* samtools-0.1.5-12 (r415)

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index 45cb05cf3dd6f8a04acfd4dd92c8d250835855a2..a3f2998687beb573186457837a844150e6245209 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -3,6 +3,7 @@
 
 #define TYPE_BAM  1
 #define TYPE_READ 2
+#define TYPE_HEX  4
 
 bam_header_t *bam_header_dup(const bam_header_t *h0)
 {
@@ -75,6 +76,7 @@ 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;
                        // write header
                        if (strstr(mode, "h")) {
                                int i;
@@ -126,7 +128,7 @@ 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(fp->header, b);
+               char *s = bam_format1_core(fp->header, b, fp->type & TYPE_HEX);
                int l = strlen(s);
                fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
                free(s);