bugs for running test case (v0.7.10)

[hh1985]

Hi,

I found two bugs when repeating the varsim example.

 File "/opt/varsim-0.7.10/varsim.py", line 458, in varsim_main
simulator_commands_files.append((art_command, os.path.join(log_dir, "art.lane%d.out" % (i)), os.path.join(log_dir, "art.lane%d.err" % (i))))
NameError: global name 'art_command' is not defined

I think art_command and dwgsim_command should be simulator_command now.

Another error is about run_randvcf:

File "/opt/varsim-0.7.10/varsim_somatic.py", line 132, in varsim_somatic_main
 os.path.realpath(args.reference.name), args.som_prop_het)])
TypeError: run_randvcf() takes exactly 7 arguments (15 given)

The definition (run_randvcf) is: def run_randvcf(sampling_vcf, out_vcf_fd, log_file_fd, seed, sex, randvcf_options, reference)

But in varsim_somatic.py, the actual command is:

monitor_processes([run_randvcf(os.path.realpath(args.cosmic_vcf), rand_vcf_stdout, rand_vcf_stderr,
args.seed, args.sex, args.som_num_snp, args.som_num_ins, args.som_num_del, args.som_num_mnp,
args.som_num_complex, 0, args.som_min_length_lim, args.som_max_length_lim,
os.path.realpath(args.reference.name), args.som_prop_het)])

The interface of run_randvcf is not consistent.

[marghoob]

Many thanks for pointing out the bugs @hh1985 ! We will fix this as soon as possible.

[marghoob]

@yunfeiguo was this fixed?