All File Changes

v291_base to v292_preview (2013-10-21 to 2013-10-28) v292

• java/src/edu/ucsc/genome/util/LiftOverTest.java
  • lines changed 1, context: html, text, full: html, text
    Fixed LiftOverTest.java to use x86 binary instead of failing on i386 binary, refs #11983
• src/blat/blat.c
  • lines changed 2, context: html, text, full: html, text
    Incorporated code review feedback. #11972
• src/gfClient/gfClient.c
  • lines changed 0, context: html, text, full: html, text
    Incorporated code review feedback. #11972
• src/gfServer/gfServer.c
  • lines changed 3, context: html, text, full: html, text
    Incorporated code review feedback. #11972
• src/hg/encode3/encPipe/sampleBam/sampleBam.c
  • lines changed 7, context: html, text, full: html, text
    Making it keep chromosome 1, and be much less likely to pick a non-aligning read for the sample.
• src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makk
  • lines changed 1, context: html, text, full: html, text
    Updating production executable location.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makk
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    Updating production executable location.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 1, context: html, text, full: html, text
    Removing special treatment of replicate named 'both'
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/makk
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    Updating production executable location.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 4, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makk
  • lines changed 3, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    Removing special treatment of replicate named 'both'
• src/hg/encode3/validateFiles/VERSION.TXT
  • lines changed 2, context: html, text, full: html, text
    ENCODE: adding ability to tolerate leading blank lines before a fastq record -- thereby also handles trailing blank lines
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 3, context: html, text, full: html, text
    ENCODE: adding ability to tolerate leading blank lines before a fastq record -- thereby also handles trailing blank lines
• src/hg/encode3/validateManifest/VERSION.TXT
  • lines changed 12, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 78, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    Making blat top out at 75k instead of 25k reads.
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 1, context: html, text, full: html, text
    Changing links for Wikipedia from hgGene details page, older link had plugin no longer working. Comment line about script that tested working links also updated to new link. refs #12003
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 1, context: html, text, full: html, text
    Changing links for Wikipedia from hgGene details page, older link had plugin no longer working. Comment line about script that tested working links also updated to new link. refs #12003
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 5, context: html, text, full: html, text
    minor improvements suggested by angie in code review
  • lines changed 7, context: html, text, full: html, text
    Looking over Galt's edits to PSL section, made a few minor wording changes, refs #11964
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 6, context: html, text, full: html, text
    Making corrections to custom track help section based on Code Review, refs #11971
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Removing reference to top right matrix cell, per Ann's request.
  • lines changed 39, context: html, text, full: html, text
    added announcement for snp138 on hg19
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    removed extra <hr> tag
  • lines changed 41, context: html, text, full: html, text
    Added job announcement for Bob.
  • lines changed 5, context: html, text, full: html, text
    Changed url + date for job announcement at Bob's request.
• src/hg/htdocs/indexNews.html
  • lines changed 78, context: html, text, full: html, text
    added announcement for snp138 on hg19, refs #11438
  • lines changed 83, context: html, text, full: html, text
    Added job announcement for Bob.
  • lines changed 6, context: html, text, full: html, text
    Changed url + date for job announcement at Bob's request.
• src/hg/htdocs/staff.html
  • lines changed 13, context: html, text, full: html, text
    updating: moving Brooke to alumni, ML manager is Luvina, Danielle's last name, Morgan grad student, kate's title
• src/hg/inc/encode3/encode3Valid.h
  • lines changed 3, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 4, context: html, text, full: html, text
    If a genePred table includes the exonFrames column, beware... it maycontain transcripts with incomplete CDS that begin out-of-frame.
    So far we've been assuming that the CDS sequence begins in frame,
    which works fine for UCSC Genes and RefSeq. However, less tidy
    sets such as Ensembl and Gencode Comprehensive have lots of
    out-of-frame CDSs.
    In order to not have incorrect translation to peptide sequence,
    we need to use a padded CDS sequence. For example, if the
    first coding exon's frame is 1, we now add an 'N' at the beginning
    of the coding sequence to align it to the correct frame. We also
    look out for subsequent surprises in exonFrames, though I expect
    those to be rare. Of course, when the coding sequence is tweaked
    like that, care must be taken when modifying it with an alt allele.
    fixes #11990
    refs #11175
    
• src/hg/lib/annoStreamDb.c
  • lines changed 2, context: html, text, full: html, text
    When doing a single-region query, if we don't get any results fromthe query, set self->eof so there isn't infinite recursion in
    asdNextRow (thanks to nextRowFromBuffer setting self->needQuery
    because the buffer is empty).
    fixes #11988
    refs #11110
    
• src/hg/lib/borf.c
  • lines changed 2, context: html, text, full: html, text
    Changed location for bestorf program and directories to a location on the hive as were in /projects/compbio before and this is no longer mounted on hgwdev.
• src/hg/lib/encode3/encode3Valid.c
  • lines changed 8, context: html, text, full: html, text
    Trying to resolve several issues for valdateManifest and validateFiles including re-factoring some enriched_in checking from edwSubmit into a library.
• src/hg/lib/gpFx.c
  • lines changed 119, context: html, text, full: html, text
    If a genePred table includes the exonFrames column, beware... it maycontain transcripts with incomplete CDS that begin out-of-frame.
    So far we've been assuming that the CDS sequence begins in frame,
    which works fine for UCSC Genes and RefSeq. However, less tidy
    sets such as Ensembl and Gencode Comprehensive have lots of
    out-of-frame CDSs.
    In order to not have incorrect translation to peptide sequence,
    we need to use a padded CDS sequence. For example, if the
    first coding exon's frame is 1, we now add an 'N' at the beginning
    of the coding sequence to align it to the correct frame. We also
    look out for subsequent surprises in exonFrames, though I expect
    those to be rare. Of course, when the coding sequence is tweaked
    like that, care must be taken when modifying it with an alt allele.
    fixes #11990
    refs #11175
    
• src/hg/lib/liftOver.c
  • lines changed 2, context: html, text, full: html, text
    fixes #11991 strand output can be wrong when -multiple used with bed6 stands and it hits multiple chains. The pattern by which the output strand has been wrong is complex. Only the strand info is incorrect. The other coordinates are OK.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    Regenerating snp138 tables with one last allele frequency fix.refs #11438, #11954
    
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 1, context: html, text, full: html, text
    Changing links for Wikipedia from hgGene details page, older link had plugin no longer working. Comment line about script that tested working links also updated to new link. refs #12003
• src/hg/makeDb/genbank/etc/dbload
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    change genbank back to using hgnfs1
• src/hg/makeDb/genbank/etc/euronode-copy
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    change genbank back to using hgnfs1
• src/hg/makeDb/genbank/etc/euronode-dbload
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    change genbank back to using hgnfs1
• src/hg/makeDb/genbank/etc/hgnfs1-copy
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    change genbank back to using hgnfs1
• src/hg/makeDb/genbank/etc/rr-dbload
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    change genbank back to using hgnfs1
• src/hg/makeDb/trackDb/apis/chainDm1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/blastzBestHuman.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/blastzHuman.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chain.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainCi2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainDm1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainDm2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainDm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chicken/galGal2/netSyntenyHg16.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chimp/panTro1/axtNetHg16.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chimp/panTro1/humanDels.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chimp/panTro2/multiz8way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainAnoGam1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainApiMel1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainApiMel2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDm1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDp2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDp3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroAna1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroAna2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroEre1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroGri1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroMoj1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroMoj2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroPer1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroSec1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroSim1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroVir1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroVir2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroYak1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/chainDroYak2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netAnoGam1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netApiMel1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netApiMel2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDp2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDp3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroAna1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroAna2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroEre1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroGri1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroMoj1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroMoj2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroPer1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroSec1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroSim1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroVir1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroVir2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroYak1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/drosophila/netDroYak2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/fugu/blastzDanRer1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/fugu/blastzDanRer2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/fugu/chainDanRer2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/blastzBestRat.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/hg16/blastzBestMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/blastzBestRn3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/blastzMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/blastzRn3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/blastzTightMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/blastzTightMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/chimpDels.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/encodeTbaAlign.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/encodeTbaCons.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/encodeTbaElements.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/humorMm3Rn3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/multizMm3Rn3GalGal2_phyloHMM.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/multizMm3Rn3Pt0.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/mzPt1Mm3Rn3Gg2_pHMM.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/netRxBestPt0.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/rBestChainPanTro1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg16/rBestNetPanTro1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/ECgene.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/hg17/blastzBestMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzBestMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzBestRn3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzDanRer1.html
  • lines changed 1, context: html, text, full: html, text
    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzDanRer2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzRn3.html
  • lines changed 1, context: html, text, full: html, text
    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzTetNig1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzTightMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzTightMm5.html
  • lines changed 1, context: html, text, full: html, text
    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/blastzTightRn3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/consIndelsHgMmCanFam.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/hg17/encodeEvoFold.html
  • lines changed 1, context: html, text, full: html, text
    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/encodeSangerChip.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/hg17/encodeTbaCons.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/encodeUcsdNgGif.html
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    Fixing links on hg17 track desciption pages
• src/hg/makeDb/trackDb/human/hg17/encode_tba23EvoFold.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/multiz10way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg17/multiz8way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/chainSelf2K.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/encodeEvoFold.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/encodeMsaTbaDec07.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/multiz17way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg18/netSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    Put orgs in Table 1 in alphabetical order. refs #11808.
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/description.html
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    Added link to GRC Assembly Terminology page (redmine #8823)
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/human/humMusL.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/humanChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/makefile
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/blastzHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm10/description.html
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    Added link to GRC Assembly Terminology page (redmine #8823)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    making snp137Common track dense on mm10
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    corrected spelling mistake
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm7/blastzSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm9/description.html
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    Added link to GRC Assembly Terminology page (redmine #8823)
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/mm9/netRn4Test.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouse/netSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouseChain.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouseNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/mouseRef.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/musHumL.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/net.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/netCi2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/netDm1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/netDm2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/netDm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/opossum/chainMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/other/braNey1/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    add ensembl mRNAs alignment for use in evaulating ucsc genbank filters
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    added gencode V17 to braNey1
• src/hg/makeDb/trackDb/other/centromeres1/description.html
  • lines changed 49, context: html, text, full: html, text
    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromeres1/gap.html
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromeres1/gold.html
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromeres1/trackDb.encode.ra
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromeres1/trackDb.ra
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromers1/description.html
  • lines changed 4, context: html, text, full: html, text
    some cosmetic changes for karen's centromere browser
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    one more cosmetic change
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    one more cosmetic centromere change
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromers1/gap.html
  • lines changed 37, context: html, text, full: html, text
    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromers1/gold.html
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromers1/trackDb.encode.ra
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/centromers1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    some cosmetic changes for karen's centromere browser
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    more cosmetics on centromer(e)s
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
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    updates to the wetlab browser
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    adding more tracks to repeats2 for wetlab
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 1, context: html, text, full: html, text
    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzBestHg15.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzBestHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzBestMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzBestMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzHg15.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzTightHg15.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzTightHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzTightMm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/blastzTightMm4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/multizHg15Mm3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn3/syntenyHg15.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/ratChain.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/ratNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/rhesus/rheMac2/multiz5waySyn.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/sacCer/sacCer3/strainAlignments.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/blastzFr1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/blastzHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/blastzMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/chainMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/tetraodon/netSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/trackDb.ra
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    hiding snp137 track
• src/hg/makeDb/trackDb/worm/cb1/blastzCe1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/cb1/ce1Chain.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/blastzSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce2/netCb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCaePb2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCb3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCe4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainCe6.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCaeJap1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCaePb1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCaePb2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCaeRem2.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCaeRem3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCb3.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCe4.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netCe6.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/worm/netPriPac1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/blastzFr1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/blastzHg17.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/blastzMm5.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/blastzTetNig1.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer3/netSelf.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.chainNet.ra
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    Updated trackDb.chainNet.ra files to fix display of older chain/nets that are still current on some older danRer assemblies
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
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    Correcting lastz link to current Miller lab website
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.chainNet.ra
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    Updated trackDb.chainNet.ra files to fix display of older chain/nets that are still current on some older danRer assemblies
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
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    Updated trackDb.chainNet.ra files to fix display of older chain/nets that are still current on some older danRer assemblies
• src/hg/pslPretty/pslPretty.c
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    Incorporated code review feedback. #11972
• src/hg/pslSort/pslSort.c
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    Incorporated code review feedback. #11972
• src/hg/qaPushQ/makefile
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    updating for new building on dev so it will use /cgi-bin-beta/, the beta build location
• src/hg/utils/otto/gwas/checkGwas.sh
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    upgrade to snp138 for GWAS use
• src/hg/utils/otto/gwas/makefile
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    upgrade to snp138 for GWAS use
• src/inc/common.mk
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    on hgwdev use the static MySQL libraries refs #11966
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    now using static ssl and crypto libs on hgwdev build refs #12005
• src/inc/linefile.h
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    Adding lineFileNextRealWithSize.
• src/inc/net.h
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    set network default read write timeout for tcp connections to browser defaults -- around 2 minutes=120 seconds. Specific applications can call the new function setReadWriteTimeouts on an open socket if they need them to be longer or shorter.
• src/lib/linefile.c
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    Adding lineFileNextRealWithSize.
• src/lib/net.c
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    set network default read write timeout for tcp connections to browser defaults -- around 2 minutes=120 seconds. Specific applications can call the new function setReadWriteTimeouts on an open socket if they need them to be longer or shorter.
• src/userApps/README
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    need mysql 5.5 on ubuntu now refs #9149
• src/utils/faToTwoBit/faToTwoBit.c
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    Incorporated code review feedback. #11972
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
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    Making this tolerate new lines in fastq files between stanzas.
• src/utils/mapViewerToGenePred/makefile
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    adding ncbi mapviewer to genepred converter
• src/utils/mapViewerToGenePred/mapViewerToGenePred
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    adding ncbi mapviewer to genepred converter
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    fix typo in help message
• src/utils/nibFrag/nibFrag.c
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    Incorporated code review feedback. #11972
• src/utils/qa/checkGenomeMysql
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    checkGenomeMysql now tests all public server IP addresses instead of hard-coding public-mysql1, etc.
• src/utils/qa/weeklybld/buildBeta.csh
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    OK to run make -j 32 for utils and beta build refs #11966
• src/utils/qa/weeklybld/buildEnv.csh
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    need to use static SQL libraries refs #11966
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    v292 preview1
• src/utils/qa/weeklybld/buildUtils.csh
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    OK to run make -j 32 for utils and beta build refs #11966

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• files changed: 336