Merge commit 'upstream/0.1.17'

[samtools.git] / glf.h

diff --git a/glf.h b/glf.h
deleted file mode 100644 (file)
index 12e5400..0000000
--- a/glf.h
+++ /dev/null
@@ -1,56 +0,0 @@
-#ifndef GLF_H_
-#define GLF_H_
-
-typedef struct {
-       unsigned char ref_base:4, dummy: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 */
-} glf1_t;
-
-#include <stdint.h>
-#include "bgzf.h"
-typedef BGZF *glfFile;
-
-#define GLF3_RTYPE_END   0
-#define GLF3_RTYPE_SUB   1
-#define GLF3_RTYPE_INDEL 2
-
-typedef struct {
-       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;
-} glf3_header_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#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
-}
-#endif
-
-#endif