* samtools-0.1.4-16 (r360)

[samtools.git] / bam_rmdup.c

diff --git a/bam_rmdup.c b/bam_rmdup.c
index 321938f3215506dbf54ebc76666c40165d2024a6..50269010d7e6760ddfa8f908df3b7349ab4d83cd 100644 (file)
--- a/bam_rmdup.c
+++ b/bam_rmdup.c
@@ -76,6 +76,11 @@ void bam_rmdup_core(bamFile in, bamFile out)
                                        fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
                                        clear_del_set(del_set);
                                }
+                               if ((int)c->tid == -1) { // append unmapped reads
+                                       bam_write1(out, b);
+                                       while (bam_read1(in, b) >= 0) bam_write1(out, b);
+                                       break;
+                               }
                                last_tid = c->tid;
                                fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
                        }