def __cmp__(self, other):
if self.type != other.type:
return self.type - other.type
else:
if self.type == vcfKey.REGULAR:
if self.chromosome == other.chromosome:
return self.position - other.position
else:
myRank = chromosomeRank.get(self.chromosome, len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome, len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
elif self.type == vcfKey.CONTIG:
myRank = chromosomeRank.get(self.chromosome, len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome, len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
elif self.type == vcfKey.OTHER_META:
# I could probably do a better job of this, but the .vcf spec doesn't require it so I don't care
return cmp(self.line, other.line)
elif self.type == vcfKey.EMPTY:
return 0
else:
raise Exception("Duplicate ##fileformat or header lines!")
def __cmp__(self, other):
if self.chromosome == other.chromosome:
return self.start - other.start
else:
myRank = chromosomeRank.get(self.chromosome, len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome, len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
def __cmp__(self, other):
if self.chromosome == other.chromosome:
return self.start - other.start
else:
myRank = chromosomeRank.get(self.chromosome, len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome,
len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
def __cmp__(self, other):
if self.type != other.type:
return self.type - other.type
else:
if self.type == vcfKey.REGULAR:
if self.chromosome == other.chromosome:
return self.position - other.position
else:
myRank = chromosomeRank.get(self.chromosome,
len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome,
len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
elif self.type == vcfKey.CONTIG:
myRank = chromosomeRank.get(self.chromosome,
len(chromosomeRank))
otherRank = chromosomeRank.get(other.chromosome,
len(chromosomeRank))
result = myRank - otherRank
if result == 0:
# we already know they're not the same chromosome; our behavior is to sort unknown chromosomes alphabetically
return cmp(self.chromosome, other.chromosome)
else:
return result
elif self.type == vcfKey.OTHER_META:
# I could probably do a better job of this, but the .vcf spec doesn't require it so I don't care
return cmp(self.line, other.line)
elif self.type == vcfKey.EMPTY:
return 0
else:
raise Exception("Duplicate ##fileformat or header lines!")