File Changes for hiram

v294_preview2 to v294_base (2014-01-06 to 2014-01-13) v294

• src/hg/inc/versionInfo.h
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    New version number v294
• src/hg/makeDb/doc/galGal4.txt
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    animalQtl reloading refs #10954
• src/hg/makeDb/doc/hg19.txt
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    liftOver to hg38 done refs #11681
• src/hg/makeDb/doc/hg38.txt
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    up to date repeat masker procedures, trf simple repeats and genscan refs #11681
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    rerunning repeat masking refs #11682
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    adding par and centromere tracks refs #11681
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    the alternate/haplotype sequence lastz chain net psl track refs #11681
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    done with rmskHmmer and added hg38.contigs.2bit build refs #11681
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    add repeat masker analysis refs #11681
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    fixup gc5BaseBw bbi directory path, and running cpgIslands on contig sequence refs #11681
• src/hg/makeDb/genbank/etc/genbank.conf
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    preparing for GRCh38/hg38 genbank run refs #11681
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
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    ignore the noSplit arguments to make it become the default refs #11681
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
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    adding alternate haplotype sequences chain net psl locations track refs #11681
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
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    documentation for the centromere track refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html
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    update the featureBits and add the class summary refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskCM.html
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    adding RepeatMasker cross-match documentation refs #11681
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    add the class summary refs #11681
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    adding HMMER rmsk documentation refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html
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    add the class summary refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskHmmer.html
  • lines changed 127, context: html, text, full: html, text
    adding HMMER rmsk documentation refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    move the rmsk experments to experimental track group refs #11681
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    adding alternate haplotype sequences chain net psl locations track refs #11681
• src/hg/makeDb/trackDb/trackDb.ra
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    add url to animalQtl refs #10954
• src/hg/utils/automation/doRepeatMasker.pl
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    need to use 32Gb and 4 CPU limits on HMMER refs #11681
• src/hg/utils/automation/makeGenomeDb.pl
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    new convention for location of bbi files, in bbi/tableName/... refs #11681
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
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    adding other genomes found on the RR for completeness refs #10272
• src/product/scripts/kentSrcUpdate.sh
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    add directory safety checks as it starts refs #9104
• src/utils/qa/weeklybld/buildEnv.csh
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    v294 final build refs #12191