Support -c/--contig also on single sample calling

src/sniffles/config.py

@@ -109,7 +109,7 @@ def add_main_args(self, parser):
         main_args.add_argument("--tandem-repeats", metavar="IN.bed", type=str, help="(Optional) Input .bed file containing tandem repeat annotations for the reference genome.", default=None)
         main_args.add_argument("--phase", help="Determine phase for SV calls (requires the input alignments to be phased)", default=False, action="store_true")
         main_args.add_argument("-t", "--threads", metavar="N", type=int, help="Number of parallel threads to use (speed-up for multi-core CPUs)", default=4)
-        main_args.add_argument("-c", "--contig", default=None, type=str, help="(Optional) Only process the specified contigs. May be given more than once. Currently only applies to merging.", action="append")
+        main_args.add_argument("-c", "--contig", default=None, type=str, help="(Optional) Only process the specified contigs. May be given more than once.", action="append")
 
     minsupport: Union[str, int]
     minsvlen: int

src/sniffles/sniffles

@@ -273,6 +273,10 @@ def Sniffles2_Main(processes: list[parallel.SnifflesWorker]):
             else:
                 task_count = max(1, math.ceil(contig.mapped / float(task_max_reads)))
             contig_str = str(contig.contig)
+
+            if config.contig and contig_str not in config.contig:
+                continue
+
             contigs.append(contig_str)
             contig_length = bam_in.get_reference_length(contig_str)
             contig_lengths.append((contig_str, contig_length))