X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;fp=sam.c;h=e8e742c80649f583b16de8fb7b1519eca9a5af10;hb=6f6733c7551a2f4697c46acb4a516fa04bba3e40;hp=a3f2998687beb573186457837a844150e6245209;hpb=941542dfbedf4ba4850d3c1d6b96981234fd6560;p=samtools.git

diff --git a/sam.c b/sam.c
index a3f2998..e8e742c 100644
--- a/sam.c
+++ b/sam.c
@@ -3,7 +3,6 @@
 
 #define TYPE_BAM  1
 #define TYPE_READ 2
-#define TYPE_HEX  4
 
 bam_header_t *bam_header_dup(const bam_header_t *h0)
 {
@@ -76,7 +75,9 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 			if (fp->x.tamr == 0) goto open_err_ret;
-			if (strstr(mode, "x")) fp->type |= TYPE_HEX;
+			if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
+			else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+			else fp->type |= BAM_OFDEC<<2;
 			// write header
 			if (strstr(mode, "h")) {
 				int i;
@@ -128,7 +129,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
 	if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 	if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 	else {
-		char *s = bam_format1_core(fp->header, b, fp->type & TYPE_HEX);
+		char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
 		int l = strlen(s);
 		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 		free(s);