forceChr = getConfigBoolOption(configParser, section, "forceChr", False)
cachePages = getConfigIntOption(configParser, section, "cachePages", 0)
forceChr = getConfigBoolOption(configParser, section, "forceChr", False)
cachePages = getConfigIntOption(configParser, section, "cachePages", 0)
snpPropertiesList = getSNPs(hitfile, uniqStartMin, totalRatioMin, doCache, cachePages, doSplices, forceChr)
for snpEntry in snpPropertiesList:
outline = "%1.2f\t%1.2f\t%s\t%d\t%d\t%d\t\t%d\t%s\n" % snpEntry
snpPropertiesList = getSNPs(hitfile, uniqStartMin, totalRatioMin, doCache, cachePages, doSplices, forceChr)
for snpEntry in snpPropertiesList:
outline = "%1.2f\t%1.2f\t%s\t%d\t%d\t%d\t\t%d\t%s\n" % snpEntry
back = "%s:%s" % (str(start), change)
uniqBaseDict = {change: 1}
totalBaseDict = {change: 1}
back = "%s:%s" % (str(start), change)
uniqBaseDict = {change: 1}
totalBaseDict = {change: 1}
- if mismatchDict.has_key(change_at):
- (uniqueReadCount, totalCount, back, uniqBaseDict, totalBaseDict) = mismatchDict[change_at]
+ if change_at in mismatchDict:
uniqBaseDict[change] += 1 # dict contains total unique read counts
back = "%s,%s" % (back, pos)
uniqBaseDict[change] += 1 # dict contains total unique read counts
back = "%s,%s" % (back, pos)