* Merge from branches/dev/

[samtools.git] / glf.h

diff --git a/glf.h b/glf.h
index d9d23c624bb0aded1b4309b68311fdc94106f115..af72a48f95385635a09ee692138969acb1c8cfde 100644 (file)
--- a/glf.h
+++ b/glf.h
@@ -8,4 +8,40 @@ typedef struct {
        unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
 } glf1_t;
 
+#include <stdint.h>
+#include "bgzf.h"
+typedef BGZF *glfFile;
+
+#define GLF_TYPE_NORMAL 0
+#define GLF_TYPE_INDEL  1
+#define GLF_TYPE_END   15
+
+typedef struct {
+       unsigned char ref_base:4, type:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
+       unsigned char max_mapQ; /** maximum mapping quality */
+       unsigned char lk[10];   /** log likelihood ratio, capped at 255 */
+       unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
+       unsigned pos; /** this is ***ZERO-BASED*** coordinate */
+} glf2_t;
+
+typedef struct {
+       int32_t l_text;
+       uint8_t *text;
+} glf_header_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+       glf_header_t *glf_header_init();
+       glf_header_t *glf_header_read(glfFile fp);
+       void glf_header_write(glfFile fp, const glf_header_t *h);
+       void glf_header_destroy(glf_header_t *h);
+       char *glf_ref_read(glfFile fp);
+       void glf_ref_write(glfFile fp, const char *str);
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif