braney: changes by commit

branch to review (2010-03-23 to 2010-03-30) v228

• a simple BAM test
  • src/hg/encode/validateFiles/tests/test3.bam 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/test3.right.txt 1.1 - lines changed: 0, context: html, text, full: html, text
• a small test for bigWig
  • src/hg/encode/validateFiles/tests/test4.bw 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/test4.right.txt 1.1 - lines changed: 0, context: html, text, full: html, text
• add a couple of tests for bigWig and BAM
  • src/hg/encode/validateFiles/makefile 1.5 - lines changed: 4, context: html, text, full: html, text
• add bigWig
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.75 - lines changed: 49, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm 1.60 - lines changed: 1, context: html, text, full: html, text
• some small edits, addition of link to protocol
  • src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html 1.2 - lines changed: 4, context: html, text, full: html, text
• fix up some printf's and add flag allowing non-native chroms
  • src/hg/encode/validateFiles/validateFiles.c 1.37 - lines changed: 12, context: html, text, full: html, text
• add support for BAM download only
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.219 - lines changed: 18, context: html, text, full: html, text