Add missing short options

build_pop.py

@@ -21,16 +21,16 @@ def parse_args():
     """
     parser = argparse.ArgumentParser(description='Generate simulated populations with SV',
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument("--nb-inds", help="Number of individuals to generate", required=True, type=int)
-    parser.add_argument("--reference", help="Reference genome", required=True)
-    parser.add_argument("--sv-list", help="File containing the SVs", required=False)
-    parser.add_argument("--coverage", help="Coverage of reads", default=15, type=int)
-    parser.add_argument("--output-directory", help="Output directory", default="res")
-    parser.add_argument("--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True,
+    parser.add_argument("-n", "--nb-inds", help="Number of individuals to generate", required=True, type=int)
+    parser.add_argument("-r", "--reference", help="Reference genome", required=True)
+    parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False)
+    parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int)
+    parser.add_argument("-o", "--output-directory", help="Output directory", default="res")
+    parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True,
                         default=False)
-    parser.add_argument("--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True,
+    parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True,
                         default=False)
-    parser.add_argument("--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001)
+    parser.add_argument("-p", "--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001)
     parser.add_argument("-l", "--read-len", help="Generate reads having a length of LEN", type=int, default=100)
     parser.add_argument("-m", "--insert-len-mean", help="Generate inserts (fragments) having an average length of LEN",
                         type=int, default=300)