All File Changes

v261_base to v262_preview (2012-01-03 to 2012-01-10) v262

• python/lib/ucscgenomics/cv.py
  • lines changed 32, context: html, text, full: html, text
    fixed small bug in cv.py
  • lines changed 1, context: html, text, full: html, text
    correct wrong type of quotes
• python/lib/ucscgenomics/ra.py
  • lines changed 50, context: html, text, full: html, text
    first draft of raMerging functions
  • lines changed 3, context: html, text, full: html, text
    had drop vs new backwards
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 94, context: html, text, full: html, text
    first draft of raMerging functions
  • lines changed 4, context: html, text, full: html, text
    no more missed duplicated comments
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 16, context: html, text, full: html, text
    Added Spikein's view and updated DAF to most up-to-date settings. Redmine 5698.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
  • lines changed 4, context: html, text, full: html, text
    Updated variables to include treatment. Redmine #4156
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated the data format for Spikeins to be doc so that they load. Redmine #5986.
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 6, context: html, text, full: html, text
    added functionality to automatically set self scheduling to 19, complains on failure, but doesn't die.
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 2, context: html, text, full: html, text
    added release number to releaseLog value of the sql file
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 442, context: html, text, full: html, text
    moved old version to .pl
  • lines changed 151, context: html, text, full: html, text
    first draft of python verison of encodeQaPrepareReleae
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease.pl
  • lines changed 442, context: html, text, full: html, text
    moved old version to .pl
• src/hg/encode/qaRaDiff/makefile
  • lines changed 27, context: html, text, full: html, text
    renamed qaRaDiff to raDiff
• src/hg/encode/qaRaDiff/qaRaDiff
  • lines changed 51, context: html, text, full: html, text
    renamed qaRaDiff to raDiff
• src/hg/encode/raDiff/makefile
  • lines changed 27, context: html, text, full: html, text
    renamed qaRaDiff to raDiff
  • lines changed 2, context: html, text, full: html, text
    fixed makefile name
• src/hg/encode/raDiff/raDiff
  • lines changed 51, context: html, text, full: html, text
    renamed qaRaDiff to raDiff
  • lines changed 0, context: html, text, full: html, text
    changed whitespace to 4 spaces instead of tabs
• src/hg/encode/raMerge/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft of raMerging functions
• src/hg/encode/raMerge/raMerge
  • lines changed 31, context: html, text, full: html, text
    first draft of raMerging functions
• src/hg/hgCustom/hgCustom.c
  • lines changed 8, context: html, text, full: html, text
    Change /goldenPath/help/customTrack.html#BED (GTF, GFF, MAF, and PSL) to /FAQ/FAQformat.html#formatN
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    Fixed bug 6501. Table display broken if any hubs were listed under My Hubs tab.
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    Change /goldenPath/help/customTrack.html#BED (GTF, GFF, MAF, and PSL) to /FAQ/FAQformat.html#formatN
• src/hg/hgTables/schema.c
  • lines changed 2, context: html, text, full: html, text
    Change /goldenPath/help/customTrack.html#BED (GTF, GFF, MAF, and PSL) to /FAQ/FAQformat.html#formatN
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    support the nextItem button on custom bigBed tracks (#947)
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    eliminate duplicate print out of html description page for bedDetail custom tracks
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 1, context: html, text, full: html, text
    Removed unnecessary up-level directories from path in URL
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Removed unnecessary up-level directories from path in URL
• src/hg/htdocs/ENCODE/submission.html
  • lines changed 13, context: html, text, full: html, text
    Merging file format docs. Changed links to point to new location.
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 53, context: html, text, full: html, text
    Added new byte-range request error section
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 85, context: html, text, full: html, text
    Merged some sections from /goldenPath/help/customTrack.html
  • lines changed 4, context: html, text, full: html, text
    Changed coordinates in example to match regulatory.txt
  • lines changed 1, context: html, text, full: html, text
    Changed coordinates in example to match regulatory.txt
• src/hg/htdocs/goldenPath/help/ColorByStrandDemo.txt
  • lines changed 12, context: html, text, full: html, text
    Merging file format documents. Adding non-example-specfic filenames and moving to same directory as other text documents. Copied from htdocsExtras/goldenPath/help/examples/ct_example5b.txt.
• src/hg/htdocs/goldenPath/help/ItemRGBDemo.txt
  • lines changed 15, context: html, text, full: html, text
    Merging file format documents. Adding non-example-specfic filenames and moving to same directory as other text documents. Copied from htdocsExtras/goldenPath/help/examples/ct_example5.txt.
  • lines changed 1, context: html, text, full: html, text
    Removed old header
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 4, context: html, text, full: html, text
    Merging file format docs. Changed links to point to new location.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 39, context: html, text, full: html, text
    Added section for byte-range request errors
  • lines changed 1, context: html, text, full: html, text
    Added hyphen
• src/hg/htdocs/goldenPath/help/fishBlats.txt
  • lines changed 3, context: html, text, full: html, text
    Merging file format documents. Modified file so it could be properly viewed in the Browser.
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 1, context: html, text, full: html, text
    Changed the number of up directories on one link
• src/hg/htdocs/goldenPath/help/hgTextHelp.html
  • lines changed 4, context: html, text, full: html, text
    Merging file format docs. Changed links to point to new location.
• src/hg/htdocs/goldenPath/help/regulatory.txt
  • lines changed 3, context: html, text, full: html, text
    Merging file format documents. Modified file so it could be properly viewed in the Browser.
  • lines changed 1, context: html, text, full: html, text
    Fixed incorrect coordinates
  • lines changed 4, context: html, text, full: html, text
    Changed coordinates
  • lines changed 1, context: html, text, full: html, text
    Changed coordinates
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 10, context: html, text, full: html, text
    Removed unnecessary up-level directories from path in URL
• src/hg/htdocs/images/Heterocephalus_glaber.jpg
  • lines changed 0, context: html, text, full: html, text
    Add hetGla1 to all.joiner, add image to the descrition page
• src/hg/htdocs/images/phylo/canFam2_4way.gif
  • lines changed 0, context: html, text, full: html, text
    Replaced old Conservation image
• src/hg/htdocs/images/phylo/fr2_5way.gif
  • lines changed 0, context: html, text, full: html, text
    Replaced old Conservation image
• src/hg/htdocs/indexNews.html
  • lines changed 35, context: html, text, full: html, text
    Added announcement for Epi Road Map in DHs, redmine #6425
  • lines changed 2, context: html, text, full: html, text
    fixed link to data hub and corrected name of consortium
• src/hg/js/hgHubConnect.js
  • lines changed 12, context: html, text, full: html, text
    Fixed Issue #5784, where pressing return was not adding a hub like user expected, but submitting the whole form and taken them to hgTracks
• src/hg/lib/customFactory.c
  • lines changed 49, context: html, text, full: html, text
    check for illegal chromosomes in bam and big* track loaders (redmine #2572)
• src/hg/lib/fileUi.c
  • lines changed 1, context: html, text, full: html, text
    use cloneString to fix a "using freed memory" problem (see redmine 6467)
• src/hg/lib/snp125Ui.c
  • lines changed 1, context: html, text, full: html, text
    add synonym for stop-loss, which appears in snp135 data (see redmine #6419)
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 43, context: html, text, full: html, text
    Finished repeat tasks.
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 375, context: html, text, full: html, text
    initial contents, running masking steps
  • lines changed 85, context: html, text, full: html, text
    masking completed
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 73, context: html, text, full: html, text
    Updated notes files to match current state of release 2.Redmine #2019.
  • lines changed 108, context: html, text, full: html, text
    Updated notes file for track, was missing some files. Redmine #2019.
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 121, context: html, text, full: html, text
    done through initial genome build
  • lines changed 240, context: html, text, full: html, text
    done with masking
  • lines changed 2, context: html, text, full: html, text
    last featureBits run for the gap measurements
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 20, context: html, text, full: html, text
    done with the sequence download
  • lines changed 445, context: html, text, full: html, text
    running repeatMasker, simpleRepeats and windowMasker
  • lines changed 47, context: html, text, full: html, text
    completed masking
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    Remove 'FROM ISAC' from the LINCRNA descrition header
  • lines changed 7, context: html, text, full: html, text
    rebuild uc genes CDS FASTA downloads again (#5004)
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 474, context: html, text, full: html, text
    initial browser build and starting masking procedures
  • lines changed 85, context: html, text, full: html, text
    done with masking
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 177, context: html, text, full: html, text
    done through initial genome build
  • lines changed 193, context: html, text, full: html, text
    masking done
  • lines changed 3, context: html, text, full: html, text
    correct done dates
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 341, context: html, text, full: html, text
    initial browser build and starting masking procedures
  • lines changed 132, context: html, text, full: html, text
    done with masking
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 6, context: html, text, full: html, text
    Getting the brackets in the right place before handing the script over to cluster-admin
  • lines changed 2, context: html, text, full: html, text
    A normal part of the UCSC Genes script is to copy the (old) known genes table into a knownGenesOld table (knownGenesOld5), and copy the (old) kgXref table into a kgXrefOld table. In this case, we didn't want to do that because we were rebuilding the new UCSC Genes, so we wanted to retain the current knownGenesOld5 and kgXrefOld5 tables. So, I commented out the lines in the build script that create those tables. Now that the new UCSC Genes data is in hg19, I'm un-commenting those lines, so the script will be ready for the next time
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 27, context: html, text, full: html, text
    setting upstreamGeneTbl for many older genomes
  • lines changed 20, context: html, text, full: html, text
    Added bosTau7
  • lines changed 5, context: html, text, full: html, text
    Added bosTau7
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce10
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce10
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 2, context: html, text, full: html, text
    improve the error messages
  • lines changed 1, context: html, text, full: html, text
    fixup error in file name information display
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Add hetGla1 to all.joiner, add image to the descrition page
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
  • lines changed 129, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chicken/galGal4/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chicken/galGal4/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/description.html
  • lines changed 129, context: html, text, full: html, text
    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 129, context: html, text, full: html, text
    Initial descriptions for bosTau7.
• src/hg/makeDb/trackDb/cow/bosTau7/gap.html
  • lines changed 64, context: html, text, full: html, text
    Initial descriptions for bosTau7.
• src/hg/makeDb/trackDb/cow/bosTau7/gold.html
  • lines changed 23, context: html, text, full: html, text
    Initial descriptions for bosTau7.
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Initial descriptions for bosTau7.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Shortned tags for small and large intenstine to accomadte 64 character limit of table names.
  • lines changed 1, context: html, text, full: html, text
    Shortned term for Placenta to allow for table names to fit 64 character limit for Mouse.
  • lines changed 19, context: html, text, full: html, text
    added HEK293T, changed HEK293TREx tag
  • lines changed 1, context: html, text, full: html, text
    Adding to HEK293T description
  • lines changed 1, context: html, text, full: html, text
    Updating H7 protocol
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 14, context: html, text, full: html, text
    Updated the numbers and the methods descriptions to keep them current
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld5.html
  • lines changed 8, context: html, text, full: html, text
    Updated the numbers and the methods descriptions to keep them current
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 145, context: html, text, full: html, text
    Added meta-data for new Junctions file formats. Redmine #2019.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1342, context: html, text, full: html, text
    added in new haib tfbs tracks
  • lines changed 59, context: html, text, full: html, text
    added in bais
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 633, context: html, text, full: html, text
    added in new open chrom dnase tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 965, context: html, text, full: html, text
    added in new tracks to sydh tfbs
  • lines changed 833, context: html, text, full: html, text
    Added 7 new submissions. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 233, context: html, text, full: html, text
    added in new uw dgf tracks
  • lines changed 25, context: html, text, full: html, text
    corrected some metadata errors
  • lines changed 13, context: html, text, full: html, text
    removed erroneous accession
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 11408, context: html, text, full: html, text
    staging Caltech RNA-seq (release 2), Redmine# 2019
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 1241, context: html, text, full: html, text
    Releasing UW Affy Exon Array (Release 2), redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
  • lines changed 3, context: html, text, full: html, text
    removed bold formatting on publication titles
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing UW Affy Exon Array (Release 2), redmine# 5314
  • lines changed 2, context: html, text, full: html, text
    staging Caltech RNA-seq (release 2), Redmine# 2019
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 10, context: html, text, full: html, text
    Changed the release date, added periods, removed white space between a period, removed an extra period, and removed unnecessary <br> tags for Caltech RNA-seq (Release 2), redmine# 2019
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
  • lines changed 3, context: html, text, full: html, text
    Changed Header tags within Display Convention and Configuration section to be h4 from h3, to match size of Line about how to find meta-data about a subTrack. Redmine #6083.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 254, context: html, text, full: html, text
    added in new haib tfbs tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 122, context: html, text, full: html, text
    added in new open chrom dnase tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 2, context: html, text, full: html, text
    modifying links to hgdownload-test to hgdownload per Vanessa's code review, #6447
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 128, context: html, text, full: html, text
    added in new tracks to sydh tfbs
  • lines changed 110, context: html, text, full: html, text
    Added 7 new submissions. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 16, context: html, text, full: html, text
    Releasing UW Affy Exon Array (Release 2), redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
  • lines changed 1, context: html, text, full: html, text
    changed the released date for UW Affy Exon Array, redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 512, context: html, text, full: html, text
    Releasing UW Affy Exon Array (Release 2), redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 85, context: html, text, full: html, text
    added in new uw dgf tracks
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Added bosTau7 to DBS.
  • lines changed 1, context: html, text, full: html, text
    adding galGal4 to the build
  • lines changed 1, context: html, text, full: html, text
    adding panTro4 to the build
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 8, context: html, text, full: html, text
    Add hetGla1 to all.joiner, add image to the descrition page
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added the first 15 submissions and track description. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2491, context: html, text, full: html, text
    Added the first 15 submissions and track description. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 3771, context: html, text, full: html, text
    Added 29 submissions to track. Redmine #5393.
  • lines changed 131, context: html, text, full: html, text
    Added 1 more submissions. Redmine #5393.
  • lines changed 211, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
  • lines changed 541, context: html, text, full: html, text
    Added 4 more submissions. Redmine #5393.
  • lines changed 651, context: html, text, full: html, text
    Added 5 new experiments for track. Redmine #5393.
  • lines changed 26, context: html, text, full: html, text
    Updated md5sum's for Mouse Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 309, context: html, text, full: html, text
    Added 2 submissions for track. Redmine #6476.
  • lines changed 617, context: html, text, full: html, text
    Added 4 submissions to track. Redmine #6476.
  • lines changed 57, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
  • lines changed 321, context: html, text, full: html, text
    Added 2 more submissions. Redmine #6476
  • lines changed 155, context: html, text, full: html, text
    Added 1 new submissions. Redmine #6476.
  • lines changed 7, context: html, text, full: html, text
    Updated md5sum's for Mouse Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 1587, context: html, text, full: html, text
    Added 12 submissions for track. Redmine #5394
  • lines changed 128, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 215, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 138, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 184, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 97, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 14, context: html, text, full: html, text
    Shortned tags for small and large intenstine to accomadte 64 character limit of table names.
  • lines changed 169, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 120, context: html, text, full: html, text
    Added 1 more submissions to track. Redmine #4469.
  • lines changed 77, context: html, text, full: html, text
    Fixed incorrect sex assigned to Patski cell line for track. Redmine #4469.
  • lines changed 29, context: html, text, full: html, text
    Shortned tags for small and large intenstine to accomadte 64 character limit of table names.
  • lines changed 113, context: html, text, full: html, text
    Updated md5sum's for all mouse tracks in preperation for the Mouse Encode Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/pseudoYale60.html
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    removed bold fotmatting from publication titles
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
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    Added 12 submissions for track. Redmine #5394
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    Added the first 15 submissions and track description. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
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    Added the first 15 submissions and track description. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
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    Added the first 15 submissions and track description. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.new.ra
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    Added 29 submissions to track. Redmine #5393.
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    Added 5 new experiments for track. Redmine #5393.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.new.ra
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.new.ra
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    Added 12 submissions for track. Redmine #5394
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
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    Shortned tags for small and large intenstine to accomadte 64 character limit of table names.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
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    Added 1 more submissions to track. Redmine #4469.
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    Fixed incorrect sex assigned to Patski cell line for track. Redmine #4469.
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    Shortned tags for small and large intenstine to accomadte 64 character limit of table names.
• src/hg/makeDb/trackDb/panda/ailMel1/gold.html
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    Fixed a broken link
• src/hg/makeDb/trackDb/worm/ce10/description.html
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    Italicized C. elegans
• src/hg/utils/automation/doSimpleRepeat.pl
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    the split command needs to be 3 digit numeric expansion to avoid .gz file name
• src/hg/utils/makeTableList/makeTableList.c
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    support -host, -user and -password
• src/hg/utils/phyloTrees/58way.nh
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    adding Atlantic Cod gadMor1
• src/inc/bamFile.h
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    add bamChromList
• src/inc/common.mk
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    SAMDIR directory needs to have $MACHTYPE in it.
• src/lib/bamFile.c
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    add bamChromList
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    suppress too verbose messages in samtools >= 0.1.18; see redmine #6491
• src/lib/blackList.c
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    a fix for a compiler warning found on 32-bit linux
• src/product/README.trackDb
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    Merging file format docs. Changed link to point to new location.
• src/utils/qa/weeklybld/buildEnv.csh
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    v262 preview1
• src/utils/userApps/bigBedWigs.txt
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    Merging file format docs. Changed link to point to new location.

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