File Changes for braney

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

• src/hg/hgTracks/hgTracks.c
  • lines changed 3, 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/inc/trackHub.h
  • 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/lib/hubConnect.c
  • lines changed 10, 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/lib/trackHub.c
  • lines changed 60, 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/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    set up mRNA defaults the way we actually want them.
• src/hg/pslToBed/pslToBed.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/utils/hubCheck/hubCheck.c
  • lines changed 1, 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/utils/isca/buildISCA.csh
  • lines changed 55, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/checkISCA.sh
  • lines changed 73, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
  • lines changed 1, context: html, text, full: html, text
    some tweaks to ISCA load and validate. Only check bed fields on validate. #6553
• src/hg/utils/isca/isca.tables
  • lines changed 9, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/iscaWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/makefile
  • lines changed 20, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/validateISCA.sh
  • lines changed 30, context: html, text, full: html, text
    first pass at ISCA otto load (#5172)
  • lines changed 5, context: html, text, full: html, text
    some tweaks to ISCA load and validate. Only check bed fields on validate. #6553
• src/lib/basicBed.c
  • lines changed 4, context: html, text, full: html, text
    look at thickStart and thickEnd when checking to see if a bed is exactly the same. (#7045)
  • lines changed 10, 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)