X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_mate.c;h=b947c9d61dad62729e190141efb5ef1d04616c6e;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=642ded68b80c0da699ba0091dc7e5dd9acc36d96;hpb=df50415f5380510f5b44bee2361413fc39c8bbcf;p=samtools.git

diff --git a/bam_mate.c b/bam_mate.c
index 642ded6..b947c9d 100644
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -1,5 +1,6 @@
 #include <stdlib.h>
 #include <string.h>
+#include <unistd.h>
 #include "kstring.h"
 #include "bam.h"
 
@@ -30,11 +31,11 @@ void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
 }
 
 // currently, this function ONLY works if each read has one hit
-void bam_mating_core(bamFile in, bamFile out)
+void bam_mating_core(bamFile in, bamFile out, int remove_reads)
 {
 	bam_header_t *header;
 	bam1_t *b[2];
-	int curr, has_prev, pre_end, cur_end;
+	int curr, has_prev, pre_end = 0, cur_end;
 	kstring_t str;
 
 	str.l = str.m = 0; str.s = 0;
@@ -46,10 +47,18 @@ void bam_mating_core(bamFile in, bamFile out)
 	curr = 0; has_prev = 0;
 	while (bam_read1(in, b[curr]) >= 0) {
 		bam1_t *cur = b[curr], *pre = b[1-curr];
-		if (cur->core.tid < 0) continue;
+		if (cur->core.tid < 0) 
+        {
+            if ( !remove_reads ) bam_write1(out, cur);
+            continue;
+        }
 		cur_end = bam_calend(&cur->core, bam1_cigar(cur));
 		if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
-		if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
+		if (cur->core.flag & BAM_FSECONDARY) 
+        {
+            if ( !remove_reads ) bam_write1(out, cur);
+            continue; // skip secondary alignments
+        }
 		if (has_prev) {
 			if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
 				cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
@@ -91,16 +100,29 @@ void bam_mating_core(bamFile in, bamFile out)
 	free(str.s);
 }
 
+void usage()
+{
+    fprintf(stderr,"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+    fprintf(stderr,"Options:\n");
+    fprintf(stderr,"       -r    remove unmapped reads and secondary alignments\n");
+    exit(1);
+}
+
 int bam_mating(int argc, char *argv[])
 {
 	bamFile in, out;
-	if (argc < 3) {
-		fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
-		return 1;
-	}
-	in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
-    out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
-	bam_mating_core(in, out);
+    int c, remove_reads=0;
+    while ((c = getopt(argc, argv, "r")) >= 0) {
+        switch (c) {
+            case 'r': remove_reads=1; break;
+        }
+    }
+    if (optind+1 >= argc) usage();
+	in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
+    out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
+	bam_mating_core(in, out, remove_reads);
 	bam_close(in); bam_close(out);
 	return 0;
 }
+
+