All File Changes

v247_preview to v247_preview2 (2011-02-01 to 2011-02-08) v247

• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 29, context: html, text, full: html, text
    encodeMkGeoPkg: Added ability to choose release number and mysql database
  • lines changed 12, context: html, text, full: html, text
    Corrected command line arguments for release and database
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 57, context: html, text, full: html, text
    Added preliminary experimant defining vars for 12 tracks.
  • lines changed 102, context: html, text, full: html, text
    Added in Crickets common track variables
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 7, context: html, text, full: html, text
    add run field
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 3, context: html, text, full: html, text
    Change the link to track settings to Katrina's suggested text.
• src/hg/hgTables/asFilter.c
  • lines changed 240, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/asFilter.h
  • lines changed 81, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/asObj.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 34, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bam.c
  • lines changed 142, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 297, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 2, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bigBed.c
  • lines changed 13, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 319, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 11, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/hgTables.c
  • lines changed 3, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 5, context: html, text, full: html, text
    Fixing a chromosome-table check that was glitching out selected fields output for bigBed data hub tracks.
  • lines changed 17, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 9, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 37, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/joining.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 13, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 2, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 4, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    adding call to setUdcCacheDir()
  • lines changed 49, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black when no frequencies were given. Now I'm wondering if I should have used a log scale, but this works so I'm checking it in.
  • lines changed 11, context: html, text, full: html, text
    Like the link to supertrack parent, added a link to the top level track list
  • lines changed 12, context: html, text, full: html, text
    Refinements of link to full track list as suggested by QA
  • lines changed 157, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added filtering by allele frequency:min/max minor allele freq and min chromosome sample count (2N).
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    Adding bam support to data hubs in hgTracks and hgc.
  • lines changed 2, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/hgTracks/encode.c
  • lines changed 26, context: html, text, full: html, text
    if you add exonArrows to broadPeak trackDb, draw the arrows on full size track #2189
• src/hg/hgTracks/gvfTrack.c
  • lines changed 4, context: html, text, full: html, text
    Track #34 (dbVar for human): Color switch agreed on by NCBI, DGV andother parties: Gain is now blue, Loss is now red.
• src/hg/hgTracks/hgTracks.c
  • lines changed 24, context: html, text, full: html, text
    adding code to ignore already failed hubs and to detect and update the status of new hub failures
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    oops... snake stuff that should have been in the earlier commit
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    add some code to draw snakes which will be used to draw Benedict's cactus graphs in ancestrla root browsers
• src/hg/hgTracks/simpleTracks.c
  • lines changed 14, context: html, text, full: html, text
    change interaction track (eg. ChiaPet) to use score to color, rather than chrom color
  • lines changed 5, context: html, text, full: html, text
    Added some functions for omimGeneClass3.
  • lines changed 4, context: html, text, full: html, text
    Added support for '*Filter' generic score filter logic to beds
  • lines changed 2, context: html, text, full: html, text
    Again the newline at the end of the file vanished. What is git up to...
  • lines changed 4, context: html, text, full: html, text
    add some code to draw snakes which will be used to draw Benedict's cactus graphs in ancestrla root browsers
  • lines changed 2, context: html, text, full: html, text
    Changed DECIPHER dup color from green to blue.
  • lines changed 169, context: html, text, full: html, text
    Added functions for omimGeneClass3, still under development...
  • lines changed 11, context: html, text, full: html, text
    Fixed bug to do with next/prev exon mouseover messages not showing the correct number of exons on reverse-strand genes.
• src/hg/hgTracks/snakeTrack.c
  • lines changed 917, context: html, text, full: html, text
    add some code to draw snakes which will be used to draw Benedict's cactus graphs in ancestrla root browsers
• src/hg/hgTracks/variation.c
  • lines changed 133, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black when no frequencies were given. Now I'm wondering if I should have used a log scale, but this works so I'm checking it in.
  • lines changed 64, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added filtering by allele frequency:min/max minor allele freq and min chromosome sample count (2N).
• src/hg/hgTracks/variation.h
  • lines changed 43, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black when no frequencies were given. Now I'm wondering if I should have used a log scale, but this works so I'm checking it in.
• src/hg/hgc/bamClick.c
  • lines changed 8, context: html, text, full: html, text
    Adding bam support to data hubs in hgTracks and hgc.
  • lines changed 2, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/hgc/bigBedClick.c
  • lines changed 9, context: html, text, full: html, text
    now using bigBed as a bedDetail system
• src/hg/hgc/gvfClick.c
  • lines changed 40, context: html, text, full: html, text
    Track #34 (dbVar for human): Nicer display of Start_range and End_range attributes.
• src/hg/hgc/hgc.c
  • lines changed 209, context: html, text, full: html, text
    Added processing logic for omimGeneClass3 subtrack.
  • lines changed 8, context: html, text, full: html, text
    Added logic for new OMIM related subtracks.
  • lines changed 14, context: html, text, full: html, text
    Updated for OMIM related tracks.
  • lines changed 2, context: html, text, full: html, text
    Fixing typo in comment.
  • lines changed 74, context: html, text, full: html, text
    Support for extraFields trackDb setting for bed items
  • lines changed 320, context: html, text, full: html, text
    Added function for new OMIM related tracks. Still under development ...
• src/hg/htdocs/ENCODE/contributors.html
  • lines changed 9, context: html, text, full: html, text
    Geographic map of ENCODE labs for portal (from ENCODE101 paper)
  • lines changed 24, context: html, text, full: html, text
    Prettify display of map, add credit
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Adding Caltech RNA-seq, hg19, Redmine #35
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 7, context: html, text, full: html, text
    added Stan/Yale TFBS to downloadsMouse.html; on index.html I fixed Preview Browser mm9 link, added Genome Browser mm9 link, enabled & reordered mouse downloads link because I released the first mouse ENCODE track (Redmine Issue #98)
• src/hg/htdocs/ENCODE/index.html
  • lines changed 4, context: html, text, full: html, text
    added Stan/Yale TFBS to downloadsMouse.html; on index.html I fixed Preview Browser mm9 link, added Genome Browser mm9 link, enabled & reordered mouse downloads link because I released the first mouse ENCODE track (Redmine Issue #98)
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 6, context: html, text, full: html, text
    Added links to genomewiki coordinate transforms page to MAF description (redmine #2632)
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 55, context: html, text, full: html, text
    Updated publication dates and links of several 2010 epubs.
  • lines changed 1, context: html, text, full: html, text
    Missing period in Raney citation.
• src/hg/htdocs/images/encodeContributorsMap.png
  • lines changed 0, context: html, text, full: html, text
    Geographic map of ENCODE labs for portal (from ENCODE101 paper)
  • lines changed 0, context: html, text, full: html, text
    Prettify display of map, add credit
• src/hg/htdocs/license/gblicense.pdf
  • lines changed 0, context: html, text, full: html, text
    Updated licensing agreement from Wil.
  • lines changed 0, context: html, text, full: html, text
    Another tiny update from Wil.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    Small change to sort column hover over header, but this does not fix IE problem with hover CSS. Should chnage our CGI HTML page doctype to strict.
• src/hg/inc/bamFile.h
  • lines changed 22, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/inc/hui.h
  • lines changed 14, context: html, text, full: html, text
    Added support for '*Filter' generic score filter logic to beds
• src/hg/inc/samAlignment.h
  • lines changed 72, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/inc/snp125Ui.h
  • lines changed 8, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black when no frequencies were given. Now I'm wondering if I should have used a log scale, but this works so I'm checking it in.
  • lines changed 3, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added filtering by allele frequency:min/max minor allele freq and min chromosome sample count (2N).
• src/hg/inc/trackDb.h
  • lines changed 7, context: html, text, full: html, text
    Added routine to get an slName list of settings from tdb tree which wildMatch an expression
• src/hg/js/hgTracks.js
  • lines changed 32, context: html, text, full: html, text
    Removing referenced javascript files from popup dialog. However, there are still problems, because the javascript is needed but getScript hoses jQuery memory some how.
  • lines changed 72, context: html, text, full: html, text
    add zoomToCodon code (redmine# 2724); this is currently turned off via the supportZoomCodon variable
• src/hg/js/utils.js
  • lines changed 18, context: html, text, full: html, text
    resize related code (redmine #2633); code is currently only used in larrym's tree
• src/hg/lib/bamFile.c
  • lines changed 165, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/encode/openChromCombinedPeaks.sql
  • lines changed 28, context: html, text, full: html, text
    Adding Open Chrom Synthesis tracks schema which is a bed 9 +.
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    check to see if HTTP_HOST is null before assuming that it isn't
• src/hg/lib/hubConnect.c
  • lines changed 48, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/hg/lib/hui.c
  • lines changed 170, context: html, text, full: html, text
    Fixed hgc downloads link bug reported in redmine 1550.7. Also refactored code in preparation for adding filters for bed n + extra fields. That code is still ifdef'd out.
  • lines changed 1, context: html, text, full: html, text
    Accidentally checked in with test code ifdef'd in. Now out.
  • lines changed 158, context: html, text, full: html, text
    Added support for '*Filter' generic score filter logic to beds
  • lines changed 10, context: html, text, full: html, text
    Fixed redmine track #98, question #56: bug in filterComposite when 'All' is selected.
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/mdb.c
  • lines changed 2, context: html, text, full: html, text
    mdb queries need to be case-sensitive for mdb objs
• src/hg/lib/ncbiIncidentDb.as
  • lines changed 9, context: html, text, full: html, text
    .as file definition used to construct bigBed file for this track
• src/hg/lib/omimAvRepl.sql
  • lines changed 13, context: html, text, full: html, text
    Added omimAvRepl.sql table for OMIM tracks.
• src/hg/lib/samAlignment.as
  • lines changed 16, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/lib/samAlignment.c
  • lines changed 189, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/samAlignment.sql
  • lines changed 22, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/lib/snp125Ui.c
  • lines changed 40, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added coloring by allele frequency:items are shaded on a scale of red (rare) to blue (common), or black when no frequencies were given. Now I'm wondering if I should have used a log scale, but this works so I'm checking it in.
• src/hg/lib/tests/expected/genePred/fromGffRegressTest.gp
  • lines changed 1, context: html, text, full: html, text
    fixed memory corruption on very long GFF attribute columns (#2694)
• src/hg/lib/tests/genePredTests.mk
  • lines changed 1, context: html, text, full: html, text
    fixed memory corruption on very long GFF attribute columns (#2694)
• src/hg/lib/tests/input/genePred/regress.gff
  • lines changed 4, context: html, text, full: html, text
    fixed memory corruption on very long GFF attribute columns (#2694)
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    add bedLogR support to composite UI
  • lines changed 52, context: html, text, full: html, text
    Added routine to get an slName list of settings from tdb tree which wildMatch an expression
• src/hg/lib/web.c
  • lines changed 6, context: html, text, full: html, text
    We should upgrade to doctyype 4.01 strict from 3.2. It does fix atleast one IE problem. But that will require a lot of testing.
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 35, context: html, text, full: html, text
    More wrangling details
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 24, context: html, text, full: html, text
    More wrangling details
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
  • lines changed 1588, context: html, text, full: html, text
    New notes file for CshlLong
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
  • lines changed 147, context: html, text, full: html, text
    Verified checksums and updated notes
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1111, context: html, text, full: html, text
    done with v61 ensembl build
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 13, context: html, text, full: html, text
    Set nomLeu1.perChromTables = no
• src/hg/makeDb/doc/oviAri1.txt
  • lines changed 7, context: html, text, full: html, text
    Add oviAri1.perChromTables = no in genbank.conf
  • lines changed 15, context: html, text, full: html, text
    Add ctgPos2 track for oviAri1
  • lines changed 6, context: html, text, full: html, text
    oviAri1 Initial Release
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 25, context: html, text, full: html, text
    Progressed a little further, added more testing steps
  • lines changed 75, context: html, text, full: html, text
    Advanced a bit further, did some additional testing
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 6, context: html, text, full: html, text
    Add oviAri1.perChromTables = no for Sheep
  • lines changed 5, context: html, text, full: html, text
    Set nomLeu1.perChromTables = no
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    add DanRer7 to non-self chains list
• src/hg/makeDb/trackDb/README
  • lines changed 8, context: html, text, full: html, text
    move ncbiIncidentDb to top level trackDb and document new bigBed option
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Update grant/lab info for reporting
  • lines changed 1, context: html, text, full: html, text
    Accepted a provisional stanza
  • lines changed 3, context: html, text, full: html, text
    Addressed code review feedback from Katrina
  • lines changed 3, context: html, text, full: html, text
    fix up GIS-Ruan, and run type
  • lines changed 2, context: html, text, full: html, text
    Update projectName for ChiaPET
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Moving a batch of changes from alpha to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 192, context: html, text, full: html, text
    approved changes to beta/cv.ra and releasing them to public - Redmine Issue #2662
• src/hg/makeDb/trackDb/human/agilentCgh.html
  • lines changed 131, context: html, text, full: html, text
    moved and renamed html for agilent track in preparation for moving trackDb entries down from human to hg* http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/human/agilentCghAlpha.html
  • lines changed 161, context: html, text, full: html, text
    moved and renamed html for agilent track in preparation for moving trackDb entries down from human to hg* http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 1, context: html, text, full: html, text
    Changed DECIPHER dup color from green to blue.
• src/hg/makeDb/trackDb/human/hg18/agilentCgh.html
  • lines changed 131, context: html, text, full: html, text
    moved and renamed html for agilent track in preparation for moving trackDb entries down from human to hg* http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 64, context: html, text, full: html, text
    Agilent track 1.moved trackDb entries down from human level to hg18 and hg19 2. removed all release tags 3. changed the priority for the subtracks for hg18 so that it was easier to follow 4. took out 'origAssembly' line from hg18 5. renames 3 tracks in hg19 to the correct name. http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
  • lines changed 161, context: html, text, full: html, text
    moved and renamed html for agilent track in preparation for moving trackDb entries down from human to hg* http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    This is the fixed metadata for Suny Albany GeneST. There are no weird duplicates
  • lines changed 5, context: html, text, full: html, text
    GisChiaPet metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 308, context: html, text, full: html, text
    Fixed a few protocol ID's to say t and added biorep where missing
  • lines changed 409, context: html, text, full: html, text
    Deleted suspect data from metaDb
  • lines changed 2730, context: html, text, full: html, text
    removed AllRawSigs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 603, context: html, text, full: html, text
    Cleaning up labels, putting some data in the attic, fixing settings
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 2208, context: html, text, full: html, text
    GisChiaPet metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 91, context: html, text, full: html, text
    Changeing GIS to Gis
  • lines changed 127, context: html, text, full: html, text
    Correcting Gis to GIS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 15, context: html, text, full: html, text
    updating post ENCODE June 2010 Freeze to Jan 2011 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 621, context: html, text, full: html, text
    Updated data version to ENCODE Jan 2011
  • lines changed 211, context: html, text, full: html, text
    Added 13 bam files that were either missing or fixed tha had already been passed on to the AWG.
  • lines changed 7, context: html, text, full: html, text
    Update the conrolId for experiments where the initial control was bad. Changed SL1780 -> SL2455 for 3 replicates.
  • lines changed 42, context: html, text, full: html, text
    Fixed 11 experiments to have correct protocol's.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 8, context: html, text, full: html, text
    Updated data version to ENCODE Jan 2011
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 39, context: html, text, full: html, text
    Updated data version to ENCODE Jan 2011
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 15, context: html, text, full: html, text
    Changed post Jun Freeze to Jan Freeze
  • lines changed 15, context: html, text, full: html, text
    Updated data version to ENCODE Jan 2011
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 9, context: html, text, full: html, text
    Fixing the CAGE to Cage
  • lines changed 2, context: html, text, full: html, text
    error in origAssembly fixed
  • lines changed 9, context: html, text, full: html, text
    updating post ENCODE June 2010 Freeze to Jan 2011 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 475, context: html, text, full: html, text
    This is the fixed metadata for Suny Albany GeneST. There are no weird duplicates
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 24, context: html, text, full: html, text
    I am checking this in broken for Tim to look at
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    Changed metadata so that the matrix links would work
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    Updated dataVersion to ENCODE Jan 2011
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 11, context: html, text, full: html, text
    Fixed cell and controlId's for experiments where UCD was lab and lab has variant B of cell, but was incorrectly labeled with non-variant cell line.
  • lines changed 11, context: html, text, full: html, text
    Reversed the corrections in commit 9f9ec89fe3b8914f8cbc37e568293082a42e087e. Waiting on labs updates.
  • lines changed 25, context: html, text, full: html, text
    Updated meta-data errors when Anshul was mapping controls.
  • lines changed 31, context: html, text, full: html, text
    Fixed wrong antibody designations in meta-data. Changed HA-F2F1 -> HA-E2F1 and MafK_(sc477) -> MafK_(SC-477)
  • lines changed 3, context: html, text, full: html, text
    Fixed wrong antibody designations in meta-data that I forgot in last commit Changed HA-F2F1 -> HA-E2F1.
  • lines changed 4663, context: html, text, full: html, text
    updating post ENCODE June 2010 Freeze to Jan 2011 Freeze
  • lines changed 3, context: html, text, full: html, text
    Replaced empty BAM file with submission 3500.
  • lines changed 63, context: html, text, full: html, text
    Added submission 3499, for missing T-REx HEK293 control input.
  • lines changed 187, context: html, text, full: html, text
    Addd submissions 3501,3497,3498. That fill gaps of missing controls for AWG.
  • lines changed 49, context: html, text, full: html, text
    Fixed incorrect controls and controlId's for MCF10A-Er-Src experiments.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Changing the new treatments to what was finally registered
  • lines changed 2, context: html, text, full: html, text
    Changing the new treatments to what was finally registered
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing for CaltechRnaSeq release, redmine issue #35
  • lines changed 1, context: html, text, full: html, text
    removing Caltech RNA-seq from public, redmine issue #35, realized gbdb files not up to date
  • lines changed 1, context: html, text, full: html, text
    preparing to release Caltech RNA-seq hg19, redmine issue# 35
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 14870, context: html, text, full: html, text
    preparing for CaltechRnaSeq release, redmine issue #35
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Removed decipher track override for hg18 lift.
  • lines changed 6, context: html, text, full: html, text
    now using bigBed as a bedDetail system
  • lines changed 3, context: html, text, full: html, text
    remove debugging BB labels
  • lines changed 11, context: html, text, full: html, text
    move ncbiIncidentDb to top level trackDb and document new bigBed option
  • lines changed 93, context: html, text, full: html, text
    Agilent track 1.moved trackDb entries down from human level to hg18 and hg19 2. removed all release tags 3. changed the priority for the subtracks for hg18 so that it was easier to follow 4. took out 'origAssembly' line from hg18 5. renames 3 tracks in hg19 to the correct name. http://redmine.soe.ucsc.edu/issues/1791#note-17
  • lines changed 13, context: html, text, full: html, text
    Matt Weirauch's TFBS for hg19... yay Matt!
  • lines changed 13, context: html, text, full: html, text
    add snake type, will be used to display Benedict's cactus graphs on the root ancestor
  • lines changed 1, context: html, text, full: html, text
    tag snake track with release alpha
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 51, context: html, text, full: html, text
    added a new composite for SUNY
  • lines changed 1, context: html, text, full: html, text
    preparing for CaltechRnaSeq release, redmine issue #35
  • lines changed 1, context: html, text, full: html, text
    removing Caltech RNA-seq from public, redmine issue #35, realized gbdb files not up to date
  • lines changed 1, context: html, text, full: html, text
    preparing to release Caltech RNA-seq hg19, redmine issue# 35
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 2, context: html, text, full: html, text
    Added 'Alignments' to display conventions at Katrina's request.
  • lines changed 5, context: html, text, full: html, text
    Added 'Raw Data' into the display conventions so that each 'view' is covered and the information is readily available on hgFileUi downloads page.
  • lines changed 2, context: html, text, full: html, text
    Fixed long labels to get this by the QA watchdogs and removed the display only views from Display Conventions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 296, context: html, text, full: html, text
    Fixed long labels to match the new and unloved std
  • lines changed 288, context: html, text, full: html, text
    Broad should not declare origAssembly=hg18 in trackDb as all were remapped on hg19, not lifted over. origAssembly=hg18 still belongs in the mdb
  • lines changed 136, context: html, text, full: html, text
    Fixed long labels to get this by the QA watchdogs and removed the display only views from Display Conventions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the viewlimits for the minus strand to be negative
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 15, context: html, text, full: html, text
    Changed the viewlimits for the minus strand to be negative
  • lines changed 21, context: html, text, full: html, text
    Changed the viewing limits to match hg18
  • lines changed 5, context: html, text, full: html, text
    Added autoscale to clean up the data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 10, context: html, text, full: html, text
    Changed the bam display settings to the lab requests
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 462, context: html, text, full: html, text
    Cleaning up labels, putting some data in the attic, fixing settings
  • lines changed 168, context: html, text, full: html, text
    Updated longLabels to new format for new submits
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 1, context: html, text, full: html, text
    add the ability to add exonArrows to broadPeak tracks, add them to wgEncodeDukeAffyExon
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 2, context: html, text, full: html, text
    color wgEncodeGisChiaPet by score
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 11, context: html, text, full: html, text
    Added Flo's email, colors and fixed heading
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 199, context: html, text, full: html, text
    changing back to matrix as lab request
  • lines changed 2, context: html, text, full: html, text
    Changed the Tier1 labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 35, context: html, text, full: html, text
    Added matrix, fixed short labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 15, context: html, text, full: html, text
    Changed defualt settings to Flo request and fixed html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Changed default track view to A459 Dex 1nM and EtOH
  • lines changed 32, context: html, text, full: html, text
    change genepred to genePred
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    Standardized longLabels and fixed defaults that Terry Furey noticed.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 141, context: html, text, full: html, text
    Standardized longLabels and fixed defaults that Terry Furey noticed.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 79, context: html, text, full: html, text
    Standardized longLabels and fixed defaults that Terry Furey noticed.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 1, context: html, text, full: html, text
    Added extraFields for hgc
  • lines changed 5, context: html, text, full: html, text
    Added pValueFilter and filterBy ocCode for extra coolness.
  • lines changed 7, context: html, text, full: html, text
    Standardized longLabels and fixed defaults that Terry Furey noticed.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 7, context: html, text, full: html, text
    Fixing the display for tracks from sub3084, changing some display settings
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
  • lines changed 21, context: html, text, full: html, text
    added missing quotes for the links to open up in new page, fixed spacing issues so that the underline links don't go beyond the periods, redmine issue #38
  • lines changed 1, context: html, text, full: html, text
    Fixed the configuration settings for Vanessa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed the configuration settings for Vanessa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 154, context: html, text, full: html, text
    added a new composite for SUNY
  • lines changed 0, context: html, text, full: html, text
    dos2unix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 438, context: html, text, full: html, text
    added a new composite for SUNY
  • lines changed 38, context: html, text, full: html, text
    Updated longLabels to new format(
  • lines changed 7, context: html, text, full: html, text
    Changing display settings
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 9, context: html, text, full: html, text
    Changed metadata so that the matrix links would work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed cell and controlId's for experiments where UCD was lab and lab has variant B of cell, but was incorrectly labeled with non-variant cell line.
  • lines changed 3, context: html, text, full: html, text
    Reversed the corrections in commit 9f9ec89fe3b8914f8cbc37e568293082a42e087e. Waiting on labs updates.
  • lines changed 9, context: html, text, full: html, text
    Updated meta-data errors when Anshul was mapping controls.
  • lines changed 9, context: html, text, full: html, text
    Added submission 3499, for missing T-REx HEK293 control input.
  • lines changed 28, context: html, text, full: html, text
    Addd submissions 3501,3497,3498. That fill gaps of missing controls for AWG.
  • lines changed 8, context: html, text, full: html, text
    Fixed incorrect controls and controlId's for MCF10A-Er-Src experiments.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 3, context: html, text, full: html, text
    Updated the labels for wgEncodeUncBsuProt
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 96, context: html, text, full: html, text
    Forced Tier 1 and Tier 2 cell lines to appear 1st and 2nd in the browswer before all tier 3 cell lines which are listed alphabetically.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 36, context: html, text, full: html, text
    Forced Tier 1 and Tier 2 cell lines to appear 1st and 2nd in the browswer before all tier 3 cell lines which are listed alphabetically.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    added omimGeneClass3 track.
  • lines changed 11, context: html, text, full: html, text
    added omimGeneClass2.
  • lines changed 11, context: html, text, full: html, text
    Added omimLocationClass2.
  • lines changed 41, context: html, text, full: html, text
    Updated for OMIM composite track.
  • lines changed 180, context: html, text, full: html, text
    Agilent track 1.moved trackDb entries down from human level to hg18 and hg19 2. removed all release tags 3. changed the priority for the subtracks for hg18 so that it was easier to follow 4. took out 'origAssembly' line from hg18 5. renames 3 tracks in hg19 to the correct name. http://redmine.soe.ucsc.edu/issues/1791#note-17
• src/hg/makeDb/trackDb/mouse/agilentCgh.html
  • lines changed 66, context: html, text, full: html, text
    removing old html for agilent track since releasing track the the rr. In next commit will git mv agilentCghAlpha.html agilentCgh.html. Had to break this commit up so that git wouldn't get confused
  • lines changed 91, context: html, text, full: html, text
    changing name of 'alpha' html to be the main html for the agilent track for mouse
• src/hg/makeDb/trackDb/mouse/agilentCghAlpha.html
  • lines changed 91, context: html, text, full: html, text
    changing name of 'alpha' html to be the main html for the agilent track for mouse
• src/hg/makeDb/trackDb/mouse/agilentCghBeta.html
  • lines changed 57, context: html, text, full: html, text
    removing old html for agilent track since releasing track the the rr. In next commit will git mv agilentCghAlpha.html agilentCgh.html. Had to break this commit up so that git wouldn't get confused
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 5, context: html, text, full: html, text
    preparing for release of Stan/Yale TFBS to RR (Redmine Issue #98)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 4442, context: html, text, full: html, text
    preparing for release of Stan/Yale TFBS to RR (Redmine Issue #98)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    releasing Stan/Yale TFBS to RR (Redmine Issue #98)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Added View for Alignments to state that it is available for download.
  • lines changed 9, context: html, text, full: html, text
    Added explanation of pooled data and link to per-replicate alignments and sequences. Also added explanation for Peaks grayscale.
  • lines changed 2, context: html, text, full: html, text
    changing tense of a sentence and case of a few words (Redmine Issue #98)
  • lines changed 1, context: html, text, full: html, text
    adding a period (Redmine Issue #98)
  • lines changed 0, context: html, text, full: html, text
    removing extraneous space (Redmine Issue #98)
  • lines changed 2, context: html, text, full: html, text
    Removed alignments from Display conventions.
  • lines changed 44, context: html, text, full: html, text
    alphabetized references (Redmine issue #98)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 57, context: html, text, full: html, text
    Fixed track longLabls to substitute Transcription Factor Binding -> TFBS by Chip-Seq
  • lines changed 2, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
  • lines changed 1, context: html, text, full: html, text
    Commented out filterComposite option and replaced with checkboxes so that track can go out.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    removing the release public stanza in trackDb for mouse agilent. Also updating the html reference. See these other related commits: 337a7eb714b1697d0796b054bf1fb3a76801383f and 4beef1042781eadaa74ead565888430b2ad1a1c3
• src/hg/makeDb/trackDb/ncbiIncidentDb.html
  • lines changed 5, context: html, text, full: html, text
    move ncbiIncidentDb to top level trackDb and document new bigBed option
• src/hg/makeDb/trackDb/rat/agilentCgh.html
  • lines changed 54, context: html, text, full: html, text
    removing old html for rat agilent track http://redmine.soe.ucsc.edu/issues/1791
  • lines changed 91, context: html, text, full: html, text
    renaming the newest html for rat aglient track to not have 'alpha' in it any more http://redmine.soe.ucsc.edu/issues/1791
• src/hg/makeDb/trackDb/rat/agilentCghAlpha.html
  • lines changed 91, context: html, text, full: html, text
    renaming the newest html for rat aglient track to not have 'alpha' in it any more http://redmine.soe.ucsc.edu/issues/1791
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 39, context: html, text, full: html, text
    removing 'release public' stanza from trackDb for rat agilent track. releasing to public http://redmine.soe.ucsc.edu/issues/1791
• src/hg/makeDb/trackDb/sheep/oviAri1/ctgPos2.html
  • lines changed 15, context: html, text, full: html, text
    Add ctgPos2 track for oviAri1
  • lines changed 1, context: html, text, full: html, text
    Track description touch up
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 2, context: html, text, full: html, text
    Track description touch up
• src/hg/makeDb/trackDb/sheep/oviAri1/gap.html
  • lines changed 2, context: html, text, full: html, text
    Track description touch up
• src/hg/makeDb/trackDb/sheep/oviAri1/gold.html
  • lines changed 2, context: html, text, full: html, text
    Track description touch up
• src/hg/makeDb/trackDb/sheep/oviAri1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Track description touch up
  • lines changed 8, context: html, text, full: html, text
    Add Cow chain to oviAri1
• src/hg/makeDb/trackDb/sheep/trackDb.chainNet.ra
  • lines changed 23, context: html, text, full: html, text
    Add Cow chain to oviAri1
• src/hg/makeDb/trackDb/sheep/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Add Cow chain to oviAri1
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    color wgEncodeGisChiaPet by score
  • lines changed 1, context: html, text, full: html, text
    add the ability to add exonArrows to broadPeak tracks, add them to wgEncodeDukeAffyExon
  • lines changed 1, context: html, text, full: html, text
    now using bigBed as a bedDetail system
  • lines changed 1, context: html, text, full: html, text
    Added extraFields for bed hgc support
  • lines changed 3, context: html, text, full: html, text
    Added 3 wildcard based tags. '*Filter' cound be pValueFilter or scoreFilter or...
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    move ncbiIncidentDb to top level trackDb and document new bigBed option
  • lines changed 1, context: html, text, full: html, text
    adjust priority for NCBI Incident track
  • lines changed 3, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): adding yet another setting necessaryfor subset tracks.
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 155, context: html, text, full: html, text
    finalize the chain/net documentation
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    finalize the chain/net documentation
• src/hg/oneShot/doOmimLocation/doOmimLocation.c
  • lines changed 304, context: html, text, full: html, text
    Created doOmimLocation.c to convert OMIM location into genomic location.
• src/hg/oneShot/doOmimLocation/makefile
  • lines changed 38, context: html, text, full: html, text
    Created makefile for doOmimLocation.
• src/hg/oneShot/freen/freen.c
  • lines changed 15, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/snp/hapmapLd/hapmapNewPhasedToOld.pl
  • lines changed 77, context: html, text, full: html, text
    Track #2648 (HapMap LD Phased): script to translate HapMap's newphased genotype format (ftp://ftp.ncbi.nlm.nih.gov/hapmap/phasing/2009-02_phaseIII/) into the older format recognized by Haploview (ftp://ftp.ncbi.nlm.nih.gov/hapmap/phasing/2007-08_rel22/).
• src/hg/trfBig/trfBig.c
  • lines changed 40, context: html, text, full: html, text
    Fixed bug with tempDir option not working. Update to current option parsing. Made help more informative
• src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh
  • lines changed 8, context: html, text, full: html, text
    Simplified the argument list
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 174, context: html, text, full: html, text
    adding v61 definitions
• src/hg/utils/automation/ncbiIncidentDb.pl
  • lines changed 177, context: html, text, full: html, text
    first version of processing sql files from xml dump from NCBI
  • lines changed 113, context: html, text, full: html, text
    adding mouse and zebrafish, it is hokey, but it works
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 81, context: html, text, full: html, text
    Added wildCardHash() routine to support tagTypes like *FilterLimits.
• src/inc/errabort.h
  • lines changed 3, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/inc/linefile.h
  • lines changed 3, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/inc/net.h
  • lines changed 13, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/dystring.c
  • lines changed 3, context: html, text, full: html, text
    Making dyString expand by at least 1.5x if it needs to expand.
• src/lib/errabort.c
  • lines changed 13, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/gff.c
  • lines changed 7, context: html, text, full: html, text
    fixed memory corruption on very long GFF attribute columns (#2694)
• src/lib/htmshell.c
  • lines changed 6, context: html, text, full: html, text
    We should upgrade to doctyype 4.01 strict from 3.2. It does fix atleast one IE problem. But that will require a lot of testing.
• src/lib/linefile.c
  • lines changed 12, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/net.c
  • lines changed 25, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/product/ex.hg.conf
  • lines changed 8, context: html, text, full: html, text
    document db.socket and db.port variables
• src/utils/bedRemoveOverlap/empty.bed
  • lines changed 1, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/one.bed
  • lines changed 1, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/test4.bed
  • lines changed 6, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/threeLast.bed
  • lines changed 3, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/twoFirst.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/twoSecond.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/unsorted.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v247 preview2

• lines changed: 46934
• files changed: 318