All File Changes

v261_preview2 to v261_base (2011-12-20 to 2012-01-03) v261

• src/hg/encode/DAFs/3.0/hg19/wgEncodeCaltechRnaSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Updated DAF to accept bigBed files for Junctions. Redmine 2019.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed DAF to have correct spelling of downloadOnly. Redmine #5986.
  • lines changed 3, context: html, text, full: html, text
    Fixed the spelling of Signal views, to mathc cv.ra.
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 2, context: html, text, full: html, text
    changed usage statement
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 15, context: html, text, full: html, text
    Added rnaExtract, localization and strain to fields.ra.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 14, context: html, text, full: html, text
    finished modifications to handle bigBed files
  • lines changed 1, context: html, text, full: html, text
    bigBeg wasn't in the list of files to get .gz appended to the target file name
• src/hg/encode/qaUpdateMetadata/makefile
  • lines changed 27, context: html, text, full: html, text
    added make file
• src/hg/hgGateway/hgGateway.c
  • lines changed 87, context: html, text, full: html, text
    add euronode redirect code (#3104); mostly written by galt with some minor changes by me. Has some debug stuff which will be taken out as I work on this. Currently only on in larrym's tree and on euronode machine
  • lines changed 7, context: html, text, full: html, text
    cleanup and comments
• src/hg/hgTracks/simpleTracks.c
  • lines changed 9, context: html, text, full: html, text
    fixed item labels in gencode tracks
• src/hg/hgc/ccdsClick.c
  • lines changed 1, context: html, text, full: html, text
    fixed missing page closes
• src/hg/hgc/gencodeClick.c
  • lines changed 17, context: html, text, full: html, text
    added annotation level to gencode details page
  • lines changed 1, context: html, text, full: html, text
    fixed missing page closes
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    Fixed bug in custom tracks bigBed item click.
• src/hg/hgc/mgcClick.c
  • lines changed 1, context: html, text, full: html, text
    fixed missing page closes
• src/hg/hgc/retroClick.c
  • lines changed 1, context: html, text, full: html, text
    fixed missing page closes
• src/hg/hgc/t2g.c
  • lines changed 2, context: html, text, full: html, text
    fixed word breaking in t2g tables, updated track desc
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 74, context: html, text, full: html, text
    Inserted script type declarations into HEAD. Inserted new euro class into links that need to be made relative.
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 3, context: html, text, full: html, text
    made changes per code review #6392
• src/hg/htdocs/goldenPath/help/hgBaseLabel.html
  • lines changed 1, context: html, text, full: html, text
    Changed capitalization of title
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 8, context: html, text, full: html, text
    Fixed formatting errors. Removed 'cse' from links.
  • lines changed 13, context: html, text, full: html, text
    Made formatting corrections
• src/hg/htdocs/goldenPath/licenses/affyagreement.html
  • lines changed 118, context: html, text, full: html, text
    Per Ann Z, deleted affyagreement.html
• src/hg/htdocs/js/staticDoc.js
  • lines changed 2, context: html, text, full: html, text
    Tim did a code review on this for Katrina and made some verbal suggestions, redmine# 6394
  • lines changed 1, context: html, text, full: html, text
    forgot to remove the code that was used for testing...this has been done in this commit, redmine# 6394
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    add euronode redirect code (#3104); mostly written by galt with some minor changes by me. Has some debug stuff which will be taken out as I work on this. Currently only on in larrym's tree and on euronode machine
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v261
• src/hg/lib/cart.c
  • lines changed 12, context: html, text, full: html, text
    add euronode redirect code (#3104); mostly written by galt with some minor changes by me. Has some debug stuff which will be taken out as I work on this. Currently only on in larrym's tree and on euronode machine
• src/hg/lib/web.c
  • lines changed 50, context: html, text, full: html, text
    add euronode redirect code (#3104); mostly written by galt with some minor changes by me. Has some debug stuff which will be taken out as I work on this. Currently only on in larrym's tree and on euronode machine
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 25, context: html, text, full: html, text
    New assemblies work.
• src/hg/makeDb/doc/encodeDccHg19/gencodeV10.txt
  • lines changed 151, context: html, text, full: html, text
    GENCODE V10 initial process by UCSC GENCODE droids
  • lines changed 4, context: html, text, full: html, text
    fixed item labels in gencode tracks
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release2.notes
  • lines changed 92, context: html, text, full: html, text
    added ntoes for genotype
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes
  • lines changed 18, context: html, text, full: html, text
    updated notes for synth
• src/hg/makeDb/doc/hetGla1.txt
  • lines changed 63, context: html, text, full: html, text
    New assemblies work.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    Fixed Bug #6417 duplicate records (6) in Human RNA editing (DARNED) track
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 43, context: html, text, full: html, text
    fixup gasAcu1 v65 business
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 57, context: html, text, full: html, text
    To clean up numerous gene-misnaming bugs, refined the way the gene symbol and description are assigned. If a transcript overlaps a RefSeq (i.e. if it has an entry in the knownToRefSeq table), take the gene symbol and description from the RefSeq record. If there isn't an overlapping transcript, then do the other things: look at whatever protein was annotated for the CDS (with the caveat that this can go badly awry within families of paralogs), look at the evidence the transcript was based on, etc. For UCSC Genes, this makes things a bit more complicated because the knownToRefSeq table must be built before the kgXref table - but later the knownToRefSeq table must be updated to match the contents of the kgXref refseq column (which is set by a more sensitive process). So, I updated the UCSC Genes script to build a preliminary version of knownToRefSeq, built the kgXref table with that preliminary knownToRefSeq, and then updated knownToRefSeq from kgXref.
  • lines changed 73, context: html, text, full: html, text
    1. Switched the genome versions for certain related organisms after those versions turned out to have incomplete datasets. 2. As a stylistic thing, where the code references the root of the kent source tree as ~/kent, replaced that with the variable , to give developers greater ease in reorganizing their source trees. 3. Rearranged some of the steps for building the isPCR files to make more explicit what must be done by a superuser and what has to be done after the superuser commands are complete
  • lines changed 24, context: html, text, full: html, text
    Fixing Redmine Bug #5180, the gist of which is that the abParts should be excluded from the knownTo* tables. Added an exclude option to hgMapToGene, which contains a list of gene names to exclude from the table
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 12, context: html, text, full: html, text
    drop the unused assemblies #6358
  • lines changed 12, context: html, text, full: html, text
    purge assemblies from active align list #6358. Also add back hg15test to genbank.conf per Mark
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 458, context: html, text, full: html, text
    drop inactive assemblies #6358
  • lines changed 18, context: html, text, full: html, text
    purge assemblies from active align list #6358. Also add back hg15test to genbank.conf per Mark
  • lines changed 5, context: html, text, full: html, text
    oops, had some truncated lines in last checkin #6358
  • lines changed 221, context: html, text, full: html, text
    follow more consistent rules about which assemblies fall into which class (low-coverage, well-ordered, finished) #6250
  • lines changed 94, context: html, text, full: html, text
    oops, typo... lowcover should be lowCover (#6250)
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 12, context: html, text, full: html, text
    drop the unused assemblies #6358
  • lines changed 12, context: html, text, full: html, text
    purge assemblies from active align list #6358. Also add back hg15test to genbank.conf per Mark
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    add an mRNA that changed from pig to panda. Simple mistake, eh?
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Added sibGene and sibTxGraph to hg$ and mm$ ignored sections
  • lines changed 1, context: html, text, full: html, text
    add a ce10 exclusion to identifier ensemblTranscriptId2
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Set speciesCodonDefault to felCat4
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Adding further explanation for cells and treatments according to ticket 1710 note 44
  • lines changed 4, context: html, text, full: html, text
    Fixing some typos
  • lines changed 7, context: html, text, full: html, text
    Finishing code review, removing provisional tags
  • lines changed 1, context: html, text, full: html, text
    Shortened tag for OlfactBulb because it was causing problems. No current data in mm9 is referencing this term.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 73, context: html, text, full: html, text
    Changes are approved and are tested. Ready fro Public site. Redmine #6387.
• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gadMor/gadMor1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gadMor/gadMor1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 6, context: html, text, full: html, text
    Fixed Ensembl version. Made a grammatical correction. Removed an extraneous baboon.
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeMetaCheckTest.ra
  • lines changed 1051, context: html, text, full: html, text
    framework for metaCheck test in encodeTest
• src/hg/makeDb/trackDb/human/encodeTest/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    framework for metaCheck test in encodeTest
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeMetaCheckTest.ra
  • lines changed 470, context: html, text, full: html, text
    framework for metaCheck test in encodeTest
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 0, context: html, text, full: html, text
    removed extra space before et al., code review #6392
• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
  • lines changed 1, context: html, text, full: html, text
    fix incorrect 'bed .' entries (redmine #6289)
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • lines changed 1, context: html, text, full: html, text
    fix incorrect 'bed .' entries (redmine #6289)
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
  • lines changed 1, context: html, text, full: html, text
    fix incorrect 'bed .' entries (redmine #6289)
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    redmine 5630: Add db name into url to TromER search for hg18 and hg19
  • lines changed 3, context: html, text, full: html, text
    dd db=hg1X to sibTxGraph external TromER link's url
  • lines changed 1, context: html, text, full: html, text
    Added include trackDb.merckPolyA.all.ra.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
  • lines changed 3, context: html, text, full: html, text
    removing link to HAIB TFBS hg18 hgTrackUi since the hg18 version of the track has been dropped from the RR
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 3, context: html, text, full: html, text
    fixed dateunrestricted date
  • lines changed 1, context: html, text, full: html, text
    forgot to regen magic number
  • lines changed 3, context: html, text, full: html, text
    forcing one experiment to be it's old expId
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 1267, context: html, text, full: html, text
    updating beta metadata - cricket removed the clusters, redmine #2020
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 7550, context: html, text, full: html, text
    preparing trackDb & metaDb for release of ENCODE RIKEN CAGE Loc (Release 2), redmine #2020
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    redmine 5630: Add db name into url to TromER search for hg18 and hg19
  • lines changed 5, context: html, text, full: html, text
    dd db=hg1X to sibTxGraph external TromER link's url
  • lines changed 2, context: html, text, full: html, text
    resolve merge conflict
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    preparing trackDb & metaDb for release of ENCODE RIKEN CAGE Loc (Release 2), redmine #2020
  • lines changed 1, context: html, text, full: html, text
    GENCODE V10 initial process by UCSC GENCODE droids
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Pointing to correct html file
  • lines changed 1, context: html, text, full: html, text
    This time for real, changing the html to the correct name
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 5, context: html, text, full: html, text
    fixed GENCODE contact address
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 265, context: html, text, full: html, text
    GENCODE V10 initial process by UCSC GENCODE droids
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 190, context: html, text, full: html, text
    GENCODE V10 initial process by UCSC GENCODE droids
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 5, context: html, text, full: html, text
    fixed GENCODE contact address
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
  • lines changed 5, context: html, text, full: html, text
    fixed GENCODE contact address
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 4, context: html, text, full: html, text
    fixed GENCODE contact address
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 3, context: html, text, full: html, text
    fixed GENCODE contact address
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 3, context: html, text, full: html, text
    fixes and stuff
  • lines changed 4, context: html, text, full: html, text
    added more information about the release changes
  • lines changed 2, context: html, text, full: html, text
    collapsed two lines into one
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 1, context: html, text, full: html, text
    fixes and stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Fixing the edits in ticket 1710 note 44
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 8, context: html, text, full: html, text
    commented out urothelia
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 60, context: html, text, full: html, text
    preparing trackDb & metaDb for release of ENCODE RIKEN CAGE Loc (Release 2), redmine #2020
  • lines changed 1, context: html, text, full: html, text
    adding date for release 2 to Release Notes section, #2020
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
  • lines changed 5, context: html, text, full: html, text
    Changing wording in the display section as per ticket 2020
  • lines changed 15, context: html, text, full: html, text
    Fixing ticket 2020 for Katrina
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 9, context: html, text, full: html, text
    Changing short label of GM12 to GM78 to accomodate incoming GM12892
  • lines changed 1, context: html, text, full: html, text
    Changing the sort order according to Katrina's wish to have view at the end
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 1240, context: html, text, full: html, text
    preparing trackDb & metaDb for release of ENCODE RIKEN CAGE Loc (Release 2), redmine #2020
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
  • lines changed 5, context: html, text, full: html, text
    Added information about 4 cells/experiments being orignally mapped and analyzed on hg18 in the reference Hanson paper. Redmine #4577.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding rheMac3 to the build
  • lines changed 1, context: html, text, full: html, text
    adding gadMor1 to the build
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added 16 experiments for UW DGF track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 2257, context: html, text, full: html, text
    Added 16 experiments for UW DGF track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 2261, context: html, text, full: html, text
    Added new 20 submissions. Redmine #4468.
  • lines changed 289, context: html, text, full: html, text
    Renamed RawSignal to Signal, as this was decided in version 1 of track, but lab used older DAF. Redmine #4468.
  • lines changed 36, context: html, text, full: html, text
    Put into the attic all replicates > 2. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 2024, context: html, text, full: html, text
    Added 17 new experiments. Redmine #4469.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Updated trackDb to have caltech release 2 on dev and release1 on beta and public.
  • lines changed 4, context: html, text, full: html, text
    Added 16 experiments for UW DGF track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated track configuration to subtrack configuration for Signals. Redmine #110, #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated track configuration to subtrack configuration for Signals. Redmine #110, #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 646, context: html, text, full: html, text
    Added 16 experiments for UW DGF track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
  • lines changed 543, context: html, text, full: html, text
    Added new 20 submissions. Redmine #4468.
  • lines changed 60, context: html, text, full: html, text
    Renamed RawSignal to Signal, as this was decided in version 1 of track, but lab used older DAF. Redmine #4468.
  • lines changed 147, context: html, text, full: html, text
    Put into the attic all replicates > 2. Redmine #4468.
  • lines changed 22, context: html, text, full: html, text
    Updated comments to include #display no for attic experiments.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 609, context: html, text, full: html, text
    Added 17 new experiments. Redmine #4469.
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhesus/rheMac3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhesus/rheMac3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/sibGene.html
  • lines changed 16, context: html, text, full: html, text
    Made some grammatical/formatting corrections. Updated the journal link.
  • lines changed 10, context: html, text, full: html, text
    Made some html formatting corrections
• src/hg/makeDb/trackDb/sibTxGraph.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 3, context: html, text, full: html, text
    minor copy-editing
  • lines changed 11, context: html, text, full: html, text
    small changes to t2g description
  • lines changed 8, context: html, text, full: html, text
    fixed word breaking in t2g tables, updated track desc
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 395, context: html, text, full: html, text
    copy taken from cons9way and updated
  • lines changed 35, context: html, text, full: html, text
    Italicized C. elegans. Changed Emsembl references from v62 to v65. Update several links.
  • lines changed 1, context: html, text, full: html, text
    Corrected caeJap3 to caeJap4
• src/hg/makeDb/trackDb/worm/ce10/gap.html
  • lines changed 4, context: html, text, full: html, text
    Made some formatting changes. Changed credit for WashU.
• src/hg/makeDb/trackDb/worm/ce10/gold.html
  • lines changed 6, context: html, text, full: html, text
    Made some formatting and wording changes
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    Removed extra 'the'
• src/hg/makeDb/trackDb/worm/est.html
  • lines changed 11, context: html, text, full: html, text
    Changed formatting. Updated some links.
• src/hg/makeDb/trackDb/worm/intronEst.html
  • lines changed 11, context: html, text, full: html, text
    Changed formatting. Updated some links.
• src/hg/makeDb/trackDb/worm/mrna.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting changes. Updated some links.
• src/hg/makeDb/trackDb/worm/refGene.html
  • lines changed 4, context: html, text, full: html, text
    Made a formatting change. Updated a journal link.
• src/hg/makeDb/trackDb/worm/rmsk.html
  • lines changed 14, context: html, text, full: html, text
    Made some formatting changes. Add Robert Hubley to the Credits section. Updated some links.
• src/hg/makeDb/trackDb/worm/xenoMrna.html
  • lines changed 11, context: html, text, full: html, text
    Changed formatting. Updated some links.
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 2, context: html, text, full: html, text
    Fixed Ensembl version. Made another minor correction.
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Per Hiram, returned to the original order of checkboxes in Multiz Alignments Configuration section
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 2, context: html, text, full: html, text
    In addition to requiring that a gene and a transcript either share a splice site or are both unspliced if they are going to be mapped together, require that they be on the same strand as well
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    Bug fix: I'd forgotten that strands are implemented as char[2], not just char. Now I'm comparing two strands properly
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    Fixing Redmine Bug #5180, the gist of which is that the abParts should be excluded from the knownTo* tables. Added an exclude option to hgMapToGene, which contains a list of gene names to exclude from the table
• src/hg/pslCDnaFilter/tests/expected/blackListTest/filt.out
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    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
• src/hg/pslCDnaFilter/tests/expected/blackListTest/keep.psl
  • lines changed 397, context: html, text, full: html, text
    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
• src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/filt.out
  • lines changed 6, context: html, text, full: html, text
    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
  • lines changed 3, context: html, text, full: html, text
    added some more interesting psl's to the decayMinCoverTest
• src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/keep.psl
  • lines changed 84, context: html, text, full: html, text
    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
  • lines changed 50, context: html, text, full: html, text
    added some more interesting psl's to the decayMinCoverTest
• src/hg/pslCDnaFilter/tests/input/blackList.psl
  • lines changed 478, context: html, text, full: html, text
    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
• src/hg/pslCDnaFilter/tests/input/blackList.txt
  • lines changed 3, context: html, text, full: html, text
    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
• src/hg/pslCDnaFilter/tests/input/decayMinCover.psl
  • lines changed 573, context: html, text, full: html, text
    added some more interesting psl's to the decayMinCoverTest
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    oops... need the makefile for the tests
  • lines changed 1, context: html, text, full: html, text
    added some more interesting psl's to the decayMinCoverTest
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 60, context: html, text, full: html, text
    To clean up numerous gene-misnaming bugs, refined the way the gene symbol and description are assigned. If a transcript overlaps a RefSeq (i.e. if it has an entry in the knownToRefSeq table), take the gene symbol and description from the RefSeq record. If there isn't an overlapping transcript, then do the other things: look at whatever protein was annotated for the CDS (with the caveat that this can go badly awry within families of paralogs), look at the evidence the transcript was based on, etc. For UCSC Genes, this makes things a bit more complicated because the knownToRefSeq table must be built before the kgXref table - but later the knownToRefSeq table must be updated to match the contents of the kgXref refseq column (which is set by a more sensitive process). So, I updated the UCSC Genes script to build a preliminary version of knownToRefSeq, built the kgXref table with that preliminary knownToRefSeq, and then updated knownToRefSeq from kgXref.
• src/lib/blackList.c
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    tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
• src/utils/qa/weeklybld/buildEnv.csh
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    v261 final build

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• files changed: 167