variant improvment

lib/Variants.py

@@ -30,6 +30,24 @@ def complement(seq):
     return ''.join(seq_list)
 
 
+class VariantGraph():
+    def __init__(self, chromosome):
+        self.chromosome = chromosome
+        self.segments = []
+
+    def length(self):
+        return len(self.chromosome)
+
+    def new_segment(self, haplotype1, haplotype2=NONE ):
+        segment = [haplotype1, haplotype2]
+        self.segment.append(segment)
+
+    def get_haplotype_segment(self, num, genotype):
+        return self.
+
+
+
+
 class Fragment:
     """
     A fragment is a chromosomal segment witha start and end are
@@ -90,9 +108,6 @@ def read_vcf(vcf_file):
         offset = record.stop + 1
 
 
-
-
-
 def main():
     parser = argparse.ArgumentParser(description="Reformat data for plink",
                                      formatter_class=argparse.RawTextHelpFormatter)