X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=glf.h;h=12e54002481b7b1edf5e4e6a76721e354253e63c;hb=50706bea83d8a1518485283876333279f4ae7137;hp=af72a48f95385635a09ee692138969acb1c8cfde;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/glf.h b/glf.h
index af72a48..12e5400 100644
--- a/glf.h
+++ b/glf.h
@@ -12,33 +12,42 @@ typedef struct {
 #include "bgzf.h"
 typedef BGZF *glfFile;
 
-#define GLF_TYPE_NORMAL 0
-#define GLF_TYPE_INDEL  1
-#define GLF_TYPE_END   15
+#define GLF3_RTYPE_END   0
+#define GLF3_RTYPE_SUB   1
+#define GLF3_RTYPE_INDEL 2
 
 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;
+	uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
+	uint8_t rms_mapQ; /** RMS mapping quality */
+	uint8_t lk[10];   /** log likelihood ratio, capped at 255 */
+	uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
+	int32_t offset; /** the first base in a chromosome has offset zero. */
+	// for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
+	int16_t indel_len[2];
+	int32_t max_len; // maximum indel len; will be modified by glf3_read1()
+	char *indel_seq[2];
+} glf3_t;
 
 typedef struct {
 	int32_t l_text;
 	uint8_t *text;
-} glf_header_t;
+} glf3_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);
+#define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
+#define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
+
+	glf3_header_t *glf3_header_init();
+	glf3_header_t *glf3_header_read(glfFile fp);
+	void glf3_header_write(glfFile fp, const glf3_header_t *h);
+	void glf3_header_destroy(glf3_header_t *h);
+	char *glf3_ref_read(glfFile fp, int *len);
+	void glf3_ref_write(glfFile fp, const char *name, int len);
+	int glf3_write1(glfFile fp, const glf3_t *g3);
+	int glf3_read1(glfFile fp, glf3_t *g3);
 
 #ifdef __cplusplus
 }