File Changes for hiram

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v301_preview to v301_preview2 (2014-05-26 to 2014-06-02) v301

src/hg/makeDb/doc/echTel2.txt
- lines changed 15, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/fr1.txt
- lines changed 27, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/galGal2.txt
- lines changed 28, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/hg16.txt
- lines changed 26, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/hg38.txt
- lines changed 138, context: html, text, full: html, text
  adding panTro4 and monDom5 lastz chain net refs #13300
- lines changed 30, context: html, text, full: html, text
  adding panTro4 and monDom5 lastz chain net refs #13300
- lines changed 2, context: html, text, full: html, text
  correct directory name for cytoBand refs #11681
src/hg/makeDb/doc/mm10.txt
- lines changed 12, context: html, text, full: html, text
  run up rheMac2 mm10 liftOver per user request refs #13319
src/hg/makeDb/doc/mm9.txt
- lines changed 16, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/ochPri2.txt
- lines changed 8, context: html, text, full: html, text
  lift over to ochPri3 refs #9347
src/hg/makeDb/doc/panTro1.txt
- lines changed 27, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/doc/rn3.txt
- lines changed 33, context: html, text, full: html, text
  unmasked CpG island track contruction refs #1268
src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
- lines changed 17, context: html, text, full: html, text
  adding in Arctic lamprey letCam1 refs #13300
src/hg/makeDb/trackDb/trackDb.chainNet.afrotheria.ra
- lines changed 176, context: html, text, full: html, text
  catching up chain net tracks refs #13300
- lines changed 118, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra
- lines changed 530, context: html, text, full: html, text
  catching up with chain net definitions refs #13300
- lines changed 126, context: html, text, full: html, text
  catching up chain net tracks refs #13300
src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra
- lines changed 353, context: html, text, full: html, text
  catching up chain net tracks refs #13300
src/hg/makeDb/trackDb/trackDb.chainNet.fish.ra
- lines changed 471, context: html, text, full: html, text
  catching up chain net tracks refs #13300
src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
- lines changed 884, context: html, text, full: html, text
  catching up chain net tracks refs #13300
- lines changed 59, context: html, text, full: html, text
  adding chlSab1 - Green monkey - Chlorocebus sabaeus and phyCat1 - Sperm whale - Physeter catodon refs #13300
- lines changed 177, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
- lines changed 59, context: html, text, full: html, text
  adding eriEur2 chain net refs #10272
src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
- lines changed 176, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
- lines changed 176, context: html, text, full: html, text
  catching up with chain net definitions refs #13300
- lines changed 59, context: html, text, full: html, text
  catching up chain net tracks refs #13300
- lines changed 59, context: html, text, full: html, text
  adding chlSab1 - Green monkey - Chlorocebus sabaeus and phyCat1 - Sperm whale - Physeter catodon refs #13300
- lines changed 59, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
- lines changed 353, context: html, text, full: html, text
  catching up chain net tracks refs #13300
- lines changed 118, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
src/hg/makeDb/trackDb/trackDb.ra
- lines changed 9, context: html, text, full: html, text
  catching up chain net tracks refs #13300
- lines changed 1, context: html, text, full: html, text
  catching up chain net track definitions refs #10272
src/hg/utils/automation/doBlastzChainNet.pl
- lines changed 3, context: html, text, full: html, text
  correctly md5sum the syntenic net downloads refs #13300
src/hg/utils/phyloTrees/130way.dissect.txt
- lines changed 1813, context: html, text, full: html, text
  raising the bar to 130 species refs #10272
src/hg/utils/phyloTrees/130wayChainNet.pl
- lines changed 212, context: html, text, full: html, text
  raising the bar to 130 species refs #10272
src/hg/utils/phyloTrees/131way.commonNames.nh
- lines changed 131, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/131way.dissect.txt
- lines changed 1827, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/131way.nh
- lines changed 131, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/131way.scientificNames.nh
- lines changed 131, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/131wayChainNet.pl
- lines changed 212, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/commonNames.sh
- lines changed 1, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/findScores.pl
- lines changed 1, context: html, text, full: html, text
  correctly parsing new style Q matrix settings refs #13300
src/hg/utils/phyloTrees/makefile
- lines changed 7, context: html, text, full: html, text
  adding sperm whale refs #10272
src/hg/utils/phyloTrees/scientificNames.sh
- lines changed 1, context: html, text, full: html, text
  adding sperm whale refs #10272
src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
  v301 preview2 refs #13189

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