Release samtools-0.1.16 (r963:234)

[samtools.git] / glf.h

diff --git a/glf.h b/glf.h
index af72a48f95385635a09ee692138969acb1c8cfde..12e54002481b7b1edf5e4e6a76721e354253e63c 100644 (file)
--- 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
 }