X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=glf.h;fp=glf.h;h=0000000000000000000000000000000000000000;hp=12e54002481b7b1edf5e4e6a76721e354253e63c;hb=e2bd290b8643f0a728c282a8b825392307750210;hpb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5

diff --git a/glf.h b/glf.h
deleted file mode 100644
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