📝 incorporated some of the PR suggestions

kids-first · Mar 28, 2024 · 5a8fcdd · 5a8fcdd
1 parent 3644424
commit 5a8fcdd
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/scripts/cnv_3_gistic_style.py b/scripts/cnv_3_gistic_style.py
@@ -112,8 +112,6 @@ def mt_adjust_cn(obj):
         data = pd.read_csv(fname, sep="\t")
     except Exception as e:
         print(e, file=sys.stderr)
-        pdb.set_trace()
-        hold=1
     data.set_index("Hugo_Symbol")
     # sample list would be cbio ids
     samp_list = list(data.columns)[1:]

diff --git a/scripts/maf_merge.py b/scripts/maf_merge.py
@@ -108,7 +108,7 @@ def process_tbl(cbio_dx, file_meta_dict, print_head):
         "-i", "--header", action="store", dest="header", help="File with maf header only"
     )
     parser.add_argument(
-        "-m", "--maf-dirs", action="store", dest="maf_dirs", help="csv of maf file directories"
+        "-m", "--maf-dirs", action="store", dest="maf_dirs", help="comma-separated list of maf file directories"
     )
     parser.add_argument(
         "-j",