X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;h=402e280606f7551dfdcc1667dcb289dc78c41a4e;hb=d07731e7c769ac5f2709ac60eb60ddd3fa0120fd;hp=ce1e1092b791386d27d8e88f61dee1ed8332dc3f;hpb=8cf329904235d82c6c781113c404f298d06bc2b0;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index ce1e109..402e280 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -119,14 +119,14 @@ static int usage(int is_long_help);
 int main_samview(int argc, char *argv[])
 {
 	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
-	int of_type = BAM_OFDEC, is_long_help = 0;
+	int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
 	int count = 0;
 	samfile_t *in = 0, *out = 0;
 	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
 
 	/* parse command-line options */
 	strcpy(in_mode, "r"); strcpy(out_mode, "w");
-	while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:")) >= 0) {
+	while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:")) >= 0) {
 		switch (c) {
 		case 's':
 			if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
@@ -157,6 +157,7 @@ int main_samview(int argc, char *argv[])
 		case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
 		case 'B': bam_no_B = 1; break;
 		case 'Q': g_qual_scale = atoi(optarg); break;
+		case '@': n_threads = strtol(optarg, 0, 0); break;
 		default: return usage(is_long_help);
 		}
 	}
@@ -214,6 +215,7 @@ int main_samview(int argc, char *argv[])
 		ret = 1;
 		goto view_end;
 	}
+	if (n_threads > 1) samthreads(out, n_threads, 256); 
 	if (is_header_only) goto view_end; // no need to print alignments
 
 	if (argc == optind + 1) { // convert/print the entire file
@@ -294,6 +296,7 @@ static int usage(int is_long_help)
 	fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
 	fprintf(stderr, "         -c       print only the count of matching records\n");
 	fprintf(stderr, "         -B       collapse the backward CIGAR operation\n");
+	fprintf(stderr, "         -@ INT   number of BAM compression threads [0]\n");
 	fprintf(stderr, "         -L FILE  output alignments overlapping the input BED FILE [null]\n");
 	fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
 	fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
@@ -364,12 +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();
@@ -379,9 +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);