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comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/glf.h @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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-1:000000000000 0:74f5ea818cea
1 #ifndef GLF_H_
2 #define GLF_H_
3
4 typedef struct {
5 unsigned char ref_base:4, dummy:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
6 unsigned char max_mapQ; /** maximum mapping quality */
7 unsigned char lk[10]; /** log likelihood ratio, capped at 255 */
8 unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
9 } glf1_t;
10
11 #include <stdint.h>
12 #include "bgzf.h"
13 typedef BGZF *glfFile;
14
15 #define GLF3_RTYPE_END 0
16 #define GLF3_RTYPE_SUB 1
17 #define GLF3_RTYPE_INDEL 2
18
19 typedef struct {
20 uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
21 uint8_t rms_mapQ; /** RMS mapping quality */
22 uint8_t lk[10]; /** log likelihood ratio, capped at 255 */
23 uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
24 int32_t offset; /** the first base in a chromosome has offset zero. */
25 // for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
26 int16_t indel_len[2];
27 int32_t max_len; // maximum indel len; will be modified by glf3_read1()
28 char *indel_seq[2];
29 } glf3_t;
30
31 typedef struct {
32 int32_t l_text;
33 uint8_t *text;
34 } glf3_header_t;
35
36 #ifdef __cplusplus
37 extern "C" {
38 #endif
39
40 #define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
41 #define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
42
43 glf3_header_t *glf3_header_init();
44 glf3_header_t *glf3_header_read(glfFile fp);
45 void glf3_header_write(glfFile fp, const glf3_header_t *h);
46 void glf3_header_destroy(glf3_header_t *h);
47 char *glf3_ref_read(glfFile fp, int *len);
48 void glf3_ref_write(glfFile fp, const char *name, int len);
49 int glf3_write1(glfFile fp, const glf3_t *g3);
50 int glf3_read1(glfFile fp, glf3_t *g3);
51
52 #ifdef __cplusplus
53 }
54 #endif
55
56 #endif