Imported Upstream version 0.5

[pysam.git] / samtools / glf.h

diff --git a/samtools/glf.h b/samtools/glf.h
new file mode 100644 (file)
index 0000000..12e5400
--- /dev/null
+++ b/samtools/glf.h
@@ -0,0 +1,56 @@
+#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