change default NM,minor bug fix

Author: Yuhe Cheng

.gitignore

@@ -0,0 +1,4 @@
+build/
+src/DupCaller.egg-info
+.prettierignore
+.pre-commit-config.yaml

get-pip.py

@@ -224,7 +224,7 @@
         "--nmflt",
         type=int,
         help="if set to a number, any read group and half of reads has a higher NM will be filtered",
-        default=10,
+        default=5,
     )
     call_parser.add_argument(
         "-w",
@@ -289,7 +289,7 @@
         nargs="+",
         type=str,
         help="contigs to consider for variant calling",
-        default=["chr" + str(_) for _ in range(1, 23, 1)] + ["chrX"],
+        default=["chr" + str(_) for _ in range(1, 23, 1)] + ["chrX","chrY"],
     )
     learn_parser.add_argument(
         "-p", "--threads", type=int, help="number of threads", default=1

nextflow/DupCaller.nf

@@ -206,13 +206,6 @@ def do_estimate(args):
                     num2trinucSbs.append(
                         minus_base + "[" + ref_base + ">" + alt_base + "]" + plus_base
                     )
-    # rf_sizes = np.zeros(len(trinuc_by_rf.columns),dtype=int)
-    # for nn,rf in enumerate(trinuc_by_rf.columns):
-    # ts = int(rf.split("+")[0])
-    # bs = int(rf.split("+")[1])
-    # rf_sizes[nn] = ts+bs
-    # sorted_index = np.argsort(rf_sizes)
-    # rf_sizes_sorted = rf_sizes[sorted_index]
     trinuc_by_rf_np = trinuc_by_rf.to_numpy()
     trinuc_mut_np = np.zeros([96, len(trinuc_by_rf.columns)], dtype=int)
     duplex_no_dict = dict()