diff --git a/bin/HATCHet.py b/bin/HATCHet.py index 0169a8b0..11db2ccc 100644 --- a/bin/HATCHet.py +++ b/bin/HATCHet.py @@ -5,6 +5,7 @@ import argparse import shutil import subprocess +import multiprocessing as mp import shlex from collections import Counter @@ -36,7 +37,7 @@ def parsing_arguments(): parser.add_argument("-tR","--toleranceRDR", type=float, required=False, default=0.08, help="RDR tolerance used for finding the clonal copy numbers (default: 0.08)") parser.add_argument("-tB","--toleranceBAF", type=float, required=False, default=0.04, help="BAF tolerance used for finding the clonal copy numbers (default: 0.04)") parser.add_argument("-p","--seeds", type=int, required=False, default=400, help="Number of seeds for coordinate-descent method (default: 400)") - parser.add_argument("-j","--jobs", type=int, required=False, default=None, help="Number of parallel jobs (default: maximum available on the machine)") + parser.add_argument("-j","--jobs", type=int, required=False, default=mp.cpu_count(), help="Number of parallel jobs (default: maximum available on the machine)") parser.add_argument("-r","--randomseed", type=int, required=False, default=None, help="Random seed (default: None)") parser.add_argument("-s","--timelimit", type=int, required=False, default=None, help="Time limit for each ILP run (default: None)") parser.add_argument("-m","--memlimit", type=int, required=False, default=None, help="Memory limit for each ILP run (default: None)") @@ -463,7 +464,7 @@ def findClonalClusters(fseg, neutral, size, tB, tR, samples, v): for cluster in clusters: rightpos = sum( (fseg[cluster][p]['rdr'] - fseg[neutral][p]['rdr']) > tR for p in samples) - leftpos = sum( (fseg[cluster][p]['rdr'] - fseg[neutral][p]['rdr']) < tR for p in samples) + leftpos = sum( (fseg[cluster][p]['rdr'] - fseg[neutral][p]['rdr']) < -tR for p in samples) eqbaf = (lambda p : abs(fseg[cluster][p]['baf'] - fseg[neutral][p]['baf']) <= tB) eqrdr = (lambda p : abs(fseg[cluster][p]['rdr'] - fseg[neutral][p]['rdr']) <= tR)