vibansal / integratedphasing Goto Github PK

Hi,

My python Python version is 3.6.8 and I found that the code in many places seems to need updating, for example, the usage of print and xrange.

TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. Did you mean "print(, file=<output_stream>)"?

File "/*/mstkruskal.py", line 47, in KruskalMST
for node in xrange(self.V): parent.append(node); rank.append(0);
NameError: name 'xrange' is not defined

Hi
My question may be out of scope of your program.
In the pipeline you mentioned
shapeit --input-vcf VCFfile -M genetic_map.txt --output-graph VCFfile.graph
I faced with this error
ERROR: You cannot phase less than 10 samples without using a reference panel!
Should I add --input-ref ?