All File Changes

v242_base to v243_preview (2010-10-12 to 2010-10-19) v243

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    adding IP-logging option
• src/gfServer/gfServer.c
  • lines changed 19, context: html, text, full: html, text
    adding IP-logging option
  • lines changed 8, context: html, text, full: html, text
    protecting against infinite loop producing up tons of logging output
  • lines changed 2, context: html, text, full: html, text
    adding more safety checks
• src/hg/bedIntersect/bedIntersect.c
  • lines changed 8, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/input/subBlocks.bed
  • lines changed 6, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/input/subBlocksWInserts.bed
  • lines changed 21, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/bedIntersect/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    Code review suggestion from Larry: errAbort if input has start==end items, but -allowStartEqualEnd not specified (thanks!).
• src/hg/blastToPsl/blastXmlToPsl.c
  • lines changed 47, context: html, text, full: html, text
    added handling of misidentified psiblast files
• src/hg/blastToPsl/tests/expected/misclassedPsiBlastTest.bscores
  • lines changed 11, context: html, text, full: html, text
    added handling of misidentified psiblast files
• src/hg/blastToPsl/tests/expected/misclassedPsiBlastTest.psl
  • lines changed 10, context: html, text, full: html, text
    added handling of misidentified psiblast files
• src/hg/blastToPsl/tests/input/misclassed.psiBlast.xml
  • lines changed 483, context: html, text, full: html, text
    added handling of misidentified psiblast files
• src/hg/blastToPsl/tests/makefile
  • lines changed 10, context: html, text, full: html, text
    added handling of misidentified psiblast files
• src/hg/encode/docId/docIdReport/docIdReport.c
  • lines changed 76, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/docIdReport/makefile
  • lines changed 18, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
  • lines changed 207, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/docIdSubmitDir/makefile
  • lines changed 19, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/inc/docId.h
  • lines changed 68, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/lib/docIdSub.as
  • lines changed 12, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/lib/docIdSub.c
  • lines changed 170, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/lib/docIdSub.sql
  • lines changed 17, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/docId/lib/makefile
  • lines changed 15, context: html, text, full: html, text
    some new code to deal with the ENCODE docId system... still primitive
• src/hg/encode/encodeMkChangeNotes/makefile
  • lines changed 13, context: html, text, full: html, text
    added alpha, install targets to makefile so that scripts don't get out of synch
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 86, context: html, text, full: html, text
    Added 6 antibodies and 3 validation documents for Snyder lab
  • lines changed 9, context: html, text, full: html, text
    Added validation document links for Bernstein (Broad) labs
  • lines changed 1, context: html, text, full: html, text
    fix typo
  • lines changed 54, context: html, text, full: html, text
    Added 17 new validation documents and standardized display names of validation processes
  • lines changed 1, context: html, text, full: html, text
    Updated the tag for Cerebellum to Cbellum to make more room for the table names.
  • lines changed 38, context: html, text, full: html, text
    Changed how GM12878 XiMat and Pat lines are registered as general cell lines rather than by clone
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    find tracks => track search
• src/hg/hgGene/pathways.c
  • lines changed 34, context: html, text, full: html, text
    Updated pathways.c to support RGD Genes.
• src/hg/hgTables/gffOut.c
  • lines changed 234, context: html, text, full: html, text
    Redmine Bug #5 (Table Browser may return GTF lines with start > end): fixed, finally. GTF2's removal of stop_codons from CDS is a real pain when codons straddle introns -- we can't just work on each exon independently and use +3/-3 to get the codon end, we have to look forwards or backwards depending on strand, and even CDS exons that don't contain the stop codon have to watch out for their neighbors. Also, instead of wasting memory building up a list of GFF and using the list only for printing out, just print as we go.
• src/hg/hgTables/pal.c
  • lines changed 1, context: html, text, full: html, text
    Added a space and a period to the users guide note.
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 1, context: html, text, full: html, text
    add track parameter to call to mapBoxJumpTo
  • lines changed 1, context: html, text, full: html, text
    Fix for broken build -- Larry also checked in a fix. Checking in so I can git pull...
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    Two paths to cleanup and both may require superTrack vis adjustments
  • lines changed 1, context: html, text, full: html, text
    add track parameter to mapBoxJumpTo
  • lines changed 8, context: html, text, full: html, text
    Freaking wierd bug of cart values disappearing and reappearing turned out to be browser cache
  • lines changed 4, context: html, text, full: html, text
    add toggle parameter to mapBoxReinvoke so we can use it for non-toggable map items (e.g. next/prev)
  • lines changed 1, context: html, text, full: html, text
    find tracks => track search
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    add track parameter to mapBoxJumpTo
  • lines changed 3, context: html, text, full: html, text
    add toggle parameter to mapBoxReinvoke so we can use it for non-toggable map items (e.g. next/prev)
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
• src/hg/hgTracks/searchTracks.c
  • lines changed 13, context: html, text, full: html, text
    Cleaned up one more ifdef
  • lines changed 2, context: html, text, full: html, text
    Remove the 'Recently Done' note at bottom.
  • lines changed 5, context: html, text, full: html, text
    Freaking wierd bug of cart values disappearing and reappearing turned out to be browser cache
  • lines changed 34, context: html, text, full: html, text
    UI tweaks; add About ... section at the bottom, join submit buttons into one piece of code and show below simple/advanced tab
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    add track parameter to mapBoxJumpTo
  • lines changed 13, context: html, text, full: html, text
    add toggle parameter to mapBoxReinvoke so we can use it for non-toggable map items (e.g. next/prev)
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Redmine Bug #1304 (alignment numbering wrong when "viewing parts ofalignment"): fixed bug I introduced into fuzzyShow.c back in 2007. Also in hgc.c, trim the "Alignment of <query> to <chrN:s-e>" message at top of alignment display frame to query bounds (not just viewing window), to be more consistent with message in whole-alignment view.
• src/hg/htdocs/ENCODE/transfragBed6CshlDiscription.html
  • lines changed 252, context: html, text, full: html, text
    Additional track description reference for CshlShortRnaSeq
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 28, context: html, text, full: html, text
    Edits to bed detail and pgSnp format descriptions. Added js lines to enable use of the Static Page JS Protocol (see the genomewiki page for details).
  • lines changed 2, context: html, text, full: html, text
    Fixed table close tags for pgSnp addition.
• src/hg/htdocs/goldenPath/help/trackSearch.html
  • lines changed 43, context: html, text, full: html, text
    starting to work on help for new Find Tracks feature
  • lines changed 102, context: html, text, full: html, text
    writing track search help page
  • lines changed 10, context: html, text, full: html, text
    making changes to the track search help, mainly in response to Larry's feedback
  • lines changed 2, context: html, text, full: html, text
    minor edits
  • lines changed 64, context: html, text, full: html, text
    edits based on Mary's feedback
  • lines changed 7, context: html, text, full: html, text
    another minor edit moving a sentence around
  • lines changed 28, context: html, text, full: html, text
    more edits
  • lines changed 14, context: html, text, full: html, text
    more edits
• src/hg/htdocs/makefile
  • lines changed 8, context: html, text, full: html, text
    Updated Makefiles to use to DOCUMENTROOT in common.mk
  • lines changed 1, context: html, text, full: html, text
    add --exclude=cpAndLinkToResourceFiles.pl
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    removing duplicated % sign
• src/hg/htdocs/style/makefile
  • lines changed 8, context: html, text, full: html, text
    Updated Makefiles to use to DOCUMENTROOT in common.mk
  • lines changed 1, context: html, text, full: html, text
    add cpAndLinkToResourceFiles.pl to the exclude list
  • lines changed 1, context: html, text, full: html, text
    remove unnecessary -exclude='makefile,cpAndLinkToResourceFiles.pl
• src/hg/inc/hui.h
  • lines changed 10, context: html, text, full: html, text
    Condensed 2 routines that did the same thing
• src/hg/inc/mdb.h
  • lines changed 2, context: html, text, full: html, text
    Fixed comment
• src/hg/inc/searchTracks.h
  • lines changed 1, context: html, text, full: html, text
    Shouuld be the one ifdef that will turn findTracks on in genome-test
• src/hg/js/hgTracks.js
  • lines changed 9, context: html, text, full: html, text
    Set focus on the OK button for poup of description text only
  • lines changed 4, context: html, text, full: html, text
    fix issues with next/prev map items
  • lines changed 8, context: html, text, full: html, text
    Remove hgsid to force a new session
• src/hg/lib/hui.c
  • lines changed 115, context: html, text, full: html, text
    Condensed 2 routines that did the same thing
• src/hg/lib/mdb.c
  • lines changed 11, context: html, text, full: html, text
    Too distinctive? Removed distinct stutter.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Shouldn't hash a var that will be freed by others
  • lines changed 34, context: html, text, full: html, text
    prototype of phoneHome() function, currently disabled
• src/hg/makeDb/doc/bruMal1.txt
  • lines changed 1, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/caePb2.txt
  • lines changed 1, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/caeRem3.txt
  • lines changed 1, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/ce6.txt
  • lines changed 18, context: html, text, full: html, text
    construct ce6 to ce9 liftOver
• src/hg/makeDb/doc/ce9.txt
  • lines changed 305, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
  • lines changed 230, context: html, text, full: html, text
    have WS210 genes on all the nematodes for 10-way frames
  • lines changed 123, context: html, text, full: html, text
    ce9 in the pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release1.notes
  • lines changed 187, context: html, text, full: html, text
    change notes for CshlShort
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release1.notes
  • lines changed 304, context: html, text, full: html, text
    new release notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaSeq.release1.notes
  • lines changed 88, context: html, text, full: html, text
    new release notes
  • lines changed 8, context: html, text, full: html, text
    added fasta files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaSeq.release1.notes.txt
  • lines changed 88, context: html, text, full: html, text
    new release notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release1.notes
  • lines changed 731, context: html, text, full: html, text
    change notes for Riken Cage
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 20, context: html, text, full: html, text
    redmine 1174 fix
• src/hg/makeDb/doc/haeCon1.txt
  • lines changed 3, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/hg18.txt
  • lines changed 45, context: html, text, full: html, text
    Redmine Track #1249 (hg19.snp131CodingDbSnp still has NCBI coords): Fixed coords in {hg18,hg19}.snp130CodingDbSnp and hg19.snp131CodingDbSnp.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 78, context: html, text, full: html, text
    Redmine Track #1249 (hg19.snp131CodingDbSnp still has NCBI coords): Fixed coords in {hg18,hg19}.snp130CodingDbSnp and hg19.snp131CodingDbSnp.
  • lines changed 9, context: html, text, full: html, text
    hg19.snp131CodingDbSnp was missing some items -- noticed while working on #1249.
  • lines changed 296, context: html, text, full: html, text
    Done RECOMBINATION RATES
• src/hg/makeDb/doc/melHap1.txt
  • lines changed 1, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/melInc1.txt
  • lines changed 1, context: html, text, full: html, text
    add links to assembly information and adding frames on ce9 10-way
• src/hg/makeDb/doc/priPac1.txt
  • lines changed 15, context: html, text, full: html, text
    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/doc/rheMac2.txt
  • lines changed 38, context: html, text, full: html, text
    added RefSeq gene predictions to Rhesus at the request of NCBI
  • lines changed 23, context: html, text, full: html, text
    converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
  • lines changed 5, context: html, text, full: html, text
    redid refseq annonotation track to include all refseq mappings
• src/hg/makeDb/doc/uniProt/sp101005.txt
  • lines changed 50, context: html, text, full: html, text
    imported new uniport
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding new chainNet definitions
  • lines changed 6, context: html, text, full: html, text
    adding blastCe9SG01
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • lines changed 7, context: html, text, full: html, text
    add a verbose to the fields option to see databases checked
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 8, context: html, text, full: html, text
    put the trix files in /hive/data/inside/trix
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 15, context: html, text, full: html, text
    rearranged the order of the description of subtracks to match order of the tracks themselves
  • lines changed 1, context: html, text, full: html, text
    grammar tweak
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 2, context: html, text, full: html, text
    removing broken link
  • lines changed 1, context: html, text, full: html, text
    updating link to paper
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metaDb on beta for wgEncodeYaleRNAseq.ra with recent changes from clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 2062, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwChIPSeq.ra
  • lines changed 573, context: html, text, full: html, text
    staging metadata clean-up that Cricket did on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDGF.ra
  • lines changed 29, context: html, text, full: html, text
    staging metadata clean-up that Cricket did on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDnaseSeq.ra
  • lines changed 2, context: html, text, full: html, text
    staging metadata clean-up that Cricket did on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleRNAseq.ra
  • lines changed 298, context: html, text, full: html, text
    staging metaDb on beta for wgEncodeYaleRNAseq.ra with recent changes from clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 6, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 2062, context: html, text, full: html, text
    preparing to release metaDb clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
  • lines changed 479, context: html, text, full: html, text
    preparing to release metaDb clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisPet.ra
  • lines changed 2308, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 97, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 279, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 1439, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeSangerGencode.ra
  • lines changed 55, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwChIPSeq.ra
  • lines changed 573, context: html, text, full: html, text
    preparing to release metaDb clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDGF.ra
  • lines changed 29, context: html, text, full: html, text
    preparing to release metaDb clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDnaseSeq.ra
  • lines changed 2, context: html, text, full: html, text
    preparing to release metaDb clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleRNAseq.ra
  • lines changed 298, context: html, text, full: html, text
    getting ready to release metadata clean-up that Cricket did
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 3, context: html, text, full: html, text
    updating links to other browsers to be links to the gateway page rather than the ftp site or conservation html pages. This is mainly for browsers that have come out since the conservation pages were created.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 33, context: html, text, full: html, text
    Changing 'enhancer' to 'enhanced' in integrated regulatory track label, and related changes.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • lines changed 8, context: html, text, full: html, text
    added documentation on directional and undirectional assays
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 6, context: html, text, full: html, text
    updating links to other browsers to be links to the gateway page rather than the ftp site or conservation html pages. This is mainly for browsers that have come out since the conservation pages were created.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 127, context: html, text, full: html, text
    added fastq information from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 157, context: html, text, full: html, text
    added bioRep for Carrie
  • lines changed 18, context: html, text, full: html, text
    more standardization changes and fixing dates for the fastqs
  • lines changed 44, context: html, text, full: html, text
    changed dates on fastqs
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    renamed the trackDb for CshlLongRna
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCshlLongRnaSeq.ra
  • lines changed 88, context: html, text, full: html, text
    added new subtracks
  • lines changed 858, context: html, text, full: html, text
    short and long labels, matrix
  • lines changed 3041, context: html, text, full: html, text
    renamed the trackDb for CshlLongRna
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 3041, context: html, text, full: html, text
    renamed the trackDb for CshlLongRna
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 62, context: html, text, full: html, text
    new track description from CSHL short
  • lines changed 1, context: html, text, full: html, text
    added broken link to supplimentaty track description
  • lines changed 1, context: html, text, full: html, text
    making link to transfragBed6CshlDiscription.html in htdocs/ENCODE work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 99, context: html, text, full: html, text
    changed short labels, the order of the matrix, alignments set to hide, all of K562 to on, prostate off
  • lines changed 2, context: html, text, full: html, text
    fixed the color display on bam
  • lines changed 2, context: html, text, full: html, text
    fixed the pros labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 147, context: html, text, full: html, text
    added new subtracks
  • lines changed 200, context: html, text, full: html, text
    first draft of wrangling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 17, context: html, text, full: html, text
    changed the H1-hESC to be a tier 1 and reflect in the ordering, and the default on status
  • lines changed 27, context: html, text, full: html, text
    Label changes: demote lab, promote exp variables in long label. Also changes to short labels
  • lines changed 9, context: html, text, full: html, text
    changed matrix order, hide for alignments, PolyA+ for Extract
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 506, context: html, text, full: html, text
    new release notes
  • lines changed 298, context: html, text, full: html, text
    short labels
  • lines changed 86, context: html, text, full: html, text
    more standardization changes and fixing dates for the fastqs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 4, context: html, text, full: html, text
    Updated track default views and order of cells in matrix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 23, context: html, text, full: html, text
    added new subtracks
• src/hg/makeDb/trackDb/makeTrixLinks
  • lines changed 42, context: html, text, full: html, text
    put the trix files in /hive/data/inside/trix
• src/hg/makeDb/trackDb/makefile
  • lines changed 8, context: html, text, full: html, text
    put the trix files in /hive/data/inside/trix
  • lines changed 3, context: html, text, full: html, text
    use /data/trix on hgwbeta
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    don't build trix for users unless they uncomment the lines
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    Changed a tiny grammar thing. Thanks, Donna\!
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    updating links to other browsers to be links to the gateway page rather than the ftp site or conservation html pages. This is mainly for browsers that have come out since the conservation pages were created.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    updating links to other browsers to be links to the gateway page rather than the ftp site or conservation html pages. This is mainly for browsers that have come out since the conservation pages were created.
• src/hg/makeDb/trackDb/rhesus/refGenePred.html
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    added RefSeq gene predictions to Rhesus at the request of NCBI
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    redid refseq annonotation track to include all refseq mappings
• src/hg/makeDb/trackDb/rhesus/refSeqAnnon.html
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    converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    added RefSeq gene predictions to Rhesus at the request of NCBI
  • lines changed 2, context: html, text, full: html, text
    converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    added RefSeq gene predictions to Rhesus at the request of NCBI
  • lines changed 5, context: html, text, full: html, text
    converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
  • lines changed 11, context: html, text, full: html, text
    redid refseq annonotation track to include all refseq mappings
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    added RefSeq gene predictions to Rhesus at the request of NCBI
  • lines changed 1, context: html, text, full: html, text
    converted rheMac2 refPreds to full RefSeq annotation track at request of NCBI
• src/hg/makeDb/trackDb/worm/caeJap3/trackDb.ra
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    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
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    initial text edited from hg19 cons46way
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    have WS210 genes on all the nematodes for 10-way frames
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    fixup type of maf net and gene annotations
• src/hg/makeDb/trackDb/worm/ce9/sangerGene.html
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    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
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    turning on frames annotations
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    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDb/worm/priPac2/trackDb.ra
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    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    have WS210 genes on all the nematodes for 10-way frames
• src/hg/makeDb/trackDbRaFormat/trackDbRaFormat.c
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    Add a precious additional character to short labels
• src/hg/near/hgNear/hgNear.c
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    adding javascript event for GeneSorter display-count dropdown
• src/hg/near/hgNear/hgNear.h
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    adding javascript event for GeneSorter display-count dropdown
• src/hg/oneShot/doRgdGene2UniProt/makefile
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    Updated makefile using the template generated by newProg.
• src/hg/protein/makefile
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    spDbAddVarSplice was not being built
• src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
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    Fixed a backwards test against NULL, that led to several UCSC Genes trascripts being assigned to the wrong UniProt identifier
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    added options to control max number of errors reports
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
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    Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
• src/hg/utils/makeTrackIndex/makefile
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    Brian added command line params to makeTrackIndex.c but needs to update this make file
• src/inc/genoFind.h
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    adding IP-logging option
• src/lib/fuzzyShow.c
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    Redmine Bug #1304 (alignment numbering wrong when "viewing parts ofalignment"): fixed bug I introduced into fuzzyShow.c back in 2007. Also in hgc.c, trim the "Alignment of <query> to <chrN:s-e>" message at top of alignment display frame to query bounds (not just viewing window), to be more consistent with message in whole-alignment view.
• src/utils/git-reports/git-reports.c
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    added option to set number of context lines, set default to 15
• src/utils/qa/weeklybld/buildEnv.csh
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    v243 preview

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• files changed: 198