All File Changes
v242_base to v243_preview (2010-10-12 to 2010-10-19) v243
- src/blat/version.doc
- 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 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 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
- 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
- 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
- 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
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaSeq.release1.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaSeq.release1.notes.txt
- 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
- 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
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
adding new chainNet definitions
- 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
- src/hg/makeDb/trackDb/human/gwasCatalog.html
- 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
- 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 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
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- 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 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
- 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
- lines changed 2, context: html, text, full: html, text
don't build trix for users unless they uncomment the lines
- src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
- lines changed 1, context: html, text, full: html, text
Changed a tiny grammar thing. Thanks, Donna\!
- lines changed 4, 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/orangutan/ponAbe2/multiz8way.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/rhesus/refGenePred.html
- lines changed 31, context: html, text, full: html, text
added RefSeq gene predictions to Rhesus at the request of NCBI
- lines changed 31, context: html, text, full: html, text
redid refseq annonotation track to include all refseq mappings
- src/hg/makeDb/trackDb/rhesus/refSeqAnnon.html
- lines changed 32, context: html, text, full: html, text
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
- lines changed 3, context: html, text, full: html, text
have WS210 genes on all the nematodes for 10-way frames
- src/hg/makeDb/trackDb/worm/ce9/cons10way.html
- lines changed 437, context: html, text, full: html, text
initial text edited from hg19 cons46way
- lines changed 10, context: html, text, full: html, text
have WS210 genes on all the nematodes for 10-way frames
- lines changed 25, context: html, text, full: html, text
fixup type of maf net and gene annotations
- src/hg/makeDb/trackDb/worm/ce9/sangerGene.html
- lines changed 2, context: html, text, full: html, text
have WS210 genes on all the nematodes for 10-way frames
- src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
- lines changed 1, context: html, text, full: html, text
turning on frames annotations
- lines changed 4, context: html, text, full: html, text
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
- lines changed 3, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
Add a precious additional character to short labels
- src/hg/near/hgNear/hgNear.c
- lines changed 21, context: html, text, full: html, text
adding javascript event for GeneSorter display-count dropdown
- src/hg/near/hgNear/hgNear.h
- lines changed 1, context: html, text, full: html, text
adding javascript event for GeneSorter display-count dropdown
- src/hg/oneShot/doRgdGene2UniProt/makefile
- lines changed 31, context: html, text, full: html, text
Updated makefile using the template generated by newProg.
- src/hg/protein/makefile
- lines changed 1, context: html, text, full: html, text
spDbAddVarSplice was not being built
- src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
- lines changed 1, context: html, text, full: html, text
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
- lines changed 19, context: html, text, full: html, text
added options to control max number of errors reports
- src/hg/utils/makeTrackIndex/makeTrackIndex.c
- lines changed 1, context: html, text, full: html, text
Resolving compiler warnings from gcc (Ubuntu 4.4.1-4ubuntu9).
- src/hg/utils/makeTrackIndex/makefile
- lines changed 3, context: html, text, full: html, text
Brian added command line params to makeTrackIndex.c but needs to update this make file
- src/inc/genoFind.h
- src/lib/fuzzyShow.c
- lines changed 1, 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/utils/git-reports/git-reports.c
- lines changed 9, context: html, text, full: html, text
added option to set number of context lines, set default to 15
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 25582
- files changed: 198