Commits for kate

v282_preview2 to v282_base (2013-04-09 to 2013-04-16) v282

• Add two more scoring methods (2 std devs, asinh). refs #10569
  • src/hg/makeDb/doc/encodeAwgHg19.txt - lines changed 12, context: html, text, full: html, text
  • src/utils/bedScore/bedScore.c - lines changed 103, context: html, text, full: html, text
• Add tests for std2 and asinh scoring methods. refs #10569
  • src/utils/bedScore/tests/expected/broadGm12878Ctcf.jan2011.asinh.narrowPeak - lines changed 40006, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/uniform.bed - lines changed 20, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/broadGm12878Ctcf.jan2011.asinh.narrowPeak - lines changed 40006, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/uniform.bed - lines changed 20, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 13, context: html, text, full: html, text
• Fix test makefile to work with default targets from build dir. refs #10569
  • src/utils/bedScore/tests/expected/encodeStd2Test.bed - lines changed 44159, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 21, context: html, text, full: html, text
• More clean-up of makefile to fit well in new makefile scheme
  • src/utils/bedScore/tests/makefile - lines changed 3, context: html, text, full: html, text
• Update md5sums after adding scores to download files. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra - lines changed 691, context: html, text, full: html, text
• Add quality term to CV. Create release notes. refs #10042
  • src/hg/makeDb/doc/encodeAwgHg19.txt - lines changed 188, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgTfbsUniform.release1.notes - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 30, context: html, text, full: html, text
• Update release notes. refs #10042
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgTfbsUniform.release1.notes - lines changed 3, context: html, text, full: html, text
• Wrap-up for QA. refs #10042
  • src/hg/makeDb/doc/encodeAwgHg19.txt - lines changed 1, context: html, text, full: html, text
• Update track description (quality, filtering). refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 5, context: html, text, full: html, text
• Fix a URL. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 1, context: html, text, full: html, text
• Wrap-up for QA. refs #10042
  • src/hg/makeDb/doc/encodeAwgHg19.txt - lines changed 1, context: html, text, full: html, text
• Add info about score to track description. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 9, context: html, text, full: html, text
• Reformat to <=100 lines. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 124, context: html, text, full: html, text
• Format corrections. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 5, context: html, text, full: html, text
• Retire older news to archive, in preparation for adding info about new FAQ page. refs #9712
  • src/hg/htdocs/ENCODE/index.html - lines changed 31, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/newsarch.html - lines changed 39, context: html, text, full: html, text
• Add news and link for new FAQ page. Also add news item for January release of AWG Dnase tracks. refs #9712
  • src/hg/htdocs/ENCODE/index.html - lines changed 69, context: html, text, full: html, text