All File Changes

v318_base to v319_preview (2015-06-22 to 2015-06-29) v319

• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 4, context: html, text, full: html, text
    Adding copyright boilerplate.
    
• src/hg/hgMirror/hgMirror
  • lines changed 62, context: html, text, full: html, text
    refs #15473: fixing the order of species in hgMirror, also making
    hgMirror partialy work at least on hgwdev to make this easier to debug.
    Moving all temp files to /tmp/hgMirror which is a lot cleaner and will
    simplify changing the temp directory when this is needed in the future.
    
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    fix click through on snake tracks to other genomes in mysql backed HAL browsers (no redmine)
    
• src/hg/hgc/transMapClick.c
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 44, context: html, text, full: html, text
    Adding announcement of Bonobo release, refs #8231
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 28, context: html, text, full: html, text
    Adding announcement of Bonobo release, refs #8231
    
• src/hg/htdocs/indexNews.html
  • lines changed 73, context: html, text, full: html, text
    Adding announcement of Bonobo release, refs #8231
    
• src/hg/htdocs/training/index.html
  • lines changed 7, context: html, text, full: html, text
    added Taxes A&M workshop
    
  • lines changed 40, context: html, text, full: html, text
    added new workshops and removed those completed
    
• src/hg/inc/genePred.h
  • lines changed 3, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/inc/transMapGene.h
  • lines changed 10, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/inc/transMapInfo.h
  • lines changed 2, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/inc/transMapSrc.h
  • lines changed 2, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/js/external/makefile
  • lines changed 2, context: html, text, full: html, text
    When using https, FaceBook's URL for React JS redirects to an http URL
    and the browser refuses to fetch from another site using http when the
    page is https. So don't rely on FaceBook's network, just host the
    React JS locally.
    refs #15557
    
• src/hg/js/external/react-with-addons-0.12.2.min.js
  • lines changed 0, context: html, text, full: html, text
    When using https, FaceBook's URL for React JS redirects to an http URL
    and the browser refuses to fetch from another site using http when the
    page is https. So don't rely on FaceBook's network, just host the
    React JS locally.
    refs #15557
    
• src/hg/js/model/lib/cart.js
  • lines changed 9, context: html, text, full: html, text
    For ease of command-line debugging, console.log the CGI param string
    (that would have been in the GET URL) when POSTing an ajax request.
    
• src/hg/lib/genePred.c
  • lines changed 36, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
  • lines changed 1, context: html, text, full: html, text
    fixed buffer overflow in extreme test case (no readmind)
    
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    fixing typo in comment
    
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    When using https, FaceBook's URL for React JS redirects to an http URL
    and the browser refuses to fetch from another site using http when the
    page is https. So don't rely on FaceBook's network, just host the
    React JS locally.
    refs #15557
    
• src/hg/lib/knownGene.as
  • lines changed 3, context: html, text, full: html, text
    make knownGene.as have more generic description to be used for both UCSC
    Genes and GENCODE Basic
    
• src/hg/lib/transMapGene.as
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapGene.c
  • lines changed 27, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapGene.sql
  • lines changed 5, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapInfo.c
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapSrc.c
  • lines changed 4, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/makeDb/doc/aquChr2/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #15096
    
• src/hg/makeDb/doc/bisBis1/initialBuild.txt
  • lines changed 45, context: html, text, full: html, text
    complete and in the pushQ 007599 with augustusGene and microsat tracks refs #15388
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 22, context: html, text, full: html, text
    adding SGP geneid gene predictions refs #15616
    
• src/hg/makeDb/doc/ce10.txt
  • lines changed 19, context: html, text, full: html, text
    adding lift over to ce11 refs #15209
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
  • lines changed 58, context: html, text, full: html, text
    added augustusGene liftOver to ce6 and ce10 and in the pushQ refs #15209
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
  • lines changed 59, context: html, text, full: html, text
    starting lastz runs refs #15209
    
• src/hg/makeDb/doc/ce6.txt
  • lines changed 18, context: html, text, full: html, text
    adding lift over to ce11 refs #15209
    
• src/hg/makeDb/doc/chlSab2/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #11172
    
• src/hg/makeDb/doc/felCat8/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #14412
    
• src/hg/makeDb/doc/hg38/geneid.SGP.genes.txt
  • lines changed 29, context: html, text, full: html, text
    adding SGP geneid gene predictions refs #13214
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 6, context: html, text, full: html, text
    Fixing default vis of clusters track (as in hg19). refs #14731
    
• src/hg/makeDb/doc/macFas5/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #11174
    
• src/hg/makeDb/doc/manPen1/initialBuild.txt
  • lines changed 62, context: html, text, full: html, text
    in the pushQ 007602 refs #15515
    
• src/hg/makeDb/doc/micMur2/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #15292
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 23, context: html, text, full: html, text
    adding SGP geneid gene predictions refs #15616
    
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
  • lines changed 24, context: html, text, full: html, text
    done and in the pushQ 007601 refs #15056
    
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #15056
    
  • lines changed 1, context: html, text, full: html, text
    adding microsat track refs #15056
    
• src/hg/makeDb/doc/nasLar1/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #14437
    
• src/hg/makeDb/doc/ornAna2/initialBuild.txt
  • lines changed 51, context: html, text, full: html, text
    in the pushQ 007603 refs #15098
    
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 10, context: html, text, full: html, text
    add the microsat track refs #8231
    
• src/hg/makeDb/doc/rhiRox1/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    adding microsat track refs #14438
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 21, context: html, text, full: html, text
    adding SGP geneid gene predictions refs #15616
    
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 286, context: html, text, full: html, text
    adding lastz chain net to nanPar1 and add microsat track refs #9868
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding panPan1 to hgwbeta genbank updates, refs #8231
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added panPan1 to RR genbank update list
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 12, context: html, text, full: html, text
    Updating to our current reference format
    
• src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Correcting the trackDb type of genomicSuperDups: it is 'bed 6 +' not
    'bed 6 .'. hgTracks and hgc didn't rely on tdb->type because they
    recognized the table name genomicSuperDups. hgTables used the
    tableDescriptions table instead. hg/lib/hAnno.c looks at tdb->type
    first to save the time of looking it up in tableDescriptions, and "."
    tells it that there are no more fields after the bed fields.
    refs #15610
    
• src/hg/makeDb/trackDb/human/hg15/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Correcting the trackDb type of genomicSuperDups: it is 'bed 6 +' not
    'bed 6 .'. hgTracks and hgc didn't rely on tdb->type because they
    recognized the table name genomicSuperDups. hgTables used the
    tableDescriptions table instead. hg/lib/hAnno.c looks at tdb->type
    first to save the time of looking it up in tableDescriptions, and "."
    tells it that there are no more fields after the bed fields.
    refs #15610
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
  • lines changed 162, context: html, text, full: html, text
    change lables on UCSC genes and GENCODE genes
    
  • lines changed 137, context: html, text, full: html, text
    first pass on GENCODE genes HTML page.
    
  • lines changed 6, context: html, text, full: html, text
    fixed a few typos
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra.alpha
  • lines changed 3, context: html, text, full: html, text
    change lables on UCSC genes and GENCODE genes
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    change release tags on knownGene in preperation to push GENCODE Basic
    
  • lines changed 2, context: html, text, full: html, text
    switch to GENCODE Basic on hg38
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    change lables on UCSC genes and GENCODE genes
    
  • lines changed 2, context: html, text, full: html, text
    change GENCODE tracks to the way they were
    
  • lines changed 2, context: html, text, full: html, text
    change lables for Gencode tracks
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.ra
  • lines changed 2, context: html, text, full: html, text
    change lables on UCSC genes and GENCODE genes
    
  • lines changed 2, context: html, text, full: html, text
    change GENCODE tracks to the way they were
    
  • lines changed 2, context: html, text, full: html, text
    change lables for Gencode tracks
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing default vis of clusters track (as in hg19). refs #14731
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding caeAng2 for alignments to ce11 refs #15209
    
• src/hg/makeDb/trackDb/microsat.html
  • lines changed 8, context: html, text, full: html, text
    Updated reference to current format
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Correcting the trackDb type of genomicSuperDups: it is 'bed 6 +' not
    'bed 6 .'. hgTracks and hgc didn't rely on tdb->type because they
    recognized the table name genomicSuperDups. hgTables used the
    tableDescriptions table instead. hg/lib/hAnno.c looks at tdb->type
    first to save the time of looking it up in tableDescriptions, and "."
    tells it that there are no more fields after the bed fields.
    refs #15610
    
  • lines changed 2, context: html, text, full: html, text
    Found a couple more instances where 'bed N .' was used but 'bed N +' should
    be used because there are extra fields.
    refs #15610
    
• src/hg/makeDb/trackDb/worm/caeAng2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding caeAng2 for alignments to ce11 refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding caeAng2 for alignments to ce11 refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding caeAng2 for alignments to ce11 refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding caeAng2 for alignments to ce11 refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    adding worm base gene track refs #15209
    
• src/hg/mouseStuff/chainToPsl/chainToPsl.c
  • lines changed 11, context: html, text, full: html, text
    fixed skipping calculation of PSL match statistic in chainToPsl because of bogus code that was just hacked around instead of fixed. (no redmine)
    
• src/hg/pslStats/pslStats.c
  • lines changed 1, context: html, text, full: html, text
    fix pslStats computation of query coverage. It was not counting based aligned to Ns (no redmine)
    
• src/hg/pslStats/tests/expected/cdna2cdnaAlignTest.stats
  • lines changed 1, context: html, text, full: html, text
    fix pslStats computation of query coverage. It was not counting based aligned to Ns (no redmine)
    
• src/hg/pslStats/tests/expected/cdna2cdnaQueryTest.stats
  • lines changed 1, context: html, text, full: html, text
    fix pslStats computation of query coverage. It was not counting based aligned to Ns (no redmine)
    
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 1, context: html, text, full: html, text
    there may be on TrfPart symlink for a simple assembly refs #15209
    
• src/hg/utils/checkStaticHtmlLinks/checkStaticHtmlLinks.c
  • lines changed 611, context: html, text, full: html, text
    adding checkStaticHtmlLinks utility.
    
• src/hg/utils/checkStaticHtmlLinks/makefile
  • lines changed 3, context: html, text, full: html, text
    adding checkStaticHtmlLinks utility.
    
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 32, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
  • lines changed 1, context: html, text, full: html, text
    fixed buffer overflow in extreme test case (no readmind)
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.gp
  • lines changed 4, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.info
  • lines changed 5, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.gp
  • lines changed 4, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.info
  • lines changed 5, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gp
  • lines changed 102, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gtf
  • lines changed 102, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/input/ensemblWithVersions.gtf
  • lines changed 38, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/hg/utils/gtfToGenePred/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/inc/gff.h
  • lines changed 3, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/lib/gff.c
  • lines changed 6, context: html, text, full: html, text
    add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v319 preview1 refs #15624
    

• lines changed: 2660
• files changed: 97