html
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• src/hg/makeDb/trackDb/worm/ce2/picTar.html
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• src/hg/makeDb/trackDb/worm/ce2/trackDb.ra
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• src/hg/makeDb/trackDb/worm/ce2/wabaCbr.html
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• src/hg/makeDb/trackDb/worm/ce4/gap.html
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• src/hg/makeDb/trackDb/worm/ce4/gold.html
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• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
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• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
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• src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
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• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
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• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
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• src/hg/makeDb/trackDb/worm/chainCaePb1.html
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• src/hg/makeDb/trackDb/worm/chainCaePb2.html
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• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
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• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
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• src/hg/makeDb/trackDb/worm/chainCb3.html
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• src/hg/makeDb/trackDb/worm/chainCe4.html
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• src/hg/makeDb/trackDb/worm/chainCe6.html
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• src/hg/makeDb/trackDb/worm/chainPriPac1.html
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• src/hg/makeDb/trackDb/worm/chainSelf.html
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• src/hg/makeDb/trackDb/worm/netCaeJap1.html
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• src/hg/makeDb/trackDb/worm/netCaePb1.html
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• src/hg/makeDb/trackDb/worm/netCaePb2.html
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• src/hg/makeDb/trackDb/worm/netCaeRem2.html
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• src/hg/makeDb/trackDb/worm/netCaeRem3.html
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• src/hg/makeDb/trackDb/worm/netCb3.html
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• src/hg/makeDb/trackDb/worm/netCe4.html
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• src/hg/makeDb/trackDb/worm/netCe6.html
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• src/hg/makeDb/trackDb/worm/netPriPac1.html
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• src/hg/makeDb/trackDb/worm/nucleosome.html
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• src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html
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• src/utils/wigToBigWig/tests/input/testBedGraph.wig
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/input/testFixed.wig
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/input/testVar.wig
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/makefile
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• src/utils/wigToBigWig/wigToBigWig.c
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.

• lines changed: 6943
• files changed: 264