All File Changes

v306_base to v307_preview (2014-09-22 to 2014-09-29) v307

• confs/preview.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Added trackLog lines at Braney's request
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 128, context: html, text, full: html, text
    add maf SNP view to maf display
• src/hg/hgVai/libifyMe.c
  • lines changed 8, context: html, text, full: html, text
    Make sure to call hReplaceGbdb on the path given to annoAssemblyNew.refs #11957
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 8, context: html, text, full: html, text
    Make sure to call hReplaceGbdb on the path given to annoAssemblyNew.refs #11957
    
  • lines changed 2, context: html, text, full: html, text
    Fixing broken hgVarAnnogrator make (not reachable by top-level make) -- textOut interface changed, and we weren't using it anyway.
• src/hg/htdocs/ebolaPortal/antibodyResources.html
  • lines changed 112, context: html, text, full: html, text
    Add Treatment Research section. Move Antibody Resources to separate page, and include working google spreadsheet
• src/hg/htdocs/ebolaPortal/ebolaPortal.css
  • lines changed 47, context: html, text, full: html, text
    Add Treatment Research section. Move Antibody Resources to separate page, and include working google spreadsheet
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 126, context: html, text, full: html, text
    Add Treatment section
  • lines changed 2, context: html, text, full: html, text
    Changing eboVir2 to eboVir3 on Ebola portal pages
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    Adding announcement for Ensembl Regulatory Build hub, refs #10311
  • lines changed 1, context: html, text, full: html, text
    Noted wrong person in our thanks section of Ensembl Regulatory Hub announcement
• src/hg/htdocs/images/ebolaBrowser.png
  • lines changed 0, context: html, text, full: html, text
    Update Ebola browser image to eboVir3
• src/hg/htdocs/inc/ebola.topbar.aux.html
  • lines changed 17, context: html, text, full: html, text
    Add Treatment Research section. Move Antibody Resources to separate page, and include working google spreadsheet
  • lines changed 1, context: html, text, full: html, text
    Changing eboVir2 to eboVir3 on Ebola portal pages
• src/hg/htdocs/inc/ebola.topbar.html
  • lines changed 1, context: html, text, full: html, text
    Add Treatment section
  • lines changed 1, context: html, text, full: html, text
    Changing eboVir2 to eboVir3 on Ebola portal pages
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    adding Ebola Portal link to light blue menu on home page
  • lines changed 1, context: html, text, full: html, text
    changing link name from Portal to Genome
  • lines changed 1, context: html, text, full: html, text
    Change Ebola item on left menu bar, as per JK request.
  • lines changed 2, context: html, text, full: html, text
    hiding Ebola link for now
• src/hg/htdocs/indexNews.html
  • lines changed 68, context: html, text, full: html, text
    Adding announcement for Ensembl Regulatory Build hub, refs #10311
  • lines changed 1, context: html, text, full: html, text
    Noted wrong person in our thanks section of Ensembl Regulatory Hub announcement
• src/hg/htdocs/license/gblicense.pdf
  • lines changed 0, context: html, text, full: html, text
    newest license from Wil Hale
• src/hg/inc/mafGene.h
  • lines changed 1, context: html, text, full: html, text
    add a mode to mafGene that let's it put out a unique character for eachcodon.
    
• src/hg/js/hgTracks.js
  • lines changed 9, context: html, text, full: html, text
    HT Hiram for noticing chrom ideogram bug in Ebola -- the ideogram's left labelchanges depending on band name, and band names with different widths cause the
    label width to change, and that causes the coords of the image areas to change;
    but the javascript was neglecting to update the ideogram image map, thinking it
    would be the same for any view on the same chromosome. Now we always update it.
    Not terribly expensive to replace an image map with only chromosome band areas.
    
• src/hg/lib/googleAnalytics.c
  • lines changed 2, context: html, text, full: html, text
    I dont think it matters, but google says the require displayfeatures is supposed to be between create and send statements refs #13120
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    fixing hgConvert gbib bug, refs #11957
• src/hg/lib/mafGene.c
  • lines changed 9, context: html, text, full: html, text
    add a mode to mafGene that let's it put out a unique character for eachcodon.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 8, context: html, text, full: html, text
    Make sure to call hReplaceGbdb on the path given to annoAssemblyNew.refs #11957
    
• src/hg/makeDb/doc/eboVir3/iedb.txt
  • lines changed 66, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/doc/eboVir3/pdb.txt
  • lines changed 11, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/doc/eboVir3/snpView.txt
  • lines changed 33, context: html, text, full: html, text
    add some doc about how to build the mafSnp track for eboVir3
  • lines changed 14, context: html, text, full: html, text
    deal with both eboVir2 maf's. Add UTR change annotation.
• src/hg/makeDb/doc/eboVir3/uniprot.txt
  • lines changed 16, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding mdbUpdate to the build refs #910
• src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
• src/hg/makeDb/trackDb/ebola/bunEbo1/trackDb.160way.ra
  • lines changed 46, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
  • lines changed 1, context: html, text, full: html, text
    turning on frames and ncbiGene refs #14011
• src/hg/makeDb/trackDb/ebola/bunEbo1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 4, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir2/arjun.html
  • lines changed 117, context: html, text, full: html, text
    desc page for netMhc track
  • lines changed 7, context: html, text, full: html, text
    Tweaks to desc. page on eboVir2. Adding desc. page for track on eboVir3.
• src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html
  • lines changed 159, context: html, text, full: html, text
    adding description page for multiple alignment pages refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir2/genbank.html
  • lines changed 17, context: html, text, full: html, text
    adding desc pages for genbank matches on eboVir2
• src/hg/makeDb/trackDb/ebola/eboVir2/genbankNotZaire.html
  • lines changed 17, context: html, text, full: html, text
    adding desc pages for genbank matches on eboVir2
• src/hg/makeDb/trackDb/ebola/eboVir2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir2/ncbiGene.html
  • lines changed 30, context: html, text, full: html, text
    Adding description page for eboVir2 NCBI Genes track
• src/hg/makeDb/trackDb/ebola/eboVir2/ncbiGenePfam.html
  • lines changed 8, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir2/pdb.html
  • lines changed 37, context: html, text, full: html, text
    desc page for eboVir2.pdb
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
  • lines changed 1, context: html, text, full: html, text
    limit chromosomes to the one this track is on refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra
  • lines changed 1, context: html, text, full: html, text
    adding description page for multiple alignment pages refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Shortening UniProt Mutations short label
  • lines changed 3, context: html, text, full: html, text
    changes after code review refs #14033
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding description page refs #14011
  • lines changed 58, context: html, text, full: html, text
    some doc that mentions the mafSnp mode
• src/hg/makeDb/trackDb/ebola/eboVir3/description.html
  • lines changed 2, context: html, text, full: html, text
    Commented out Downloads/Credits section until we provide these in the docs.
• src/hg/makeDb/trackDb/ebola/eboVir3/gap.html
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir3/gold.html
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcell.html
  • lines changed 27, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcellNeg.html
  • lines changed 25, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellI.html
  • lines changed 29, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellII.html
  • lines changed 27, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/ncbiGene.html
  • lines changed 20, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir3/ncbiGenePfam.html
  • lines changed 42, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
• src/hg/makeDb/trackDb/ebola/eboVir3/pdb.html
  • lines changed 37, context: html, text, full: html, text
    pdb desc page
• src/hg/makeDb/trackDb/ebola/eboVir3/spAnnot.html
  • lines changed 65, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/spMut.html
  • lines changed 66, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/spStruct.html
  • lines changed 57, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 3, context: html, text, full: html, text
    eliminate tree diagram png image reference refs #14011
  • lines changed 2, context: html, text, full: html, text
    trackDb modifications to support mafSnp mode on eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 71, context: html, text, full: html, text
    moving iedb,uniprot,pdb tracks to eboVir3
  • lines changed 1, context: html, text, full: html, text
    Changing shortLabel on eboVir3 track
  • lines changed 5, context: html, text, full: html, text
    Making genscan and windowmasker tracks only visible on dev. Removing release tag for spAnnot track.
  • lines changed 2, context: html, text, full: html, text
    Changing visibilities for tracks on eboVir3
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 1, context: html, text, full: html, text
    add snpTable mode to ebola 160 way
  • lines changed 1, context: html, text, full: html, text
    adding description page refs #14011
  • lines changed 3, context: html, text, full: html, text
    eliminate tree diagram png image reference refs #14011
  • lines changed 1, context: html, text, full: html, text
    Changing visibilities for tracks on eboVir3
  • lines changed 2, context: html, text, full: html, text
    trackDb modifications to support mafSnp mode on eboVir3
• src/hg/makeDb/trackDb/ebola/gire2014.html
  • lines changed 41, context: html, text, full: html, text
    Adding description pages for eboVir3 tracks. Tweaking links on gap/gold tracks. Changing shortLabel for one immunology track
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling mistake per code review, refs #14039
• src/hg/makeDb/trackDb/ebola/gire2014FixedMissense.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gire2014KikwitMissense.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gire2014MayingaMissense.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gire2014Missense.html
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling mistake per code review, refs #14039
• src/hg/makeDb/trackDb/ebola/gire2014PolymorphicMissense.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gire2014SpecificSnps.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gireIntraHost.html
  • lines changed 45, context: html, text, full: html, text
    Tweaks to desc. page on eboVir2. Adding desc. page for track on eboVir3.
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling mistake per code review, refs #14039
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 0, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
  • lines changed 1, context: html, text, full: html, text
    Edited Baize ref.
• src/hg/makeDb/trackDb/ebola/gireZebov.html
  • lines changed 10, context: html, text, full: html, text
    Added include files gireMethods & gireReferences to all track gire*.html files.
• src/hg/makeDb/trackDb/ebola/gireZebovMissense.html
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling mistake per code review, refs #14039
• src/hg/makeDb/trackDb/ebola/marVir1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene refs #14011
• src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
• src/hg/makeDb/trackDb/ebola/resEbo1/trackDb.160way.ra
  • lines changed 46, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 2, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/resEbo1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 4, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
• src/hg/makeDb/trackDb/ebola/sudEbo1/trackDb.160way.ra
  • lines changed 46, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene and frames refs #14011
• src/hg/makeDb/trackDb/ebola/sudEbo1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 4, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
• src/hg/makeDb/trackDb/ebola/taiEbo1/trackDb.160way.ra
  • lines changed 46, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
  • lines changed 1, context: html, text, full: html, text
    turning on frames and added ncbiGene refs #14011
• src/hg/makeDb/trackDb/ebola/taiEbo1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 160way tracks on all the separate Ebo virus browsers refs #10411
  • lines changed 4, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/trackDb.ncbiGene.ra
  • lines changed 11, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html
  • lines changed 197, context: html, text, full: html, text
    adding description page for 160-way refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/trackDb.160way.ra
  • lines changed 46, context: html, text, full: html, text
    adding 160-way refs #13996
  • lines changed 1, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/ebola/zaiEbo1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 160-way refs #13996
  • lines changed 4, context: html, text, full: html, text
    adding ncbiGene where they fit and frames on for 160-way refs #10411
• src/hg/makeDb/trackDb/human/HInvGeneMrna.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
  • lines changed 13, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld6.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
  • lines changed 19, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hg19/peptideAtlas.html
  • lines changed 74, context: html, text, full: html, text
    Add PeptideAtlas 2014 build
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 60, context: html, text, full: html, text
    Add PeptideAtlas 2014 build
  • lines changed 4, context: html, text, full: html, text
    Tidying up after my comrades so hg19 trackDb can be built again.
  • lines changed 14, context: html, text, full: html, text
    Retiring in progress track temporarily to sort out config problems.
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 49, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/hgdpGeo.html
  • lines changed 40, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/illuminaProbes.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/laminB1Super.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/omimAvSnp.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 17, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/omimLocation.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/human/phastBias.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 20, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    add snpTable mode to ebola 160 way
  • lines changed 4, context: html, text, full: html, text
    Tidying up after my comrades so hg19 trackDb can be built again.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Making genscan and windowmasker tracks only visible on dev. Removing release tag for spAnnot track.
• src/hg/makeDb/trackDb/ucscGenePfam.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on human (hg19) track description pages. Adjust arrangement of references on mouse (mm9) track description page
• src/hg/ratStuff/mafGene/mafGene.c
  • lines changed 6, context: html, text, full: html, text
    add a mode to mafGene that let's it put out a unique character for eachcodon.
    
• src/hg/ratStuff/mafToSnpBed/mafToSnpBed.c
  • lines changed 165, context: html, text, full: html, text
    add mafToSnpBed tool that takes a maf and outputs a bed with someinformation about the functional region that the SNPS fall into.
    
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    polish mafToSnpBed ... remove some unneccesary stuff
• src/hg/ratStuff/mafToSnpBed/makefile
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    add mafToSnpBed tool that takes a maf and outputs a bed with someinformation about the functional region that the SNPS fall into.
    
• src/inc/dnautil.h
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    add a mode to mafGene that let's it put out a unique character for eachcodon.
    
• src/lib/annoAssembly.c
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    fixing gbib bug in vai, refs #11957
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    fixing Vai gbib error, refs #11957
• src/lib/dnautil.c
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    add a mode to mafGene that let's it put out a unique character for eachcodon.
    
• src/oneShot/bedFixBlockOverlaps/bedFixBlockOverlaps
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    moving small tools into utils directory
• src/oneShot/bedFixBlockOverlaps/makefile
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    moving small tools into utils directory
• src/utils/bedFixBlockOverlaps
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    moving small tools into utils directory
• src/utils/makefile
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    adding a pslScore and pslScore.pl function refs #14011
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    moving small tools into utils directory
• src/utils/pslScore/makefile
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/pslScore/pslScore.c
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/pslScore/pslScore.pl
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/pslScore/tests/expectOut.tab
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/pslScore/tests/makefile
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/pslScore/tests/test.psl
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    adding a pslScore and pslScore.pl function refs #14011
• src/utils/qa/weeklybld/buildEnv.csh
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    v307 preview1 refs #14072
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    Changing to run hgTablesTest on hg19
• src/utils/qa/weeklybld/doZip.csh
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    allow previous versions of source packages to remain existing refs #13954
• src/utils/uniprotLift
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    moving small tools into utils directory
• src/utils/uniprotLift/makefile
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    moving small tools into utils directory
• src/utils/uniprotLift/uniprotLift
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    moving small tools into utils directory

• lines changed: 5096
• files changed: 168