Changes

#Inspect length, defined as length of alternate allele minus length of reference allele.

#Inspect length, defined as length of alternate allele minus length of reference allele.

##if length = 0

##if length = 0

###if length(ref) = 1 and nucleotides differ, classify as SNP

###if length(ref) = 1 and nucleotides differ, classify as SNP (count ts and tv too)

###if length(ref) > 1  

###if length(ref) > 1  

####if all nucleotides differ, classify as MNP

####if all nucleotides differ, classify as MNP (count ts and tv too)

####if not all nucleotides differ, classify as CLUMPED

####if not all nucleotides differ, classify as CLUMPED (count ts and tv too)

##if length <math>\ne</math> 0, classify as INDEL

##if length <math>\ne</math> 0, classify as INDEL

###if shorter allele is of length 1

###if shorter allele is of length 1

####if shorter allele does not match either of the end nucleotides of the longer allele, classify as SNP  

####if shorter allele does not match either of the end nucleotides of the longer allele, classify as SNP  

###if shorter allele length > 1

###if shorter allele length > 1

####compare the shorter allele sequence with the subsequence in the 5' end of the longer allele

####compare the shorter allele sequence with the subsequence in the 5' end of the longer allele (count ts and tv too)

#####if all nucleotides differ, classify as MNP

#####if all nucleotides differ, classify as MNP

#####if not all nucleotides differ, classify as CLUMPED

#####if not all nucleotides differ, classify as CLUMPED