All File Changes

v291_preview2 to v291_base (2013-10-14 to 2013-10-21) v291

• src/blat/blat.c
  • lines changed 35, context: html, text, full: html, text
    Fixed some typos and formatting probs in conjunction with updating blat spec.
• src/gfClient/gfClient.c
  • lines changed 11, context: html, text, full: html, text
    Fixed some typos and formatting probs in conjunction with updating blat spec.
• src/gfServer/gfServer.c
  • lines changed 27, context: html, text, full: html, text
    Fixed some typos and formatting probs in conjunction with updating blat spec.
• src/hg/hgTables/hal.c
  • lines changed 64, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/hgTables/hgTables.c
  • lines changed 4, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/hgTables/joining.c
  • lines changed 12, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/hgTables/mainPage.c
  • lines changed 8, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    implement maf output in table browser
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 37, context: html, text, full: html, text
    Added bigDataUrl example in mulitple places on page, updated some track type links and added a note about sharing custom tracks through sessions, refs #10293,#10902
  • lines changed 40, context: html, text, full: html, text
    Adding problem/solution sections about Dropbox and Google Drive as hints to users, per note 30 refs #10078
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 6, context: html, text, full: html, text
    Added Brennan et al. pub at David's request.
• src/hg/inc/gpFx.h
  • lines changed 5, context: html, text, full: html, text
    Another fix for ML #11775: use a real alternate allele for intergenicvariants, so users aren't misled by the VEP placeholder "-".
    
• src/hg/inc/mdb.h
  • lines changed 12, context: html, text, full: html, text
    Speeding up trix file generation by using the mdb and cv lib code. Redmine #11951
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v291
• src/hg/lib/annoGratorGpVar.c
  • lines changed 33, context: html, text, full: html, text
    Another fix for ML #11775: use a real alternate allele for intergenicvariants, so users aren't misled by the VEP placeholder "-".
    
• src/hg/lib/gpFx.c
  • lines changed 4, context: html, text, full: html, text
    Heroic ML #11775 users provoked yet another bug: an insertion at theCDS/UTR boundary was falling through the cracks and nothing was output
    for it. It should be classified as UTR.
    refs #11775
    
  • lines changed 1, context: html, text, full: html, text
    Another fix for ML #11775: use a real alternate allele for intergenicvariants, so users aren't misled by the VEP placeholder "-".
    
• src/hg/lib/mdb.c
  • lines changed 33, context: html, text, full: html, text
    Speeding up trix file generation by using the mdb and cv lib code. Redmine #11951
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 126, context: html, text, full: html, text
    running up melGal1 and taeGut2 chain net refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 46, context: html, text, full: html, text
    1. Rebuilding ucscAlleleFreq (and hence snp138) because when updatingthe allele frequencies in August, I forgot to use the new -deDupTGP
    command line arg.
    2. As b0b suggested, I'm including variants in snp138Common if they
    are 100% non-reference. Technically their MAF is 0 -- but differing
    from the reference sure is common! And those wishing to filter out
    common variants would want to filter those out.
    refs #11438
    
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    take out verbose flag on rsyncs to eurotoad
• src/hg/makeDb/genbank/etc/euronode-dbload
  • lines changed 2, context: html, text, full: html, text
    take out verbose flag on rsyncs to eurotoad
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 138, context: html, text, full: html, text
    reorganize the genbank db lists to be prioritized
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 161, context: html, text, full: html, text
    reorganize the genbank db lists to be prioritized
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Uncommented lines that Fan had previously commented out. The underlying problem that caused them to be commented out no longer exists. (redmine #11675)
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cat/felCat3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau5/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/elephant/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 2, context: html, text, full: html, text
    Correcting link on Ensembl genes description page
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/horse/equCab1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/horse/equCab2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added include statement for new trackDb.chainNet.ra (redmine #11913)
• src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/human/altGraphX.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60Pval.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60PvalStrict.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SignalStrict.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60Sites.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SitesStrict.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/consIndelsHgMmCanFam.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/encodeAffyRnaSignal.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/encodeAffyRnaTransfrags.html
  • lines changed 1, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganAlign.html
  • lines changed 2, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • lines changed 3, context: html, text, full: html, text
    fixing some broken links on hg17 description pages
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing URL lines so links to old DGV database are not presented in hgc for hg17 refs #11200
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 4, context: html, text, full: html, text
    fixup name lists in gene tracks codon translation table refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 27, context: html, text, full: html, text
    reset phyloP track default on refs #10272
• src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/opossum/monDom1/description.html
  • lines changed 2, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/opossum/monDom4/description.html
  • lines changed 2, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • lines changed 2, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/panda/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/rabbit/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/rat/rn3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/rat/rn4/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/sheep/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • lines changed 13, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Round 2 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/zebrafish/danRer3/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/zebrafish/danRer4/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/zebrafish/danRer5/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
  • lines changed 1, context: html, text, full: html, text
    fixing NHGRI photo credit links for a lot of species, refs #10410
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
  • lines changed 2, context: html, text, full: html, text
    Added include statement for new trackDb.chainNet.ra (redmine #11913)
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    Round 1 of trackDb.chainNet.ra changes for release of mm10 chain/nets (redmine #11913)
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    now using mysql_config to find MYSQLINC and MYSQLLIBS refs #11899 #9149
• src/hg/pslPretty/makefile
  • lines changed 20, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/pslPretty.c
  • lines changed 11, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/hg/pslPretty/test/expected/bad.axt
  • lines changed 0, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/bad.output
  • lines changed 2, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/dnax.axt
  • lines changed 8, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/empty.axt
  • lines changed 0, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/empty.output
  • lines changed 1, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/justComments.axt
  • lines changed 0, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/expected/justComments.output
  • lines changed 0, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/input/bad.psl
  • lines changed 1, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/input/empty.psl
  • lines changed 0, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslPretty/test/input/justComments.psl
  • lines changed 2, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/hg/pslReps/pslReps.c
  • lines changed 17, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/hg/pslSort/pslSort.c
  • lines changed 12, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/hg/sqlEnvTest.sh
  • lines changed 4, context: html, text, full: html, text
    now using mysql_config to find MYSQLINC and MYSQLLIBS refs #11899 #9149
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 8, context: html, text, full: html, text
    fixup previous releaseidentity check and correctly find species name when not in dbDb refs #11675
• src/hg/utils/automation/categorizeSnps.pl
  • lines changed 82, context: html, text, full: html, text
    1. Rebuilding ucscAlleleFreq (and hence snp138) because when updatingthe allele frequencies in August, I forgot to use the new -deDupTGP
    command line arg.
    2. As b0b suggested, I'm including variants in snp138Common if they
    are 100% non-reference. Technically their MAF is 0 -- but differing
    from the reference sure is common! And those wishing to filter out
    common variants would want to filter those out.
    refs #11438
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 2, context: html, text, full: html, text
    1. Rebuilding ucscAlleleFreq (and hence snp138) because when updatingthe allele frequencies in August, I forgot to use the new -deDupTGP
    command line arg.
    2. As b0b suggested, I'm including variants in snp138Common if they
    are 100% non-reference. Technically their MAF is 0 -- but differing
    from the reference sure is common! And those wishing to filter out
    common variants would want to filter those out.
    refs #11438
    
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 10, context: html, text, full: html, text
    fixup previous releaseidentity check and correctly find species name when not in dbDb refs #11675
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 1, context: html, text, full: html, text
    revCompSnp's reversing of the sorted reverse-complemented alleleswas enough to maintain sorting of [ACGT] alleles, but not when '-'
    is in the mix. When merging lists that weren't correctly sorted,
    we ended up with two entries for '-' in the combined output.
    Now we're outright sorting them so that won't happen again.
    refs #11943, #11954
    
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • lines changed 45, context: html, text, full: html, text
    Speeding up trix file generation by using the mdb and cv lib code. Redmine #11951
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 3, context: html, text, full: html, text
    check in some changes to the GWAS otto scripts
• src/hg/utils/otto/gwas/makefile
  • lines changed 1, context: html, text, full: html, text
    check in some changes to the GWAS otto scripts
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 4, context: html, text, full: html, text
    check in some changes to the GWAS otto scripts
• src/hg/utils/otto/gwas/validateGwas.sh
  • lines changed 1, context: html, text, full: html, text
    check in some changes to the GWAS otto scripts
• src/inc/common.mk
  • lines changed 13, context: html, text, full: html, text
    now using mysql_config to find MYSQLINC and MYSQLLIBS refs #11899 #9149
  • lines changed 3, context: html, text, full: html, text
    fixup slow behavior in make clean with new mysql_config business refs #11899 #9149
  • lines changed 8, context: html, text, full: html, text
    avoid dynamic MySQL libraries on Mac OSX refs #11899 149
• src/lib/psl.c
  • lines changed 14, context: html, text, full: html, text
    fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
    
• src/product/README.building.source
  • lines changed 26, context: html, text, full: html, text
    mention the new mysql_config business refs #11899 #9149
• src/utils/faToNib/faToNib.c
  • lines changed 2, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/utils/faToTwoBit/faToTwoBit.c
  • lines changed 4, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/utils/nibFrag/nibFrag.c
  • lines changed 3, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
• src/utils/qa/checkTrackUiLinks.csh
  • lines changed 55, context: html, text, full: html, text
    working with Matt. removed checking of local ucsc links, esp topbar pulldowns. checking links one-by-one instead of all at once (was using checkLinks option on htmlCheck) so we can fix timeout on slow links later. now checking on beta if RR is specified, so it doesn't hammer RR unnecessarily. renamed some variables so they are easier to understand when reading script. dropped hgw7&8 from RR list. merged description.html into tables list, even though that's a different cgi. refs #11809
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v291 preview2
  • lines changed 3, context: html, text, full: html, text
    v291 final build
• src/utils/twoBitToFa/twoBitToFa.c
  • lines changed 10, context: html, text, full: html, text
    Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.

• lines changed: 1423
• files changed: 140