All File Changes

v236_base to v237_preview (2010-07-20 to 2010-07-27) v237

• src/blat/blat.c
  • lines changed 2, context: html, text, full: html, text
    adding max query size limit to help
  • lines changed 5, context: html, text, full: html, text
    adding needed checks on query sizes against the maximum single piece size for use with -fastMap
• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    adding needed checks on query sizes against the maximum single piece size for use with -fastMap
• src/hg/encode/DAFs/2.0/YdhrRnaSeq.daf
  • lines changed 59, context: html, text, full: html, text
    This is a modern daf for the Yale RNA seq data that includes a description of the ddf and updates for hg19 (bam, bigwig) and the addition of rnaExtract and treatment
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • lines changed 6, context: html, text, full: html, text
    This DAF is updated to look like what we have actually been using withColin and to add the Transfrags view.|
• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Commented out the Revision history line that was causing problems
  • lines changed 3, context: html, text, full: html, text
    Updated the validateFiles for fastq to check 1 in 1000 rather than the first 1000 lines, which was breaking (refer to Bug:390)
• src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
  • lines changed 58, context: html, text, full: html, text
    This is a DAF for the YaleRNA-Seq. I think that it will change a lot from here.
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 1, context: html, text, full: html, text
    look for *.bigWig instead of *.bw
  • lines changed 3, context: html, text, full: html, text
    special case type for bam index file
  • lines changed 1, context: html, text, full: html, text
    add .bai files to those included in the output files
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 19, context: html, text, full: html, text
    don't gzip BAM or bigWigs
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 13, context: html, text, full: html, text
    don't gzip BAM or bigWigs
• src/hg/encode/encodeMdbToDdf/encodeMdbToDdf
  • lines changed 5, context: html, text, full: html, text
    .gz exntensions are now removed from the files
  • lines changed 152, context: html, text, full: html, text
    program to make a DDF given a composite name and a list of metadata vars
• src/hg/encode/encodeMdbToDdf/makefile
  • lines changed 18, context: html, text, full: html, text
    added missing makefile
• src/hg/encode/encodeMkGeoPkg/makefile
  • lines changed 22, context: html, text, full: html, text
    added makefile
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updated type of termP to term
  • lines changed 279, context: html, text, full: html, text
    Added 22 cell lines from UW.
  • lines changed 1, context: html, text, full: html, text
    Fixed description for TAM treamtent for quantity of 2uM to 1 uM.
  • lines changed 5, context: html, text, full: html, text
    Added 1 new treatment tamoxifen for Myers lab
  • lines changed 8, context: html, text, full: html, text
    Remvoed orderUrl for GM12878 registered cell lines, not applicable
  • lines changed 69, context: html, text, full: html, text
    Added 4 new cell lines for X-inactivation in GM12878 cell lines registered by the Myers lab
  • lines changed 18, context: html, text, full: html, text
    Updated the Mouse cell type controlled vocabulary to be consistent with what was registered as well as update the CGIs to display the correct headers for mouse Cell Type
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 6, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId as optional field
• src/hg/encode/encodeValidate/config/ripAntibody.cv.ra
  • lines changed 1220, context: html, text, full: html, text
    This is the draft of how I think the rip Antibody cv should look. This will hopefully become part of cv.ra after approval.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    Updated Validtor to check assembly and if hg19 and 3 composites require inputType
  • lines changed 11, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId as optional field
  • lines changed 3, context: html, text, full: html, text
    don't output a separate metadata line for bam index files
  • lines changed 18, context: html, text, full: html, text
    don't gzip BAM or bigWigs
  • lines changed 12, context: html, text, full: html, text
    Added special case restriction to avoid HAIB TFBS ever submitting again without inputType
  • lines changed 1, context: html, text, full: html, text
    Updated the check for Mouse Tissue category to spell out Tissue to match cv.ra, previously T was used.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    Updated the Mouse cell type controlled vocabulary to be consistent with what was registered as well as update the CGIs to display the correct headers for mouse Cell Type
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 15, context: html, text, full: html, text
    add some options to let some errors pass through
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
  • lines changed 1, context: html, text, full: html, text
    Temporarily changing the otherOrg databases that go with the blastTab tables rebuild back to their values at the v234 CGI release. Leaving out zebrafish archive.ensembl otherUrl links because Fan, Hiram and I think that these should go to the latest ensembl page.
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
  • lines changed 1, context: html, text, full: html, text
    Temporarily changing the otherOrg databases that go with the blastTab tables rebuild back to their values at the v234 CGI release. Leaving out zebrafish archive.ensembl otherUrl links because Fan, Hiram and I think that these should go to the latest ensembl page.
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
  • lines changed 2, context: html, text, full: html, text
    Temporarily changing the otherOrg databases that go with the blastTab tables rebuild back to their values at the v234 CGI release. Leaving out zebrafish archive.ensembl otherUrl links because Fan, Hiram and I think that these should go to the latest ensembl page.
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
  • lines changed 2, context: html, text, full: html, text
    Temporarily changing the otherOrg databases that go with the blastTab tables rebuild back to their values at the v234 CGI release. Leaving out zebrafish archive.ensembl otherUrl links because Fan, Hiram and I think that these should go to the latest ensembl page.
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/hgPcr/hgPcr.c
  • lines changed 1, context: html, text, full: html, text
    fixing broken link
• src/hg/hgTracks/imageV2.c
  • lines changed 20, context: html, text, full: html, text
    Replaced clenseQuotes with htmlEncode as suggested by Brian
• src/hg/htdocs/ENCODE/index.html
  • lines changed 261, context: html, text, full: html, text
    udpated news: +2 items to 3/18 post, +2 new posts, -2 posts from index.html one had be added to newsarch.html, collapsed 2 posts & added full posts to newsarch.html
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 151, context: html, text, full: html, text
    udpated news: +2 items to 3/18 post, +2 new posts, -2 posts from index.html one had be added to newsarch.html, collapsed 2 posts & added full posts to newsarch.html
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 14, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    added blurb about big paper
  • lines changed 5, context: html, text, full: html, text
    tweaked news item about workshops
  • lines changed 95, context: html, text, full: html, text
    added announcement of free workshops and archived that and happy birthday genome message
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 25, context: html, text, full: html, text
    Added bigwig pub. Updated Epub refs that now have print versions.
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 14, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/indexNews.html
  • lines changed 29, context: html, text, full: html, text
    added blurb about big paper
  • lines changed 3, context: html, text, full: html, text
    tweaked news item about workshops
  • lines changed 27, context: html, text, full: html, text
    added announcement of free workshops and archived that and happy birthday genome message
• src/hg/htdocs/util.html
  • lines changed 5, context: html, text, full: html, text
    updating link to source downloads to include executables in the language as well
  • lines changed 5, context: html, text, full: html, text
    adding link to our source tree downloads so it is easier to find
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    added sqlDump to assist in debuging connection cache/profile problems
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    Made dragReorder action which causes whole page scroll, scroll a bit faster.
• src/hg/js/hui.js
  • lines changed 69, context: html, text, full: html, text
    Fixed redmine 385 where Changing view affected unchecked ABC dimensions.
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    fixed URLs for hgEncodeVocab so that they can use the sandbox
  • lines changed 1, context: html, text, full: html, text
    Fixed redmine 385 where Changing view affected unchecked ABC dimensions.
• src/hg/lib/jksql.c
  • lines changed 45, context: html, text, full: html, text
    added sqlDump to assist in debuging connection cache/profile problems
• src/hg/makeDb/doc/bosTau5.txt
  • lines changed 448, context: html, text, full: html, text
    bosTau4 LIFTOVER to bosTau5
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 33, context: html, text, full: html, text
    Use ensGene to annotate calJac3
  • lines changed 16, context: html, text, full: html, text
    adding Ensembl genes v58 to calJac3 and phyloP30way to mm9
• src/hg/makeDb/doc/ce6.txt
  • lines changed 5, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/makeDb/doc/ce9.txt
  • lines changed 9, context: html, text, full: html, text
    masked sequence available
• src/hg/makeDb/doc/dm3.txt
  • lines changed 17, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 327, context: html, text, full: html, text
    fix duplicat EST track problem
  • lines changed 136, context: html, text, full: html, text
    start Phylogenetic
  • lines changed 97, context: html, text, full: html, text
    Done gene annotation to multiz6way
• src/hg/makeDb/doc/hg18.txt
  • lines changed 2, context: html, text, full: html, text
    add tiny piece of information about UCSF Brain Methyl since we don't have Ting's load info
• src/hg/makeDb/doc/hg19.txt
  • lines changed 74, context: html, text, full: html, text
    Added uniGene for hg19.
  • lines changed 270, context: html, text, full: html, text
    adding patch1 sequence to hg19
  • lines changed 36, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 17, context: html, text, full: html, text
    adding Ensembl genes v58 to calJac3 and phyloP30way to mm9
• src/hg/makeDb/doc/mm8.txt
  • lines changed 41, context: html, text, full: html, text
    fixing bug in doSameSpeciesLiftOver - redid mm8->mm9 liftOver
• src/hg/makeDb/doc/mm9.txt
  • lines changed 17, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
  • lines changed 25, context: html, text, full: html, text
    adding Ensembl genes v58 to calJac3 and phyloP30way to mm9
• src/hg/makeDb/doc/rn4.txt
  • lines changed 6, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/makeDb/doc/sacCer2.txt
  • lines changed 16, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
  • lines changed 5, context: html, text, full: html, text
    bare output file from RepeatMasker has different header spacing compared to liftUp produced header
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    added lines for Decipher track.
  • lines changed 1, context: html, text, full: html, text
    bosTau4 LIFTOVER to bosTau5
• src/hg/makeDb/trackDb/cat/felCat4/ctgPos2.html
  • lines changed 11, context: html, text, full: html, text
    Done gene annotation to multiz6way
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    fix duplicat EST track problem
  • lines changed 25, context: html, text, full: html, text
    Done gene annotation to multiz6way
• src/hg/makeDb/trackDb/cow/bosTau5/description.html
  • lines changed 82, context: html, text, full: html, text
    bosTau4 LIFTOVER to bosTau5
• src/hg/makeDb/trackDb/cow/bosTau5/gap.html
  • lines changed 40, context: html, text, full: html, text
    bosTau4 LIFTOVER to bosTau5
• src/hg/makeDb/trackDb/cow/bosTau5/gold.html
  • lines changed 4, context: html, text, full: html, text
    bosTau4 LIFTOVER to bosTau5
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 1099, context: html, text, full: html, text
    Changed inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 281, context: html, text, full: html, text
    added missing insertLength values
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 1231, context: html, text, full: html, text
    Changed inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 1403, context: html, text, full: html, text
    Changed inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 1123, context: html, text, full: html, text
    Changed inputType to controlId
  • lines changed 41, context: html, text, full: html, text
    Corrected 40 metadata settings
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 11, context: html, text, full: html, text
    Fixed cells marked as BJ-tert but supposed to be BJ
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 2151, context: html, text, full: html, text
    Changed inputType to controlId
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    change UCSF Brain Methyl table names
  • lines changed 27, context: html, text, full: html, text
    edits from Mary
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    removing release tags to include lines because I forgot that this functionality doesn't exist yet ;)
  • lines changed 3, context: html, text, full: html, text
    added release tags to include statements for Yale RNA-seq
  • lines changed 78, context: html, text, full: html, text
    Added release tags for the YaleRnaSeq Track and pulled out the track into two files
  • lines changed 6, context: html, text, full: html, text
    Final changes for the Yale labels to make the long labels have full words
  • lines changed 12, context: html, text, full: html, text
    Changed the short labels to show the treatment as well.
  • lines changed 6, context: html, text, full: html, text
    Changed the short labels from PolyA to PolyA-
  • lines changed 7, context: html, text, full: html, text
    I changed the long labels to PolyA- from Poly A
  • lines changed 6, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
  • lines changed 1, context: html, text, full: html, text
    added html line to wgEncodeRegMarkPromoter block of Regulation Super Track because html desc is not equal to track line of trackDb block
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.new.ra
  • lines changed 2, context: html, text, full: html, text
    Stephen from the lab says that one of the tracks should have a + afterall
  • lines changed 88, context: html, text, full: html, text
    Added release tags for the YaleRnaSeq Track and pulled out the track into two files
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.ra
  • lines changed 0, context: html, text, full: html, text
    This is part of the change to add release tags to the YaleRnaSeq track
  • lines changed 88, context: html, text, full: html, text
    Added release tags for the YaleRnaSeq Track and pulled out the track into two files
• src/hg/makeDb/trackDb/human/hg18/ucsfBrainMethyl.html
  • lines changed 137, context: html, text, full: html, text
    completely re-doing the description page so that more detailed and accurate
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 177, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 138, context: html, text, full: html, text
    take metadata out of trackDb
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
  • lines changed 1954, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • lines changed 1, context: html, text, full: html, text
    fixed typo, a period mid-sentence
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 5, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k27ac.html
  • lines changed 2, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me1.html
  • lines changed 2, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me3.html
  • lines changed 2, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTxn.html
  • lines changed 2, context: html, text, full: html, text
    reworded some sentences on the regulation track description pages and fixed the redirected link to standford
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.new.ra
  • lines changed 2273, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.new.ra
  • lines changed 221, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 1704, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • lines changed 1, context: html, text, full: html, text
    Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source.
• src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html
  • lines changed 69, context: html, text, full: html, text
    The RRBS tracks were in an enc file instead of a wgEncodefile. I moved them from one to the other. There is one more file that should be in this commit which is the newly labeled wgEncodeHaibMethylRrbs.html. There are new tracks in the RRBS trackDb.ra and there is a new include statement in the main trackDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    copy from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 1873, context: html, text, full: html, text
    copy from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1343, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
  • lines changed 272, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 399, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 72, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 121, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 16, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 33, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 6, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 12, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 44, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 44, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1553, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
  • lines changed 206, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 206, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
  • lines changed 420, context: html, text, full: html, text
    Updated the metaData to be compliant with Hudson Alpha Expectations
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 143, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
  • lines changed 59, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 66, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 31, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 17, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 169, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
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    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 2077, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
  • lines changed 452, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 5, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 15, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 72, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 144, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1311, context: html, text, full: html, text
    Changed inputType to controlId and added labExpId
  • lines changed 140, context: html, text, full: html, text
    add fileIndex for BAM files
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    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 156, context: html, text, full: html, text
    Removed old track for HAIB Methyl RRBS labeled encHaibRrbs from trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    The RRBS tracks were in an enc file instead of a wgEncodefile. I moved them from one to the other. There is one more file that should be in this commit which is the newly labeled wgEncodeHaibMethylRrbs.html. There are new tracks in the RRBS trackDb.ra and there is a new include statement in the main trackDb.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra
  • lines changed 573, context: html, text, full: html, text
    The RRBS tracks were in an enc file instead of a wgEncodefile. I moved them from one to the other. There is one more file that should be in this commit which is the newly labeled wgEncodeHaibMethylRrbs.html. There are new tracks in the RRBS trackDb.ra and there is a new include statement in the main trackDb.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra
  • lines changed 7, context: html, text, full: html, text
    Updated the metaData to be compliant with Hudson Alpha Expectations
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the defaults for the tracks to be default, as the composite is set to default hide.
  • lines changed 22, context: html, text, full: html, text
    Updated all Histone tracks to be consistent within the given super track. Short Labels and matrix display( factor and cell type order)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 2, context: html, text, full: html, text
    Updated the defaults for the tracks to be default, as the composite is set to default hide.
  • lines changed 148, context: html, text, full: html, text
    Updated all Histone tracks to be consistent within the given super track. Short Labels and matrix display( factor and cell type order)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 92, context: html, text, full: html, text
    transfer hg18 page over to hg19...
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 65, context: html, text, full: html, text
    oops, this was supposed to be in there a while ago
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 119, context: html, text, full: html, text
    transfer hg18 page over to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 69, context: html, text, full: html, text
    This was really just a rename that should have been a git mv.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 8, context: html, text, full: html, text
    fix up some of the metadata
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 2, context: html, text, full: html, text
    Updated compsites to be default dense while supertrack is hide
  • lines changed 1, context: html, text, full: html, text
    Updated Open Chrom FAIRE-seq track short labels to match DNase-Seq. Also standardized treatment display headers between the two tracks
  • lines changed 111, context: html, text, full: html, text
    Updated the short lables and consistency notes.
  • lines changed 647, context: html, text, full: html, text
    Changed OpenChromFaire to OpenChromDnase and visversa to be consistent with the data that is within each ra file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 2, context: html, text, full: html, text
    Updated compsites to be default dense while supertrack is hide
  • lines changed 1, context: html, text, full: html, text
    Updated long label for track
  • lines changed 2, context: html, text, full: html, text
    Updated the order of the cell types in the matrix display.
  • lines changed 67, context: html, text, full: html, text
    Updated Open Chrom FAIRE-seq track short labels to match DNase-Seq. Also standardized treatment display headers between the two tracks
  • lines changed 649, context: html, text, full: html, text
    Changed OpenChromFaire to OpenChromDnase and visversa to be consistent with the data that is within each ra file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Updated compsites to be default dense while supertrack is hide
  • lines changed 219, context: html, text, full: html, text
    Updated the short lables and consistency notes.
  • lines changed 234, context: html, text, full: html, text
    Updated short labels and display standards for the UW DNaseI track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the defaults for the tracks to be default, as the composite is set to default hide.
  • lines changed 9, context: html, text, full: html, text
    Updated all Histone tracks to be consistent within the given super track. Short Labels and matrix display( factor and cell type order)
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 4, context: html, text, full: html, text
    Changes to default wiggle settings requested by Ed Green.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 5, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 10, context: html, text, full: html, text
    take .gz off bigWig and BAM files
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 23, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 51, context: html, text, full: html, text
    take .gz off bigWig and BAM files
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 81, context: html, text, full: html, text
    adding release tags to separate out different 30way multiz
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Setting rat mrnas to dense, since pack is huge at the default position for rn4. This may have turned from dense to pack when visibility.ra got folded back into trackDb.ra last December.
• src/hg/makefile
  • lines changed 2, context: html, text, full: html, text
    added hgsqlTableDate and hgsqlSwapTables to the make file
• src/hg/near/hgNear/hgNearData/C_elegans/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/near/hgNear/hgNearData/D_melanogaster/dm3/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/near/hgNear/hgNearData/Mouse/columnDb.ra
  • lines changed 2, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/near/hgNear/hgNearData/S_cerevisiae/columnDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updated for xxBlastpTab tables rebuild using danRer6.
• src/hg/pslCDnaFilter/usage.txt
  • lines changed 2, context: html, text, full: html, text
    fixed documentation error
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 31, context: html, text, full: html, text
    fixing cross-post bug in show-sizes for add (edit already worked)
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 2, context: html, text, full: html, text
    fixing splitSize for doSameSpeciesLiftOver.pl - chunk size cannot exceed 5000 for blat -fastMap
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 58, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
  • lines changed 221, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
• src/hg/utils/gff3ToPsl/makefile
  • lines changed 22, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
• src/hg/utils/gff3ToPsl/tests/README
  • lines changed 2, context: html, text, full: html, text
    take out spurious comment
  • lines changed 13, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt
  • lines changed 21329, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 1, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/locusNameAndSize.txt
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/twoBitMask/twoBitMask.c
  • lines changed 5, context: html, text, full: html, text
    bare .out from RepeatMasker has extra space in header compared to liftUp .out file
• src/inc/genoFind.h
  • lines changed 3, context: html, text, full: html, text
    adding needed checks on query sizes against the maximum single piece size for use with -fastMap
• src/inc/htmshell.h
  • lines changed 6, context: html, text, full: html, text
    Extended htmlEncode to handle single quotes properly
• src/jkOwnLib/gfBlatLib.c
  • lines changed 1, context: html, text, full: html, text
    adding needed checks on query sizes against the maximum single piece size for use with -fastMap
• src/lib/gff3.c
  • lines changed 5, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
• src/lib/htmshell.c
  • lines changed 67, context: html, text, full: html, text
    Extended htmlEncode to handle single quotes properly
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v237 preview

• lines changed: 56727
• files changed: 249