All File Changes

v245_preview2 to v245_base (2010-12-21 to 2011-01-04) v245

• src/hg/encode/DAFs/2.0/buOrchid.daf
  • lines changed 13, context: html, text, full: html, text
    changed to accept bigWig
• src/hg/encode/DAFs/2.0/haibMethylArray.daf
  • lines changed 2, context: html, text, full: html, text
    Change the dafs to have new dataType and new views
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
  • lines changed 35, context: html, text, full: html, text
    Change the dafs to have new dataType and new views
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 3, context: html, text, full: html, text
    Removed replicate identification for Peaks and Signals, as data is pooled.
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 3, context: html, text, full: html, text
    Removed replicate identification for Peaks and Signals, as data is pooled.
• src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated validation settings.
• src/hg/encode/DAFs/2.0/uncBsuProt.daf
  • lines changed 40, context: html, text, full: html, text
    Added the subcellular localization variable to the unc/bsu proteogenomics daf file. Adding this variable represents expanding the metadata for this track. Shortened the track name so that there might be room for the localizations in the short names
• src/hg/encode/DAFs/2.0/uncBsuProtgeno.daf
  • lines changed 40, context: html, text, full: html, text
    Added the first version of the UNC/BSU proteogenomics DAF, which was recently reviewed by both Cricket and Kate
  • lines changed 2, context: html, text, full: html, text
    Minor tweaks: changed the data type to peptideMapping (which should be registered now, I hope)
  • lines changed 40, context: html, text, full: html, text
    Added the subcellular localization variable to the unc/bsu proteogenomics daf file. Adding this variable represents expanding the metadata for this track. Shortened the track name so that there might be room for the localizations in the short names
• src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
  • lines changed 5, context: html, text, full: html, text
    Change long labels, raw signal to signal
• src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
  • lines changed 2, context: html, text, full: html, text
    got rid of docIdTable global in library, added md5sum calculation in docIdTidy
• src/hg/encode/docId/docIdTidy/docIdTidy.c
  • lines changed 109, context: html, text, full: html, text
    got rid of docIdTable global in library, added md5sum calculation in docIdTidy
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 1, context: html, text, full: html, text
    got rid of docIdTable global in library, added md5sum calculation in docIdTidy
• src/hg/encode/docId/inc/docId.h
  • lines changed 4, context: html, text, full: html, text
    got rid of docIdTable global in library, added md5sum calculation in docIdTidy
• src/hg/encode/docId/lib/docIdSub.c
  • lines changed 10, context: html, text, full: html, text
    got rid of docIdTable global in library, added md5sum calculation in docIdTidy
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 15, context: html, text, full: html, text
    change missing checksums to warnings and not errors
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 7, context: html, text, full: html, text
    added vars for wgEncodeUwDnase
  • lines changed 5, context: html, text, full: html, text
    added vars for wgEncodeCshlLongRnaSeq
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    add peptideMapping
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 16, context: html, text, full: html, text
    catch errors that come from closing a gzip pipe before the whole file is read #390
  • lines changed 46, context: html, text, full: html, text
    add report information for fastq's and bigWig's #145
• src/hg/genePredHisto/makefile
  • lines changed 3, context: html, text, full: html, text
    hg/utils tests were not automatically run
• src/hg/genePredHisto/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    hg/utils tests were not automatically run
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 2036 (silent javascript errors because lib code was inappropriately including hu.js for hgTables merge list. Added feature for redmine 2062. Now hgc and hgTrackUi will show pennantIcon with note.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    fix problem where codon numbering failed to be inherited from composite track (see redmine 1728#note-4)
• src/hg/hgc/hgc.c
  • lines changed 0, context: html, text, full: html, text
    added space between 'feature' and assembly name
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 2036 (silent javascript errors because lib code was inappropriately including hu.js for hgTables merge list. Added feature for redmine 2062. Now hgc and hgTrackUi will show pennantIcon with note.
  • lines changed 2, context: html, text, full: html, text
    otherOrg is actually thisOrg
• src/hg/hgc/wiggleClick.c
  • lines changed 2, context: html, text, full: html, text
    Corrected a bug, reversing the display values of Minimum span and maximum span.
• src/hg/htdocs/admin/403.html
  • lines changed 11, context: html, text, full: html, text
    fixing misleading 403 message
• src/hg/htdocs/images/phylo/danRer7_8way.png
  • lines changed 0, context: html, text, full: html, text
    adding 8-way alignment phylo tree for danRer7
• src/hg/inc/clonePos.h
  • lines changed 20, context: html, text, full: html, text
    Changes associated with the lift of the clonePos (coverage) track to hg19
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 2036 (silent javascript errors because lib code was inappropriately including hu.js for hgTables merge list. Added feature for redmine 2062. Now hgc and hgTrackUi will show pennantIcon with note.
• src/hg/inc/peptideMapping.h
  • lines changed 70, context: html, text, full: html, text
    Adding a header file for a new peptide mapping data type, for results of peptides identified in mass spec experiments mapped to the genome
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v245
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    fix problem caused when cytoband track is visible
  • lines changed 7, context: html, text, full: html, text
    Larry fixed the cytoBand bug, but I extended the premise to all cytoBands
• src/hg/lib/clonePos.c
  • lines changed 45, context: html, text, full: html, text
    Changes associated with the lift of the clonePos (coverage) track to hg19
• src/hg/lib/clonePos.sql
  • lines changed 4, context: html, text, full: html, text
    Changes associated with the lift of the clonePos (coverage) track to hg19
• src/hg/lib/encode/peptideMapping.as
  • lines changed 14, context: html, text, full: html, text
    Added a data type for the proteogenomic peptide hits to the genome
• src/hg/lib/encode/peptideMapping.c
  • lines changed 166, context: html, text, full: html, text
    Adding a c file for a new peptide mapping data type, for results of peptides identified in mass spec experiments mapped to the genome
• src/hg/lib/encode/peptideMapping.sql
  • lines changed 20, context: html, text, full: html, text
    Added a data type for the proteogenomic peptide hits to the genome
  • lines changed 1, context: html, text, full: html, text
    Changed the key for the peptide mapping, since it appears that the combination of chrom, chromStart, and precursorMz is not unique
• src/hg/lib/fileUi.c
  • lines changed 22, context: html, text, full: html, text
    Added standardized preamble for the files downloads page.
• src/hg/lib/hgRelate.c
  • lines changed 4, context: html, text, full: html, text
    removed comment that is no longer true
• src/hg/lib/hui.c
  • lines changed 35, context: html, text, full: html, text
    Fix for redmine 2036 (silent javascript errors because lib code was inappropriately including hu.js for hgTables merge list. Added feature for redmine 2062. Now hgc and hgTrackUi will show pennantIcon with note.
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 1333.12. While encode gencode subtracks can now be configured, they cannot be filtered by popup. Long term either filterBoxes need to be made popup compatible or tracks with filterBoxes should not offer filter by popup.
  • lines changed 1, context: html, text, full: html, text
    fix problem where codon numbering failed to be inherited from composite track (see redmine 1728#note-4)
• src/hg/lib/liftOver.c
  • lines changed 3, context: html, text, full: html, text
    strand mixup on multiple mappings
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added peptideMapping to the make file
• src/hg/makeDb/doc/danRer6.txt
  • lines changed 12, context: html, text, full: html, text
    liftOver from danRer6 to danRer7 and fr2 lastz to danRer7 and preparing for 8-way alignment
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 255, context: html, text, full: html, text
    liftOver from danRer6 to danRer7 and fr2 lastz to danRer7 and preparing for 8-way alignment
  • lines changed 83, context: html, text, full: html, text
    running autoMultiz for 8-way
  • lines changed 73, context: html, text, full: html, text
    8-way done and annotated with Irows
  • lines changed 643, context: html, text, full: html, text
    completed 8-way phastCons and phyloP
  • lines changed 297, context: html, text, full: html, text
    have phastCons and phyloP 8way on danRer7 for vert and fish groups
  • lines changed 167, context: html, text, full: html, text
    started human proteins
  • lines changed 3, context: html, text, full: html, text
    fixup up comments about tree diagrams
  • lines changed 6, context: html, text, full: html, text
    finished tblastn... now doing chaining
  • lines changed 15, context: html, text, full: html, text
    finished Human protiens
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • lines changed 5, context: html, text, full: html, text
    Fixed mysterious change of subId 193 from released to loaded
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 78, context: html, text, full: html, text
    Broad hg19 to the pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release1.notes
  • lines changed 1735, context: html, text, full: html, text
    Notes made from Krish's encodeMkChangeNotes for pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV5.txt
  • lines changed 30, context: html, text, full: html, text
    loading doc for Gencode V5
  • lines changed 20, context: html, text, full: html, text
    load metadata
  • lines changed 14, context: html, text, full: html, text
    table name changes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release1.notes
  • lines changed 537, context: html, text, full: html, text
    Added wgEncodeRikenCageK562NucleolusTotalAlnRep1
  • lines changed 574, context: html, text, full: html, text
    added a track
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release1.notes
  • lines changed 18, context: html, text, full: html, text
    Added 16 previously missing fastq's to release notes and director.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release1.notes
  • lines changed 26, context: html, text, full: html, text
    Added 24 previously missing fastq's to release notes and director.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 26, context: html, text, full: html, text
    instructions for DECIPHER hg18->hg19
  • lines changed 22, context: html, text, full: html, text
    changed fosEndPairs lift instructions a bit.
  • lines changed 6, context: html, text, full: html, text
    have phastCons and phyloP 8way on danRer7 for vert and fish groups
  • lines changed 19, context: html, text, full: html, text
    Changes associated with the lift of the clonePos (coverage) track to hg19
  • lines changed 17, context: html, text, full: html, text
    Stuff to do with MGI Mouse QTL lift to hg19
  • lines changed 15, context: html, text, full: html, text
    Changes for lifting the H-Inv track to hg19
  • lines changed 26, context: html, text, full: html, text
    Added SIB Alt-Splicing lift to hg19 stuff
  • lines changed 27, context: html, text, full: html, text
    Changes for Illumina WG-6 lift to hg19
  • lines changed 20, context: html, text, full: html, text
    Added stuff for EIO/JCVI NAS hg19 lift.
  • lines changed 16, context: html, text, full: html, text
    Chages for ORegAnno hg19 lift
  • lines changed 30, context: html, text, full: html, text
    Changes associated with the NK Nuc Lamina lift to hg19
  • lines changed 64, context: html, text, full: html, text
    Changes for lifting UCSF Brain Methylation track
  • lines changed 69, context: html, text, full: html, text
    Changes for lifted SNP Arrays track
• src/hg/makeDb/doc/mm9.txt
  • lines changed 128, context: html, text, full: html, text
    Added Yale Pseudogenes track based on Ensembl Release 60.
  • lines changed 3, context: html, text, full: html, text
    Documented added pseudogenes classes to tagTypes.tab file.
• src/hg/makeDb/doc/panTro2.txt
  • lines changed 5, context: html, text, full: html, text
    adding denisova track for chimp
• src/hg/makeDb/doc/proteins/090821.txt
  • lines changed 58, context: html, text, full: html, text
    Updated Reactome related tables for Release 35
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 11, context: html, text, full: html, text
    Cleaned up some handling of Rfam to remove species-specific hardcoded references. Replaced a sql-level join with a csh-level bedIntersect
  • lines changed 13, context: html, text, full: html, text
    Set up a better mechanism to get the blocks that are syntenic to mm9
  • lines changed 4, context: html, text, full: html, text
    Attempted a more elegant way to select the hg19 blocks that are syntenic to mm9. At this time, I'm not pleased with the results. I generate a bed file in which the bed blocks are delineated consistently with the mm9 subtrack in the consensus track, but this bed file contains items that map to gaps in the mm9 subtrack
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    enable automatic generation of upstream files for danRer7
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    adding felCat4 to list of assemblies that get genbank updates http://redmine.soe.ucsc.edu/issues/2209
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    adding danRer7
  • lines changed 1, context: html, text, full: html, text
    Changed the rgdQtlId minCheck from 0.89 to 0.88 to accomodate the items that did not lift from hg18 to hg19. See redmine #1782.
• src/hg/makeDb/trackDb/chimp/trackDb.denisova.ra
  • lines changed 21, context: html, text, full: html, text
    adding denisova track for chimp
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding denisova track for chimp
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 99, context: html, text, full: html, text
    (1) Set up a stanza for the UNC/BSU lab, replacing the Giddings-m lab. (2) Registered five new antibodies for the Myers lab
  • lines changed 2, context: html, text, full: html, text
    Fixing a bug noticed by Katrina in code review: an erroneous line break in a hyperlink for the new SETDB1 validation document
  • lines changed 5, context: html, text, full: html, text
    Fixed a number of cases where the antibody target name was of the form <target>_(<vendor_id>), such as ELF1_(SC-631). In these cases, the target should just be <target>, such as ELF1 (or perhaps <target>_(<interaction residues>). This came from a bug in a script that erroneously just copied the entire antibody name into the target field.
  • lines changed 10, context: html, text, full: html, text
    Added two new treatments for the Myers lab
  • lines changed 10, context: html, text, full: html, text
    Removed two rnaExtracts at lab request, 2 have been merged in the metaDb
  • lines changed 1, context: html, text, full: html, text
    Changed the sex for the WERI-Rb-1 from male to female, by request of Richard Sandstrom
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 121, context: html, text, full: html, text
    Periodic cv update, everything should be stable
  • lines changed 1, context: html, text, full: html, text
    Periodic copying of updates from the alpha version of cv.ra
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 196, context: html, text, full: html, text
    pushing changes out to public
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    setting data for fr2 danRer7 chain net
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    minor grammar edit for code review: http://redmine.soe.ucsc.edu/issues/2174
• src/hg/makeDb/trackDb/human/bamSLDenisova.html
  • lines changed 24, context: html, text, full: html, text
    Denisova track description tweaks
  • lines changed 2, context: html, text, full: html, text
    adding denisova track for chimp
• src/hg/makeDb/trackDb/human/denisovaModernHumans.html
  • lines changed 44, context: html, text, full: html, text
    Denisova track description tweaks
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 4, context: html, text, full: html, text
    added Jakob's new affiliation
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Added stuff for EIO/JCVI NAS hg19 lift.
  • lines changed 35, context: html, text, full: html, text
    Changes associated with the NK Nuc Lamina lift to hg19
  • lines changed 203, context: html, text, full: html, text
    Changes for lifting UCSF Brain Methylation track
  • lines changed 93, context: html, text, full: html, text
    Changes for lifted SNP Arrays track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    I had to add 'release alpha' to the top-level composite stanza for each of these files. By doing that, I was then able to do a 'make beta' on hgwbeta. Hope I didn't mess anyting up!
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra
  • lines changed 1, context: html, text, full: html, text
    I had to add 'release alpha' to the top-level composite stanza for each of these files. By doing that, I was then able to do a 'make beta' on hgwbeta. Hope I didn't mess anyting up!
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.new.ra
  • lines changed 1, context: html, text, full: html, text
    I had to add 'release alpha' to the top-level composite stanza for each of these files. By doing that, I was then able to do a 'make beta' on hgwbeta. Hope I didn't mess anyting up!
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    I had to add 'release alpha' to the top-level composite stanza for each of these files. By doing that, I was then able to do a 'make beta' on hgwbeta. Hope I didn't mess anyting up!
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.ra
  • lines changed 1, context: html, text, full: html, text
    I had to add 'release alpha' to the top-level composite stanza for each of these files. By doing that, I was then able to do a 'make beta' on hgwbeta. Hope I didn't mess anyting up!
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 178, context: html, text, full: html, text
    Fixed commit a274c43385c1eccb4868875039705057d7381e13 by addign back deleted rows in the trackDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 137, context: html, text, full: html, text
    removed subID 2410
  • lines changed 2991, context: html, text, full: html, text
    added submissions 3151 3149 3148 3146 3145 3147 3143 3144 3142 3140 3137 3139 3136 3135 3134 3133 3131 3130 3129 3128 3127 3125 3124
  • lines changed 613, context: html, text, full: html, text
    Added new experiments
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 45, context: html, text, full: html, text
    changing short to shortTotal to be consistent with hg18 at lab request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 109, context: html, text, full: html, text
    updated the release dates to reflect origassembly information
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2477, context: html, text, full: html, text
    Added 12 submissions to track and meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 88, context: html, text, full: html, text
    Added one more track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 33, context: html, text, full: html, text
    Added fastq files missing for K562 and GM06990 cell lines
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 353, context: html, text, full: html, text
    Added meta-data for missing fastq's.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 529, context: html, text, full: html, text
    Added meta-data for 24 missing fastq's.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed release alpha from fishClones track.
  • lines changed 4, context: html, text, full: html, text
    Changes associated with the lift of the clonePos (coverage) track to hg19
  • lines changed 4, context: html, text, full: html, text
    Stuff to do with MGI Mouse QTL lift to hg19
  • lines changed 4, context: html, text, full: html, text
    Changes for lifting the H-Inv track to hg19
  • lines changed 13, context: html, text, full: html, text
    Added SIB Alt-Splicing lift to hg19 stuff
  • lines changed 4, context: html, text, full: html, text
    Changes for Illumina WG-6 lift to hg19
  • lines changed 4, context: html, text, full: html, text
    Added stuff for EIO/JCVI NAS hg19 lift.
  • lines changed 4, context: html, text, full: html, text
    Chages for ORegAnno hg19 lift
  • lines changed 4, context: html, text, full: html, text
    Changes associated with the NK Nuc Lamina lift to hg19
  • lines changed 4, context: html, text, full: html, text
    Changes for lifting UCSF Brain Methylation track
  • lines changed 4, context: html, text, full: html, text
    Changes for lifted SNP Arrays track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    add GencodeV5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    add ability to pairEndsByName
  • lines changed 44, context: html, text, full: html, text
    removed the subID 2410, lab says it was mislabeled in wet lab
  • lines changed 984, context: html, text, full: html, text
    added submissions 3151 3149 3148 3146 3145 3147 3143 3144 3142 3140 3137 3139 3136 3135 3134 3133 3131 3130 3129 3128 3127 3125 3124
  • lines changed 24, context: html, text, full: html, text
    Added new experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDnaMethylSuper.html
  • lines changed 1, context: html, text, full: html, text
    adding simicolon after italic in my css attribute (Redmine #2163)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 103, context: html, text, full: html, text
    added the track description, changed short labels, added noInherit on
  • lines changed 1, context: html, text, full: html, text
    Fixed a link and added a scoreFilter setting after approval call
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 21, context: html, text, full: html, text
    added the track description, changed short labels, added noInherit on
  • lines changed 55, context: html, text, full: html, text
    Fixed a link and added a scoreFilter setting after approval call
  • lines changed 1, context: html, text, full: html, text
    Changed Androgen=Methyltrienolone and Estrogen=Estradiol_100nM according to issue 2518
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV5.ra
  • lines changed 150, context: html, text, full: html, text
    add GencodeV5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
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    Description for Yale pseudogenes track based on Ensembl release 60.
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    have phastCons and phyloP 8way on danRer7 for vert and fish groups
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