src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: avoid merging adjacent TAD together

src/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py

@@ -185,7 +185,7 @@ def merge_tads(tad_files: Path, name_file: str) -> Path:
     """
     merged_tad = tad_files.parent / tad_files.name.replace("_overlapped.bed",
                                                            ".bed")
-    cmd = f"bedtools merge -i {tad_files} > {merged_tad}"
+    cmd = f"bedtools merge -i {tad_files} -d -1 > {merged_tad}"
     sp.check_call(cmd, shell=True)
     df = pd.read_csv(merged_tad, sep="\t", names=["chr", "start", "stop"])
     new_name = name_file.replace("_grch38.hic", "")