medvedevgroup / varmatch Goto Github PK

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.

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.

Hi,
I noticed two issues with the test data set example, maybe you can help.

1. minor, a typo on the test_data page where you say parameter -r "> VarMatch_Directory/varmatch -r ref.fa -b baseline.fa -q query.fa -o output -f" but the tool expects -g for the reference. Probably leftover from an update pf some sort.
2. is the ref example file intended to contain only Ns?

Thanks!

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

-s 3, still output stat.output

varmatch python script does not check if file exists, if not, it should exist and send an error

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