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License: Apache License 2.0
robust matching of small variant datasets using flexible scoring schemes
License: Apache License 2.0
If the baseline vcf or the query vcf contain no variants, varmatch will crash due to a division by zero error when calculating specificity/sensitivity.
Pull request #8 fixes this issue.
-s 3, still output stat.output
Hi,
I noticed two issues with the test data set example, maybe you can help.
Thanks!
in whole genome mode, out.match, chromosome name not printed
Hi,
it would be helpful if you would consider tagging releases. This would enable users and distributors (I intend to package varmatch for Debian) to differentiate between code that is intended for user consumption from random development releases.
Thanks for considering, Andreas.
Varmatch does not run under python3 due to inconsistent print usage.
pull request #10 addresses this issue, allowing varmatch to be used with python2 or python3
varmatch python script does not check if file exists, if not, it should exist and send an error
git clone https://github.com/medvedevgroup/varmatch.git
cd varmatch
make all
I try to run tool to see help:
./varmatch -h
File "./varmatch", line 24
from __future__ import print_function
SyntaxError: from __future__ imports must occur at the beginning of the file
Python 2.7.13
uname -a
Linux hgrcgridlogin 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 GNU/Linux
gcc version 6.3.0 20170516 (Debian 6.3.0-18)
edited:
Following lines from script/vardiff
file work in python shell:
from __future__ import print_function
import sys
import textwrap as _textwrap
import argparse
import os
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