All File Changes

v290_preview2 to v290_base (2013-09-23 to 2013-09-30) v290

• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 85, context: html, text, full: html, text
    Making it so that you can overlay new metadata on an older file by just resubmitting it with different tags. It will flag an error if the new metadata doesn't match the old metadata unless the new update option is used.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makk
  • lines changed 1, context: html, text, full: html, text
    Changing target for production executable.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 10, context: html, text, full: html, text
    Adding size parameter to edwGotFile to support efforts to reduce duplications of large files.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 27, context: html, text, full: html, text
    Adding size parameter to edwGotFile to support efforts to reduce duplications of large files.
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    fixing problem with msyql-injection prevention checks. cmpVal has already been vetted above and it is really a sql fragment itself, not an identifier, so suppress checking with %-s
• src/hg/hgTracks/pslTrack.c
  • lines changed 5, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/hgTracks/retroGene.c
  • lines changed 1, context: html, text, full: html, text
    fix problem with transMap and retroGenes that I introduced when I addedcode to string version numbers off Genbank accessions.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    fixes #7472 deals with bed4 and bed9 when element has size=0 start==end
• src/hg/hgTracks/snakeTrack.c
  • lines changed 8, context: html, text, full: html, text
    make sure the timeout message makes it to the user in snake drawingcode.
    
• src/hg/hgTracks/transMapTracks.c
  • lines changed 1, context: html, text, full: html, text
    fix problem with transMap and retroGenes that I introduced when I addedcode to string version numbers off Genbank accessions.
    
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
  • lines changed 2, context: html, text, full: html, text
    fixes #7472 deals with bed4 and bed9 when element has size=0 start==end
• src/hg/hgc/mgcClick.c
  • lines changed 8, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Adding update date to pubs for ENCODE per Mike Pazin request, updating main pubs date too
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 1, context: html, text, full: html, text
    Adding update date to pubs for ENCODE per Mike Pazin request
  • lines changed 4, context: html, text, full: html, text
    Correcting publications per code review refs #11797
  • lines changed 4, context: html, text, full: html, text
    Pubs corrections code review refs #11797
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 1, context: html, text, full: html, text
    Adding update date to pubs for ENCODE per Mike Pazin request
  • lines changed 2, context: html, text, full: html, text
    Correcting publication information Code Review refs #11797
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Adding news release and credits/FAQ updates for new alligator assembly allMis1 refs #8750
• src/hg/htdocs/conditions.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken license link, per Luvina.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 57, context: html, text, full: html, text
    Adding news release and credits/FAQ updates for new alligator assembly allMis1 refs #8750
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    Adding news release and credits/FAQ updates for new alligator assembly allMis1 refs #8750
• src/hg/htdocs/indexNews.html
  • lines changed 60, context: html, text, full: html, text
    Adding news release and credits/FAQ updates for new alligator assembly allMis1 refs #8750
• src/hg/inc/annoGratorGpVar.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/gpFx.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/snakeUi.h
  • lines changed 1, context: html, text, full: html, text
    change the default bar coloring in snakes (per David)
• src/hg/inc/soTerm.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/variant.h
  • lines changed 6, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v290
• src/hg/lib/annoFormatVep.c
  • lines changed 47, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 54, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/gpFx.c
  • lines changed 633, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    fixes #7472 deals with bed4 and bed9 when element has size=0 start==end
• src/hg/lib/soTerm.c
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/variant.c
  • lines changed 8, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 55, context: html, text, full: html, text
    downloads constructed for 100-way refs #10272
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
  • lines changed 1, context: html, text, full: html, text
    allMis1 doesn't have refGene so it can be used to make the upstreamfiles
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding allMis1 to genbank updates on beta, refs# 8750
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding allMis1 to RR genbank updates, refs# 8750
• src/hg/makeDb/genbank/src/dbload/gbAlignData.c
  • lines changed 3, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
  • lines changed 13, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.h
  • lines changed 1, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 3, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
  • lines changed 4, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.h
  • lines changed 2, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
  • lines changed 2, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Excluded mm10 from knownGeneOld5Id since knownGene5 never existed on mm10
  • lines changed 1, context: html, text, full: html, text
    Adjusted ce2 threshold to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted dm1 threshold to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted dm2/dm3 threshold to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted hg17 threshold to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted hg18 threshold to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Adjusted hg19 threshold to fix joinerCheck error
  • lines changed 2, context: html, text, full: html, text
    Added macEug1 to notEnsemblTranscriptId2 group to fix joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Added hg16,hg17,hg18,mm7,mm8 to ensGeneDb group to fix joinerCheck error
  • lines changed 5, context: html, text, full: html, text
    Added ce4 and hg19 to the notFlyBaseGeneId group; created new flyBase2004IdDmDb group and moved the list of databases from the appropriate line of the section into the group - added ce4 and hg19 to the group; created a minCheck value for flyBase2004IdDm.mmBlatTab.query
  • lines changed 1, context: html, text, full: html, text
    Added rn3 to ensGeneDb list
• src/hg/makeDb/trackDb/chicken/galGal2/bgiGene.html
  • lines changed 1, context: html, text, full: html, text
    Correcting broken URL for galGal2 per Code Review, refs #11798
• src/hg/makeDb/trackDb/chicken/galGal2/bgiSnp.html
  • lines changed 2, context: html, text, full: html, text
    Correcting broken URL for galGal2 per Code Review, refs #11798
• src/hg/makeDb/trackDb/gator/allMis1/description.html
  • lines changed 2, context: html, text, full: html, text
    Adding line about recommendation for Rysnc for allMis1 descp page refs #8750
• src/hg/makeDb/trackDb/other/braNey1/trackDb.genbank.ra
  • lines changed 115, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/makeDb/trackDb/other/braNey1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    more tweaks to optionally add version numbers to id's in genbank tables
• src/hg/utils/pslMap/pslMap.c
  • lines changed 50, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/pslMap/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/pslMap/usage.txt
  • lines changed 2, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/uniprotMutations/liftUniprotMut.py
  • lines changed 3, context: html, text, full: html, text
    tiny changes to scripts for easier re-running
• src/hg/utils/uniprotMutations/makeUniProtToHg.sh
  • lines changed 2, context: html, text, full: html, text
    tiny changes to scripts for easier re-running
• src/inc/cheapcgi.h
  • lines changed 16, context: html, text, full: html, text
    Adding cgiDictionary - something you can make from a cgi-encoded string.
• src/inc/common.mk
  • lines changed 3, context: html, text, full: html, text
    missing UNAME_S variable setting refs #11792
• src/lib/annoStreamVcf.c
  • lines changed 4, context: html, text, full: html, text
    Code review feedback, thanks Tim.refs #11800
    
• src/lib/bPlusTree.c
  • lines changed 1, context: html, text, full: html, text
    fix error in the size of a buffer allocation
• src/lib/cheapcgi.c
  • lines changed 24, context: html, text, full: html, text
    Adding cgiDictionary - something you can make from a cgi-encoded string.
• src/lib/vcf.c
  • lines changed 2, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/utils/qa/2bitCompare
  • lines changed 1, context: html, text, full: html, text
    Made correction to variable name for output of file date,size for gbdb on beta (redmine #6508)
• src/utils/qa/getJoinerKeyErrors.pl
  • lines changed 1, context: html, text, full: html, text
    Updated environment statement
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v290 final build

• lines changed: 1427
• files changed: 80