Beagle multithreading

[RetGiraffe11235]

Hello, thank you for developing great software. I tried to run germline genotyping using 16 threads, but it did not work multithreading on Beagle phasing step. I think it forgets to set "args.nthreads" on Beagle parameter "nthreads" in Monopgen.py. If you have other aims, I'm sorry for saying things that aren't necessary.

original

cmd3 = java + " -Xmx20g -jar " + beagle 
 +  " gl=" +  out + "/germline/" +  jobid + ".gl.vcf.gz"  
 +  " ref=" +  imputation_vcf   
 + "  chrom=" + record[0] 
 + " out="   +  out + "/germline/" + jobid 
 + ".gp " + "impute=false  modelscale=2  nthreads=1  gprobs=true  niterations=0"

cmd5 = java + " -Xmx20g -jar " + beagle 
 +  " gt=" +  out + "/germline/" +  jobid + ".germline.vcf"  
 +  " ref=" +  imputation_vcf    
 +  "  chrom=" + record[0]  
 + " out="   +  out + "/germline/" + jobid+ ".phased " 
 + "impute=false  modelscale=2  nthreads=1  gprobs=true  niterations=0"

palliative solution

cmd3 = java + " -Xmx20g -jar " + beagle 
 +  " gl=" +  out + "/germline/" +  jobid + ".gl.vcf.gz"  
 +  " ref=" +  imputation_vcf   
 + "  chrom=" + record[0] 
 + " out="   +  out + "/germline/" + jobid 
 + ".gp " + "impute=false  modelscale=2  nthreads=" + str(args.nthreads) + "  gprobs=true  niterations=0"

cmd5 = java + " -Xmx20g -jar " + beagle 
 +  " gt=" +  out + "/germline/" +  jobid + ".germline.vcf"  
 +  " ref=" +  imputation_vcf    
 +  "  chrom=" + record[0]  
 + " out="   +  out + "/germline/" + jobid+ ".phased " 
 + "impute=false  modelscale=2  nthreads=" + str(args.nthreads) + "  gprobs=true  niterations=0"

Best, Tomoki