optionally surpress /[12] in bam2fq

diff --git a/sam_view.c b/sam_view.c
index d1178ffd4dd36c8805ef00230c51ff161af226c6..402e280606f7551dfdcc1667dcb289dc78c41a4e 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -367,12 +367,14 @@ int main_bam2fq(int argc, char *argv[])
        bam_header_t *h;
        bam1_t *b;
        int8_t *buf;
-       int max_buf;
+       int max_buf, c, no12 = 0;
+       while ((c = getopt(argc, argv, "n")) > 0)
+               if (c == 'n') no12 = 1;
        if (argc == 1) {
                fprintf(stderr, "Usage: samtools bam2fq <in.bam>\n");
                return 1;
        }
-       fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+       fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
        if (fp == 0) return 1;
        h = bam_header_read(fp);
        b = bam_init1();
@@ -382,9 +384,12 @@ int main_bam2fq(int argc, char *argv[])
                int i, qlen = b->core.l_qseq;
                uint8_t *seq;
                putchar('@'); fputs(bam1_qname(b), stdout);
-               if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
-               else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
-               else putchar('\n');
+               if (no12) putchar('\n');
+               else {
+                       if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
+                       else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
+                       else putchar('\n');
+               }
                if (max_buf < qlen + 1) {
                        max_buf = qlen + 1;
                        kroundup32(max_buf);