X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_stat.c;h=ea9deee9d712c71bfd51f7574a5cae055a2c2ace;hb=b6f550edaa9384857879894bf01399fad76dac37;hp=a4522daa49257b920ab26586a6062d046a26d9e3;hpb=02884d7b923597d15ccecd598e73675b5074a1eb;p=samtools.git

diff --git a/bam_stat.c b/bam_stat.c
index a4522da..ea9deee 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -1,3 +1,5 @@
+#include <unistd.h>
+#include <assert.h>
 #include "bam.h"
 
 typedef struct {
@@ -14,7 +16,7 @@ typedef struct {
 			if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good;		\
 			if ((c)->flag & BAM_FREAD1) ++(s)->n_read1;					\
 			if ((c)->flag & BAM_FREAD2) ++(s)->n_read2;					\
-			if ((c)->flag & BAM_FMUNMAP) ++(s)->n_sgltn;				\
+			if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn;	\
 			if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
 				++(s)->n_pair_map;										\
 				if ((c)->mtid != (c)->tid) {							\
@@ -33,13 +35,15 @@ bam_flagstat_t *bam_flagstat_core(bamFile fp)
 	bam_flagstat_t *s;
 	bam1_t *b;
 	bam1_core_t *c;
+	int ret;
 	s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
 	b = bam_init1();
 	c = &b->core;
-	while (bam_read1(fp, b) >= 0) {
+	while ((ret = bam_read1(fp, b)) >= 0)
 		flagstat_loop(s, c);
-	}
 	bam_destroy1(b);
+	if (ret != -1)
+		fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
 	return s;
 }
 int bam_flagstat(int argc, char *argv[])