Commits for braney

v274_base to v275_preview (2012-10-09 to 2012-10-16) v275

• look at thickStart and thickEnd when checking to see if a bed is exactly the same. (#7045)
  • src/lib/basicBed.c - lines changed 4, context: html, text, full: html, text
• first pass at ISCA otto load (#5172)
  • src/hg/utils/isca/buildISCA.csh - lines changed 55, context: html, text, full: html, text
  • src/hg/utils/isca/checkISCA.sh - lines changed 73, context: html, text, full: html, text
  • src/hg/utils/isca/isca.tables - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/isca/iscaWrapper.sh - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/isca/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/isca/validateISCA.sh - lines changed 30, context: html, text, full: html, text
• set up mRNA defaults the way we actually want them.
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 2, context: html, text, full: html, text
• this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 60, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 1, context: html, text, full: html, text
• tweak how pslToBed generates non-coding beds so the browser displays them properly, twich bedExact to compare non-coding beds just by checking if both of them have thickStart==thickEnd. (#7045)
  • src/hg/pslToBed/pslToBed.c - lines changed 1, context: html, text, full: html, text
  • src/lib/basicBed.c - lines changed 10, context: html, text, full: html, text
• some tweaks to ISCA load and validate. Only check bed fields on validate. #6553
  • src/hg/utils/isca/checkISCA.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/isca/validateISCA.sh - lines changed 5, context: html, text, full: html, text