All File Changes

v270_preview to v270_preview2 (2012-07-03 to 2012-07-10) v270

• src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromChip.daf
  • lines changed 5, context: html, text, full: html, text
    correcting some errors in the open chrom chip daf
  • lines changed 1, context: html, text, full: html, text
    fixing validation settings
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 1, context: html, text, full: html, text
    Fixed a '\N' problem preventing clean compile.
  • lines changed 2, context: html, text, full: html, text
    Fixed the two slash N issues
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 736, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): Major UI work done in adev branch over the past month.
    1. For new "lite" sections, use CSS instead of 3-level nested tables.
    2. Use classes and CSS properties instead of extra divs just to add
    vertical space.
    3. CGI parses JSON from UI into hierarchical data structures and builds
    contents from those data structures instead of ever-growing arg lists.
    4. Proper use of name instead of id for non-uniquely named elements.
    5. Filter inputs: CGI builds up Javascript object literal vars describing
    available (not yet configured) and active (configured by user) filters.
    Javascript uses the vars to display active filters and offer choices
    when user clicks "Add Filter". New filters configured by user are
    sent back to CGI in querySpec JSON.
    Note: filters aren't yet applied when executing queries! (don't work)
    6. Javascript handles updates to intersectSel elements when there's a new
    primary source. Ajax to CGI still needed for updating which output
    formats are possible given types of inputs.
    7. Better handling of error 500's (give user something to paste so we can
    reproduce, instead of pulling entire err500 HTML page into warnBox).
    8. Make it possible for an annoFilter to be a function on an entire row
    instead of anchored to a single column. This will enable more flexible
    filters such as comparing cdsEnd to cdsStart, extracting minor allele freq
    from snpNNN's comma-sep list column, etc.
    
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 5, context: html, text, full: html, text
    Added line for FSU Replication Timing (redmine #6627)
• src/hg/htdocs/ENCODE/index.html
  • lines changed 208, context: html, text, full: html, text
    Update ENCODE News on the portal
  • lines changed 27, context: html, text, full: html, text
    Made some corrections to Kate's additions
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 241, context: html, text, full: html, text
    Update ENCODE News on the portal
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 15, context: html, text, full: html, text
    Removed references to using the wiki to log in for sessions.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    Removed references to using the wiki to log in for sessions.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 18, context: html, text, full: html, text
    Brian's valuable suggestions incorporated.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 49, context: html, text, full: html, text
    Brian's valuable suggestions incorporated.
  • lines changed 4, context: html, text, full: html, text
    And removed a note that was only meant to underline my own ignorance.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 13, context: html, text, full: html, text
    adding announcement about retiring hgText
  • lines changed 2, context: html, text, full: html, text
    added link to original hgTables release announcement in archives
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    added ASCII codes for two euro-letters that were rendering wrong
• src/hg/htdocs/images/Gadus_morhua.jpg
  • lines changed 0, context: html, text, full: html, text
    public domain painting from wikigallery painter Andreas Ludwig Kruger
• src/hg/htdocs/images/Melopsittacus_undulatus.jpg
  • lines changed 0, context: html, text, full: html, text
    public domain photograph from Wikimedia commons by Jen Smith
• src/hg/htdocs/indexNews.html
  • lines changed 28, context: html, text, full: html, text
    adding announcement about retiring hgText. added some end-paragraph tags
  • lines changed 2, context: html, text, full: html, text
    added link to original hgTables release announcement in archives
• src/hg/inc/cart.h
  • lines changed 24, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/cv.h
  • lines changed 1, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/fileUi.h
  • lines changed 2, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/mdb.h
  • lines changed 90, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/search.h
  • lines changed 9, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/trackDb.h
  • lines changed 23, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/inc/web.h
  • lines changed 2, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/js/ajax.js
  • lines changed 5, context: html, text, full: html, text
    Added abort method to loadingImage. (for #6152)
• src/hg/js/hgVarAnnogrator.js
  • lines changed 280, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): Major UI work done in adev branch over the past month.
    1. For new "lite" sections, use CSS instead of 3-level nested tables.
    2. Use classes and CSS properties instead of extra divs just to add
    vertical space.
    3. CGI parses JSON from UI into hierarchical data structures and builds
    contents from those data structures instead of ever-growing arg lists.
    4. Proper use of name instead of id for non-uniquely named elements.
    5. Filter inputs: CGI builds up Javascript object literal vars describing
    available (not yet configured) and active (configured by user) filters.
    Javascript uses the vars to display active filters and offer choices
    when user clicks "Add Filter". New filters configured by user are
    sent back to CGI in querySpec JSON.
    Note: filters aren't yet applied when executing queries! (don't work)
    6. Javascript handles updates to intersectSel elements when there's a new
    primary source. Ajax to CGI still needed for updating which output
    formats are possible given types of inputs.
    7. Better handling of error 500's (give user something to paste so we can
    reproduce, instead of pulling entire err500 HTML page into warnBox).
    8. Make it possible for an annoFilter to be a function on an entire row
    instead of anchored to a single column. This will enable more flexible
    filters such as comparing cdsEnd to cdsStart, extracting minor allele freq
    from snpNNN's comma-sep list column, etc.
    
• src/hg/lib/cart.c
  • lines changed 92, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/cv.c
  • lines changed 51, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/fileUi.c
  • lines changed 171, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    Bug #8420 (BAM checkbox behavior): Fixed as suggested by Tim, thanks!
• src/hg/lib/mdb.c
  • lines changed 310, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/search.c
  • lines changed 54, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/trackDbCustom.c
  • lines changed 6, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/lib/web.c
  • lines changed 76, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/makeDb/doc/canFam2.txt
  • lines changed 19, context: html, text, full: html, text
    Track #8279 (canFam2 snp131): added missing doc, thx Greg for noticing it was missing.
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 23, context: html, text, full: html, text
    lastz hg19 to canFam3 complete
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 24, context: html, text, full: html, text
    swap hg19 lastz done
  • lines changed 0, context: html, text, full: html, text
    remove blanks at end of lines
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUmassDekker5C.release2.notes
  • lines changed 194, context: html, text, full: html, text
    Added release notes for Release 2 of track. Redmine #8071.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 9, context: html, text, full: html, text
    completed echTel1 chain net
  • lines changed 60, context: html, text, full: html, text
    lastz hg19 to canFam3 complete
• src/hg/makeDb/doc/mm10.txt
  • lines changed 533, context: html, text, full: html, text
    done with phyloP phastCons 60-way rework
  • lines changed 116, context: html, text, full: html, text
    download files ready to go for the 60-way
  • lines changed 53, context: html, text, full: html, text
    hgPal downloads constructed for the 60-way
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 2, context: html, text, full: html, text
    Run run makeDownloads.pl from top directory /hive/data/genomes/sarHar1.
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    need the fully qualified name to get to hgwdev from Europa
  • lines changed 14, context: html, text, full: html, text
    make the euronode copy and load scripts update the genbank etc, bin, and lib directories before starting to do their work
• src/hg/makeDb/genbank/etc/euronode-dbload
  • lines changed 8, context: html, text, full: html, text
    make the euronode copy and load scripts update the genbank etc, bin, and lib directories before starting to do their work
• src/hg/makeDb/genbank/etc/euronode.crontab
  • lines changed 1, context: html, text, full: html, text
    mail from Europa needs to have fully qualified names
• src/hg/makeDb/genbank/src/align/gbAlignGet.c
  • lines changed 1, context: html, text, full: html, text
    fixed a typo
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 1, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 6, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 9, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 6, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
  • lines changed 119, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
  • lines changed 119, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
  • lines changed 119, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 133, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/description.html
  • lines changed 116, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 36, context: html, text, full: html, text
    Added iPS cells for Gilbert lab. Redmine #7663.
• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
  • lines changed 116, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
  • lines changed 116, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
  • lines changed 115, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
  • lines changed 2, context: html, text, full: html, text
    Removing numeric tags from the old Affy tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • lines changed 2, context: html, text, full: html, text
    Removing numeric tags from the old Affy tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    Separating out the mdb files for the REG tracks into separate files and adding a composite object for the RegTxn track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 736, context: html, text, full: html, text
    Adding the new metaData in for reporting
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1093, context: html, text, full: html, text
    adding new track for haib tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 867, context: html, text, full: html, text
    added in new tracks for duke dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 1068, context: html, text, full: html, text
    added in new faire tarcks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 9, context: html, text, full: html, text
    Removing freeze date which is not related to this data
  • lines changed 295, context: html, text, full: html, text
    Separating out the mdb files for the REG tracks into separate files and adding a composite object for the RegTxn track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegDnaseClustered.ra
  • lines changed 37, context: html, text, full: html, text
    Separating out the mdb files for the REG tracks into separate files and adding a composite object for the RegTxn track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegTfbsClustered.ra
  • lines changed 53, context: html, text, full: html, text
    Separating out the mdb files for the REG tracks into separate files and adding a composite object for the RegTxn track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegTxn.ra
  • lines changed 211, context: html, text, full: html, text
    Separating out the mdb files for the REG tracks into separate files and adding a composite object for the RegTxn track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    make K562 FASP download only
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
  • lines changed 9, context: html, text, full: html, text
    Cricket removed freeze dates from the metadata (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUmassDekker5C.ra
  • lines changed 463, context: html, text, full: html, text
    Staging UMass 5C Interactions (Release 2) on beta (redmine #8071)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlShortRnaSeq.ra
  • lines changed 20597, context: html, text, full: html, text
    Staging on public Cold Spring Harbor RNA-seq Short (Release 3) RM# 5556
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
  • lines changed 9, context: html, text, full: html, text
    Cricket removed freeze dates from the metadata (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUmassDekker5C.ra
  • lines changed 463, context: html, text, full: html, text
    Releasing UMass 5C Interactions (Release 2) to the RR (redmine #8071)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging UMass 5C Interactions (Release 2) on beta (redmine #8071)
  • lines changed 2, context: html, text, full: html, text
    Making Release 3 of track displayable.
  • lines changed 2, context: html, text, full: html, text
    Staging UCSC Regulation Transcription Track (Release 3) on beta (redmine #7990)
  • lines changed 2, context: html, text, full: html, text
    Releasing UMass 5C Interactions (Release 2) to the RR (redmine #8071)
  • lines changed 2, context: html, text, full: html, text
    Staging on public Cold Spring Harbor RNA-seq Short (Release 3) RM# 5556
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
  • lines changed 160, context: html, text, full: html, text
    Adding Tier2.5 and tag changes to caltech with out introducing other changes
  • lines changed 3, context: html, text, full: html, text
    Cleaning up the dimA dimB strangeness
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.html
  • lines changed 3, context: html, text, full: html, text
    fixed some html thigns for qa
  • lines changed 27, context: html, text, full: html, text
    more html qa fixes
  • lines changed 1, context: html, text, full: html, text
    moved contacts to be under credits
  • lines changed 2, context: html, text, full: html, text
    Adding three links and fixing the Signals to say Plus and Minus
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 9, context: html, text, full: html, text
    Changing the bedRnaElements to bed 6
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 89, context: html, text, full: html, text
    Changing tags and Tier 2 in Cell line for this track, this results in some realphebetization
  • lines changed 1, context: html, text, full: html, text
    Steve asked that we correct the other alphabetization errors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 200, context: html, text, full: html, text
    adding new track for haib tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
  • lines changed 176, context: html, text, full: html, text
    added in new tracks for duke dnase
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 218, context: html, text, full: html, text
    added in new faire tarcks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release3.ra
  • lines changed 2, context: html, text, full: html, text
    Adding Steves changes from ticket 7990, mostly spelling and grammar
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
  • lines changed 14, context: html, text, full: html, text
    Adding Steves changes from ticket 7990, mostly spelling and grammar
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 13, context: html, text, full: html, text
    Changing the tags on Uchicago to not begin with numerals
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.release2.html
  • lines changed 1, context: html, text, full: html, text
    Meta-data fixes for FSU Repli-Chip, fixed miss-spelling in html description page and fixed wording of Umass Dekker 5c description page. Redmine #8391.
  • lines changed 47, context: html, text, full: html, text
    Fixes for Redmine #8071
    4. added comma after based on observations
    6. Removed Nature in citation
    7. Added comma et. al
    8. Added paretheses around i.e and comma
    10. Changed is to was
    11. Changed altering to altered
    12. Added hyphen between manually-picked
    13. Added hyphen between randomly-picked
    14. Changed allows to allowd
    15. Changed allows to allowed
    16. Hyphenated paired-end
    17. Add the in Release notes section
    18. Added parethess after e.g, and commad and space before V2
    19. Changed UMASS to UMass
    20. Updated Dekker site link
    22. Made references in alphabetic order
    23. Used new version of getTrackReferences for author list about 8 authors
    
  • lines changed 4, context: html, text, full: html, text
    Fixes issues in Redmine #8071
    8b. Removed paretheses at end of sentence and moved to end of regions
    11b. Changed were to was
    20b. Removed period at end of hyperlink for Dekker lab`
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixes for Redmine #8071. 1. Fixed spelling and representation of H1-hESC cell line.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 7, context: html, text, full: html, text
    make K562 FASP download only
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 19, context: html, text, full: html, text
    update H1-hESC subId 6542 dataset, strange, the metaDb was updated but the trackDb wasn't, prior to this update
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • lines changed 129, context: html, text, full: html, text
    Removing numeric tags from the old Affy tracks
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
  • lines changed 114, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/megabat/pteVam1/description.html
  • lines changed 114, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 486, context: html, text, full: html, text
    initial contents
  • lines changed 149, context: html, text, full: html, text
    cleaned up pretty much done
  • lines changed 11, context: html, text, full: html, text
    correct ensGene version indication
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 138, context: html, text, full: html, text
    new versions of phastCons and phyloP for subsets and adding subset vertebrate
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra
  • lines changed 3, context: html, text, full: html, text
    Meta-data fixes for FSU Repli-Chip, fixed miss-spelling in html description page and fixed wording of Umass Dekker 5c description page. Redmine #8391.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 289, context: html, text, full: html, text
    update of new submissions of past week
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1302, context: html, text, full: html, text
    update last weeks submission
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    correct strain name for MEL
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeFsuRepliChip.ra
  • lines changed 3, context: html, text, full: html, text
    Venkat made some metadata changes (redmine #6627)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    Ruihua changed some strain info in the metadata (redmine #4469)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Releasing FSU Replication Timing (Release 1) to the RR (redmine #6627)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeFsuRepliChip.ra
  • lines changed 1724, context: html, text, full: html, text
    Releasing FSU Replication Timing (Release 1) to the RR (redmine #6627)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.html
  • lines changed 1, context: html, text, full: html, text
    Meta-data fixes for FSU Repli-Chip, fixed miss-spelling in html description page and fixed wording of Umass Dekker 5c description page. Redmine #8391.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.ra
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    Fixed typo in shortlabel adding i. Fixes for QA. Redmine #6627.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
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    update of new submissions of past week
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
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    update last weeks submission
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.html
  • lines changed 4, context: html, text, full: html, text
    editing in responding to Steve's points 13-17, note 62, #4469
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    add reference for SAM format
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    fix link
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    fix order in cell matrix
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    fix orders of matrix labels, long labels, in responding to Steves point 1, 4-6, 8-11
  • lines changed 9, context: html, text, full: html, text
    fix numeric tag, note 65, #4469
  • lines changed 10, context: html, text, full: html, text
    fix order of 416B cell
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    fix labels, sort order in responding to Steve's points 3, 10b, 18, #4469
  • lines changed 25, context: html, text, full: html, text
    fixed order of cell/tissue types
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    fix replication box
  • lines changed 3, context: html, text, full: html, text
    fix autoscale in responding to Steve's point 12, note 62, #4469
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    change default view to 0:50 from 0:500, turn off alignment of default display subtracks
  • lines changed 1, context: html, text, full: html, text
    capitalize first letter in strain
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    add age rep column to file sort list
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    remove S from S129
  • lines changed 1, context: html, text, full: html, text
    change S129=S129 to A129=129
  • lines changed 1, context: html, text, full: html, text
    change back label, testing
  • lines changed 5, context: html, text, full: html, text
    change S129=S129 to A129=129 and updated corresponding stanzas
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    change Replicate to Rep
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    change Rep to Replicate
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    change rep to replicate
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    change A129 to A1S129
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    remove S from S129
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    fix short labels
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • lines changed 113, context: html, text, full: html, text
    contents from minimal makeGenomeDb.pl script
• src/hg/makeDb/trackDb/pika/ochPri2/description.html
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    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 119, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
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    correct assembly number 310688
• src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html
  • lines changed 114, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
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    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
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    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
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    brought up to date with all current settings
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    new sGroups for mm10 60-way Glire and Placental
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    removed too many tag types
• src/hg/makeDb/trackDb/tarsier/tarSyr1/description.html
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    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html
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    minimal page from makeGenomeDb.pl
• src/hg/utils/automation/configFiles/choHof1.config.ra
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    brought up to date with all current settings
• src/hg/utils/automation/configFiles/dasNov3.config.ra
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    up to date with current parameters
• src/hg/utils/automation/configFiles/dipOrd1.config.ra
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    up to date with current required settings
• src/hg/utils/automation/configFiles/eriEur1.config.ra
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    updated ancient contents to new style
• src/hg/utils/automation/configFiles/felCat5.config.ra
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    up to date with current required parameters
• src/hg/utils/automation/configFiles/gadMor1.config.ra
  • lines changed 22, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/melUnd1.config.ra
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    up to date with current parameters
• src/hg/utils/automation/configFiles/micMur1.config.ra
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    updated ancient contents to new style
• src/hg/utils/automation/configFiles/nomLeu2.config.ra
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    up to date with required parameters
• src/hg/utils/automation/configFiles/ochPri2.config.ra
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    up to date with current required variables
• src/hg/utils/automation/configFiles/otoGar3.config.ra
  • lines changed 22, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/panTro4.config.ra
  • lines changed 25, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/proCap1.config.ra
  • lines changed 24, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/pteVam1.config.ra
  • lines changed 23, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/rheMac3.config.ra
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    up to date with required parameters
• src/hg/utils/automation/configFiles/saiBol1.config.ra
  • lines changed 26, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/sorAra1.config.ra
  • lines changed 25, context: html, text, full: html, text
    updated ancient contents to new style
• src/hg/utils/automation/configFiles/tarSyr1.config.ra
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    up to date with required parameters
• src/hg/utils/automation/configFiles/tupBel1.config.ra
  • lines changed 25, context: html, text, full: html, text
    updated ancient contents to new style
• src/inc/annoFilter.h
  • lines changed 18, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): Major UI work done in adev branch over the past month.
    1. For new "lite" sections, use CSS instead of 3-level nested tables.
    2. Use classes and CSS properties instead of extra divs just to add
    vertical space.
    3. CGI parses JSON from UI into hierarchical data structures and builds
    contents from those data structures instead of ever-growing arg lists.
    4. Proper use of name instead of id for non-uniquely named elements.
    5. Filter inputs: CGI builds up Javascript object literal vars describing
    available (not yet configured) and active (configured by user) filters.
    Javascript uses the vars to display active filters and offer choices
    when user clicks "Add Filter". New filters configured by user are
    sent back to CGI in querySpec JSON.
    Note: filters aren't yet applied when executing queries! (don't work)
    6. Javascript handles updates to intersectSel elements when there's a new
    primary source. Ajax to CGI still needed for updating which output
    formats are possible given types of inputs.
    7. Better handling of error 500's (give user something to paste so we can
    reproduce, instead of pulling entire err500 HTML page into warnBox).
    8. Make it possible for an annoFilter to be a function on an entire row
    instead of anchored to a single column. This will enable more flexible
    filters such as comparing cdsEnd to cdsStart, extracting minor allele freq
    from snpNNN's comma-sep list column, etc.
    
• src/lib/annoFilter.c
  • lines changed 134, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): Major UI work done in adev branch over the past month.
    1. For new "lite" sections, use CSS instead of 3-level nested tables.
    2. Use classes and CSS properties instead of extra divs just to add
    vertical space.
    3. CGI parses JSON from UI into hierarchical data structures and builds
    contents from those data structures instead of ever-growing arg lists.
    4. Proper use of name instead of id for non-uniquely named elements.
    5. Filter inputs: CGI builds up Javascript object literal vars describing
    available (not yet configured) and active (configured by user) filters.
    Javascript uses the vars to display active filters and offer choices
    when user clicks "Add Filter". New filters configured by user are
    sent back to CGI in querySpec JSON.
    Note: filters aren't yet applied when executing queries! (don't work)
    6. Javascript handles updates to intersectSel elements when there's a new
    primary source. Ajax to CGI still needed for updating which output
    formats are possible given types of inputs.
    7. Better handling of error 500's (give user something to paste so we can
    reproduce, instead of pulling entire err500 HTML page into warnBox).
    8. Make it possible for an annoFilter to be a function on an entire row
    instead of anchored to a single column. This will enable more flexible
    filters such as comparing cdsEnd to cdsStart, extracting minor allele freq
    from snpNNN's comma-sep list column, etc.
    
• src/product/ex.hg.conf
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    Removed old but duplicate comment on genomewiki.
• src/utils/qa/weeklybld/buildEnv.csh
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    v270 preview2
• src/utils/qa/weeklybld/cherryPickCommits.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doNewBranch.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doNewReview.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doSearchRobot.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
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    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • lines changed 1, context: html, text, full: html, text
    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/moveBranchTag.csh
  • lines changed 1, context: html, text, full: html, text
    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.
• src/utils/qa/weeklybld/patchBranch.csh
  • lines changed 1, context: html, text, full: html, text
    Added BUILDMEISTER to the lists of mail receipients. Making the 'build' user run the build process, the env variable BUILDMEISTER is needed to declare who is actually kickin iff scripts.

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• files changed: 201