larrym: changes by commit

review to branch (2009-04-21 to 2009-04-28) v205

• support -chromSize option
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.12 - lines changed: 28, context: html, text, full: html, text
• modify code to support the normal two column chromSize file format
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.13 - lines changed: 12, context: html, text, full: html, text
• use hgsql --host option instead of doing a ssh
  • src/hg/encode/encodeStatus/encodeStatus.pl 1.7 - lines changed: 1, context: html, text, full: html, text
• fix typo
  • src/hg/encode/encodeStatus/encodeStatus.pl 1.8 - lines changed: 1, context: html, text, full: html, text
• add DESTDIR so we can add this to userApps
  • src/hg/bedItemOverlapCount/makefile 1.8 - lines changed: 3, context: html, text, full: html, text
• add BINDIR so we can add this to userApps
  • src/hg/utils/bedExtendRanges/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
• fix mysql 'Commands out of sync' problem
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c 1.69 - lines changed: 3, context: html, text, full: html, text
• add colors
  • src/hg/encode/encodeValidate/config/cv.ra 1.90 - lines changed: 3, context: html, text, full: html, text
• add some colors
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.269 - lines changed: 3, context: html, text, full: html, text
• aampp => aamp
  • src/hg/encode/encodeValidate/config/labs.ra 1.6 - lines changed: 1, context: html, text, full: html, text
• some HAMethylSeq colors
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.270 - lines changed: 11, context: html, text, full: html, text