All File Changes

v253_preview2 to v253_base (2011-06-21 to 2011-06-28) v253

• src/hg/checkCoverageGaps/checkCoverageGaps.c
  • lines changed 10, context: html, text, full: html, text
    Responding to Mark's feedback.
• src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Added 2 new views plus and minus raw signal for Strand specific signal.
  • lines changed 2, context: html, text, full: html, text
    Updated bam validation to be 5 mismatches and 99.9% of bam complies.
• src/hg/encode/antibodyWikiParser.py
  • lines changed 30, context: html, text, full: html, text
    Added the functionality to download multiple validation sub-files and combine them as a single pdf file
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 8, context: html, text, full: html, text
    Rename modify command to update and add an example to usage to clarify
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    Rename modify command to update and add an example to usage to clarify
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 14, context: html, text, full: html, text
    As per last weeks code review (note to self), fixed cvNormalize routines to not return values on the stack. Added 'const' to all the cv routines in appropriate places. Kept validateCv compiling even though it is unused. Made hgEncodeVocab use the one true cvFile() call so that it gets the same cv file as other CGIs.
• src/hg/encode/validateCv/validateCv.c
  • lines changed 6, context: html, text, full: html, text
    As per last weeks code review (note to self), fixed cvNormalize routines to not return values on the stack. Added 'const' to all the cv routines in appropriate places. Kept validateCv compiling even though it is unused. Made hgEncodeVocab use the one true cvFile() call so that it gets the same cv file as other CGIs.
• src/hg/hgGene/makefile
  • lines changed 4, context: html, text, full: html, text
    Changed rsync -ar to -aO on Jorge's advice. This eliminates an error when making demo sandboxes.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 10, context: html, text, full: html, text
    Added label selections for omimGene2 track.
• src/hg/hgTracks/bedGraph.c
  • lines changed 2, context: html, text, full: html, text
    properly recognize custom tracks, and allow close of bigWig files after load time
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 12, context: html, text, full: html, text
    properly recognize custom tracks, and allow close of bigWig files after load time
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixes in response to code review with Angie #4352. Thanks Angie!
• src/hg/hgTracks/retroGene.c
  • lines changed 2, context: html, text, full: html, text
    remove itemAdd hardcoding and fix buffer overflow
• src/hg/hgTracks/simpleTracks.c
  • lines changed 68, context: html, text, full: html, text
    Added label processing for omimGene2 track.
• src/hg/hgTracks/snakeTrack.c
  • lines changed 13, context: html, text, full: html, text
    fixes in response to code review with Angie #4352. Thanks Angie!
• src/hg/hgTracks/wigTrack.c
  • lines changed 2, context: html, text, full: html, text
    properly recognize custom tracks, and allow close of bigWig files after load time
• src/hg/hgc/bamClick.c
  • lines changed 8, context: html, text, full: html, text
    redmine #4036: per data provider's request, skip printing sequence quality score in the bam file
  • lines changed 1, context: html, text, full: html, text
    redmine #4036: per data provider's request, skip printing alignment quality for NumtS item bam detail page
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Fixed Bug #1232 Unaligned mRNA Search Results problem.
  • lines changed 10, context: html, text, full: html, text
    Track #4036 remove score field from item detail page
  • lines changed 79, context: html, text, full: html, text
    redmine track #4036: Consolidate numtSeq item display logic for hg18, hg19 amd mm9.
  • lines changed 4, context: html, text, full: html, text
    redmine track #4036 Put back score field of item detail page.
• src/hg/hgc/makefile
  • lines changed 3, context: html, text, full: html, text
    Changed rsync -ar to -aO on Jorge's advice. This eliminates an error when making demo sandboxes.
• src/hg/hgc/retroClick.c
  • lines changed 8, context: html, text, full: html, text
    remove itemAdd hardcoding and fix buffer overflow
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 9, context: html, text, full: html, text
    adding hg18 and hg19 Broad ChromHmm, redmine 2882
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 11, context: html, text, full: html, text
    adding LICR Histone to downloads, redmine# 975
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 2, context: html, text, full: html, text
    added the name of the app in two places to avoid any confusion over which program the note was referring to. Related to Redmine issue 4425.
  • lines changed 2, context: html, text, full: html, text
    added the name of the input file for clarification, per Ann's request. Related to Redmine issue 4425.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    making the range read from low to high instead of high to low per code review: http://redmine.soe.ucsc.edu/issues/4363
  • lines changed 3, context: html, text, full: html, text
    Added a couple line breaks in a printed url as Safari was not wrapping the text and making the page fly off the browser window to the right.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    added a description of where to find the tracks
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    added a description of where to find the tracks
• src/hg/htdocs/staff.html
  • lines changed 2, context: html, text, full: html, text
    Removed Trevor's name from alumni list at his request.
• src/hg/inc/cv.h
  • lines changed 16, context: html, text, full: html, text
    As per last weeks code review (note to self), fixed cvNormalize routines to not return values on the stack. Added 'const' to all the cv routines in appropriate places. Kept validateCv compiling even though it is unused. Made hgEncodeVocab use the one true cvFile() call so that it gets the same cv file as other CGIs.
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    Added support for CSS styles in filterBy drop downs. While this has iffy support in old DDCL, the jquery upgrade should be able to make use of this CSS style.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v253
• src/hg/js/hui.js
  • lines changed 3, context: html, text, full: html, text
    Fix for redmine 4381: subtrack cfg open shouldn't also open metadata.
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    Make sure sandboxes get static js files at root of htdocs-{sandbox}/js dir
• src/hg/js/ui.dropdownchecklist.js
  • lines changed 23, context: html, text, full: html, text
    Added support for CSS styles in filterBy drop downs. While this has iffy support in old DDCL, the jquery upgrade should be able to make use of this CSS style.
• src/hg/js/utils.js
  • lines changed 11, context: html, text, full: html, text
    Fix for redmine 4381: subtrack cfg open shouldn't also open metadata.
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    print out the bogus url in the protocol check for bigDataUrl so the user can find it in their submission
• src/hg/lib/cv.c
  • lines changed 45, context: html, text, full: html, text
    As per last weeks code review (note to self), fixed cvNormalize routines to not return values on the stack. Added 'const' to all the cv routines in appropriate places. Kept validateCv compiling even though it is unused. Made hgEncodeVocab use the one true cvFile() call so that it gets the same cv file as other CGIs.
• src/hg/lib/encode/encodeExp.c
  • lines changed 1, context: html, text, full: html, text
    As per last weeks code review (note to self), fixed cvNormalize routines to not return values on the stack. Added 'const' to all the cv routines in appropriate places. Kept validateCv compiling even though it is unused. Made hgEncodeVocab use the one true cvFile() call so that it gets the same cv file as other CGIs.
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    Good idea to specify the db in the link to hgFileUi for downloadable files.
  • lines changed 136, context: html, text, full: html, text
    Added support for CSS styles in filterBy drop downs. While this has iffy support in old DDCL, the jquery upgrade should be able to make use of this CSS style.
  • lines changed 57, context: html, text, full: html, text
    Removed commented out code that was checked in by accident.
• src/hg/makeDb/doc/bosTau4.txt
  • lines changed 17, context: html, text, full: html, text
    Added SEGMENTAL DUPLICATIONS track.
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 4, context: html, text, full: html, text
    A little bit of old notes that should be checked in, in case Matt wants to share this doc.
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 10, context: html, text, full: html, text
    A little bit of old notes that should be checked in, in case Matt wants to share this doc.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 13, context: html, text, full: html, text
    Track #1091 (MGI/Jackson Lab Tracks update): Bob Sinclair told me thatsome of the files on the FTP site were left over from a previous release and should have been removed. Removed the files locally and reprocessed.
• src/hg/makeDb/hgCgiData/makefile
  • lines changed 4, context: html, text, full: html, text
    Changed rsync -ar to -aO on Jorge's advice. This eliminates an error when making demo sandboxes.
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    Removed trackDb definition and text for omimGene now that omimGene2 is out (the corresponding tables have also been dropped). Also removed the omimGeneId identifier from all.joiner per Fan (redmine #2153, note-167).
  • lines changed 85, context: html, text, full: html, text
    add Gencode V7
  • lines changed 5, context: html, text, full: html, text
    Minor edits per Brook's suggestions.
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    Shorten shortlabel for numtSeq tracks, change track name from NumtSeq to numtSeq, rephrase the note in README
  • lines changed 20, context: html, text, full: html, text
    Added support for CSS styles in filterBy drop downs. While this has iffy support in old DDCL, the jquery upgrade should be able to make use of this CSS style.
• src/hg/makeDb/trackDb/cow/bosTau4/genomicSuperDups.html
  • lines changed 57, context: html, text, full: html, text
    Created cow/bosTau4/genomicSuperDups.html.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 10, context: html, text, full: html, text
    Added 2 new protocols provided by Myers lab.
  • lines changed 40, context: html, text, full: html, text
    Just updated a whole slew of antibody validation documents, plus added two new antibodies
  • lines changed 7, context: html, text, full: html, text
    Added age 18.5 for submission presented by UW for their RNA-seq submissions.
  • lines changed 67, context: html, text, full: html, text
    Looking at this week's code review, I reviewed myself and fixed a few errors that I'd made last week. One shouldn't try to resolve a code review when sick...
  • lines changed 17, context: html, text, full: html, text
    Changing UCD to USC
  • lines changed 7, context: html, text, full: html, text
    Fixing broken links
  • lines changed 19, context: html, text, full: html, text
    Fixed broken links and commented out SK-SY5Y
  • lines changed 25, context: html, text, full: html, text
    Updated view descriptions
  • lines changed 109, context: html, text, full: html, text
    Added 5 cell types, 1 strain and 2 new ages.
  • lines changed 2, context: html, text, full: html, text
    Added descriptions to view descriptions
  • lines changed 1, context: html, text, full: html, text
    Added the Thymus protocol for the Stam lab.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 1917, context: html, text, full: html, text
    releasng changes to public
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeq.html
  • lines changed 2, context: html, text, full: html, text
    corrected citations with dates (if they were known)
• src/hg/makeDb/trackDb/human/hg18/evoCpg.html
  • lines changed 2, context: html, text, full: html, text
    Corrected citation format
  • lines changed 1, context: html, text, full: html, text
    Moved period and italicized journal name
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 105, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 105, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 550, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 550, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 10, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 3, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 3, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 283, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 283, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 534, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 534, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 26, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 26, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 56, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 56, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
  • lines changed 55, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 55, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 35, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 35, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 117, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 117, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 25, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 4, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 905, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 453, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 7, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 7, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 7, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 7, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 86, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 86, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 13, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 12, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 12, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 556, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 556, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • lines changed 29, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 29, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 371, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 371, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 1076, context: html, text, full: html, text
    added dcc accessions to a lot of hg18 tracks
  • lines changed 1076, context: html, text, full: html, text
    didn't need to add dcc accession with the expid's went a bit overboard there. Sorry.
  • lines changed 169, context: html, text, full: html, text
    Changing UCD to USC and adding related expIds
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeSangerGencode.ra
  • lines changed 32, context: html, text, full: html, text
    pushing out updated metaDb for Genocde, hg18 redmine# 2390
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing metadata for release, redmine #2882
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBroadHmm.ra
  • lines changed 168, context: html, text, full: html, text
    preparing metadata for release, redmine #2882
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeSangerGencode.ra
  • lines changed 32, context: html, text, full: html, text
    pushing out updated metaDb for Genocde, hg18 redmine# 2390
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Turned off score filter for evoCpg track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 13, context: html, text, full: html, text
    The UW Southerns track has been made obsolete. This is experiment level validation data that Venkat will wrangle into the hg18 UW DNase composite.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
  • lines changed 3, context: html, text, full: html, text
    Update the citation which has been published (in Nature) by now.
  • lines changed 3, context: html, text, full: html, text
    Changes to longLabels and description as requested by Katrina. 'Chromatin' Modeling' has been changed to 'Chromatin State Segmentation'
  • lines changed 2, context: html, text, full: html, text
    truncating the authors a reference to 10 and fixing a typo
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 1, context: html, text, full: html, text
    removing UCSC Accession column from hg18 hgFileUi, redmine 2882
  • lines changed 10, context: html, text, full: html, text
    Changing shortLabels from Broad HMM to Broad ChromHMM as per Katrina's request
  • lines changed 10, context: html, text, full: html, text
    Changes to longLabels and description as requested by Katrina. 'Chromatin' Modeling' has been changed to 'Chromatin State Segmentation'
• src/hg/makeDb/trackDb/human/hg19/genomicSuperDups.html
  • lines changed 56, context: html, text, full: html, text
    Created hg19 human/hg19/genomicSuperDups.html.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 25, context: html, text, full: html, text
    filled in some dcc accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    reversed 2 name changes that made object name too long
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 12, context: html, text, full: html, text
    fixed replicate errors LID8831 = rep1
  • lines changed 12, context: html, text, full: html, text
    changed another replicate nubmer error
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 65, context: html, text, full: html, text
    filled in some dcc accessions
  • lines changed 23, context: html, text, full: html, text
    re-added 3861
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 342, context: html, text, full: html, text
    gencode metadata and trackDb.
  • lines changed 202, context: html, text, full: html, text
    some clean up, add submission id
  • lines changed 126, context: html, text, full: html, text
    fix up metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 23, context: html, text, full: html, text
    Straightening out hg19 mapability issues before creating pushQ entry.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 15, context: html, text, full: html, text
    filled in some dcc accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 37, context: html, text, full: html, text
    filled in some dcc accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 7, context: html, text, full: html, text
    resubmitted the 2 bigwig files subID 4351
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 483, context: html, text, full: html, text
    Adding the Stanford tags where needed
  • lines changed 4, context: html, text, full: html, text
    Removing the (Farnham)
  • lines changed 1025, context: html, text, full: html, text
    Changing UCD to USC and adding related expIds
  • lines changed 495, context: html, text, full: html, text
    correct a whole bunch of labs in sydh tfbs
  • lines changed 15, context: html, text, full: html, text
    changed some objects to lab=harvard
  • lines changed 445, context: html, text, full: html, text
    Adding more expIds for the ones that we think are valid
  • lines changed 31, context: html, text, full: html, text
    added in some missing expid's
  • lines changed 19, context: html, text, full: html, text
    changed some lab's in sydh tfbs
  • lines changed 19, context: html, text, full: html, text
    changed some experiments to lab=Harvard
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 67, context: html, text, full: html, text
    added in 4349 and 4350
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    added in 4349 and 4350
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing metadata for release, redmine #2882
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHmm.ra
  • lines changed 186, context: html, text, full: html, text
    preparing metadata for release, redmine #2882
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Change NumtS SNP track default
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    gencode metadata and trackDb.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 3, context: html, text, full: html, text
    Update the citation which has been published (in Nature) by now.
  • lines changed 3, context: html, text, full: html, text
    Changes to longLabels and description as requested by Katrina. 'Chromatin' Modeling' has been changed to 'Chromatin State Segmentation'
  • lines changed 2, context: html, text, full: html, text
    truncating the authors a reference to 10 and fixing a typo
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    Changing shortLabels from Broad HMM to Broad ChromHMM as per Katrina's request
  • lines changed 10, context: html, text, full: html, text
    Changes to longLabels and description as requested by Katrina. 'Chromatin' Modeling' has been changed to 'Chromatin State Segmentation'
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra
  • lines changed 129, context: html, text, full: html, text
    gencode metadata and trackDb.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 9, context: html, text, full: html, text
    gencode metadata and trackDb.
  • lines changed 1, context: html, text, full: html, text
    got rid of annotation metadata item
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 13, context: html, text, full: html, text
    fixed some html issues as jacob requested in redmine #1708
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 5, context: html, text, full: html, text
    Added 'ENCODE' to the composite longLabel to make it more prominent.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 10, context: html, text, full: html, text
    added validation snippet to the html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 22, context: html, text, full: html, text
    resubmitted the 2 bigwig files subID 4351
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 3, context: html, text, full: html, text
    updated peggy farnham's information
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 52, context: html, text, full: html, text
    Minor updates in the track description page, at request of the lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 10, context: html, text, full: html, text
    added in 4349 and 4350
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 10, context: html, text, full: html, text
    added in 4349 and 4350
• src/hg/makeDb/trackDb/human/omimGene.html
  • lines changed 122, context: html, text, full: html, text
    Removed trackDb definition and text for omimGene now that omimGene2 is out (the corresponding tables have also been dropped). Also removed the omimGeneId identifier from all.joiner per Fan (redmine #2153, note-167).
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Removed trackDb definition and text for omimGene now that omimGene2 is out (the corresponding tables have also been dropped). Also removed the omimGeneId identifier from all.joiner per Fan (redmine #2153, note-167).
  • lines changed 9, context: html, text, full: html, text
    Shorten shortlabel for numtSeq tracks, change track name from NumtSeq to numtSeq, rephrase the note in README
  • lines changed 1, context: html, text, full: html, text
    Use 'NumtS Sequence' as label for the composite track numtSeq
  • lines changed 3, context: html, text, full: html, text
    Change NumtS SNP track default
  • lines changed 3, context: html, text, full: html, text
    Track #4036 remove score field from item detail page
  • lines changed 3, context: html, text, full: html, text
    redmine track #4036 Put back score field of item detail page.
  • lines changed 1, context: html, text, full: html, text
    redmine #4036: per data provider's request, skip printing sequence quality score in the bam file
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    releasing LICR Histone mm9, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrHistone.ra
  • lines changed 4968, context: html, text, full: html, text
    releasing LICR Histone mm9, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 5, context: html, text, full: html, text
    redmine #4036: No need to have Verification section in mm9's Numt Sequence track detail html description
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Shorten shortlabel for numtSeq tracks, change track name from NumtSeq to numtSeq, rephrase the note in README
  • lines changed 1, context: html, text, full: html, text
    Use 'NumtS Sequence' as label for the composite track numtSeq
  • lines changed 3, context: html, text, full: html, text
    Change NumtS SNP track default
  • lines changed 3, context: html, text, full: html, text
    Track #4036 remove score field from item detail page
  • lines changed 3, context: html, text, full: html, text
    redmine track #4036 Put back score field of item detail page.
  • lines changed 1, context: html, text, full: html, text
    redmine #4036: per data provider's request, skip printing sequence quality score in the bam file
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 9, context: html, text, full: html, text
    Added periods (.) after Journal title for all references. Also removed 'the' before darker in Peak description. Redmine 101, note 23, 24.
  • lines changed 14, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
  • lines changed 0, context: html, text, full: html, text
    removed a space, redmine# 975
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 4, context: html, text, full: html, text
    Updated both tracks with correct range for Signals for Peaks as well as add a score filter and Shading percentage at 11%. User can now update grey scale of peaks to be darker in browswer. Redmine 975, note 17.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
  • lines changed 6, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
  • lines changed 4, context: html, text, full: html, text
    Moved periods (.) after article names out of hyper link. Redmine 3629, note 9.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Removed treatment in fileSortOrder, this is not relevant for this track. Redmine 3629, note 10.
  • lines changed 20, context: html, text, full: html, text
    Track checkboxes are either fully filled in or empty. Removed the grayed out checkboxes for Alignments view. View was hidden by default, but subtracks where on. Redmine 3629, note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 6, context: html, text, full: html, text
    Used rewording from LICR Histone track description provide by Vanessa to make it more readable.
  • lines changed 9, context: html, text, full: html, text
    Added periods (.) after Journal title for all references. Also removed 'the' before darker in Peak description. Redmine 101, note 23, 24.
  • lines changed 14, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    Updated both tracks with correct range for Signals for Peaks as well as add a score filter and Shading percentage at 11%. User can now update grey scale of peaks to be darker in browswer. Redmine 975, note 17.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 12, context: html, text, full: html, text
    Updated Reference ordering to be alphabetically. Redmine 191, note #26.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 4, context: html, text, full: html, text
    Updated score range to be 100:1000 for Peaks and HotSpots to match actuall values. Updated Score filter to be min of 100, just as befor min was 500 and score filter was set to 500. Redmine #191 note 23.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    redmine #4036: per data provider's request, skip printing sequence quality score in the bam file
• src/hg/near/hgNear/makefile
  • lines changed 4, context: html, text, full: html, text
    Changed rsync -ar to -aO on Jorge's advice. This eliminates an error when making demo sandboxes.
• src/utils/qa/getYield.csh
  • lines changed 12, context: html, text, full: html, text
    removed :cds from reference table. changed output to say intersection instead of union
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v253 final build

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• files changed: 212