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