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1 #ifndef BAM_TVIEW_H
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2 #define BAM_TVIEW_H
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3
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4 #include <ctype.h>
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5 #include <assert.h>
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6 #include <string.h>
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7 #include <math.h>
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8 #include <unistd.h>
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9 #include <stdarg.h>
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10 #include "bam.h"
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11 #include "faidx.h"
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12 #include "bam2bcf.h"
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13 #include "sam_header.h"
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14 #include "khash.h"
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15
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16 KHASH_MAP_INIT_STR(kh_rg, const char *)
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17
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18 typedef struct AbstractTview {
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19 int mrow, mcol;
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20
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21 bam_index_t *idx;
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22 bam_lplbuf_t *lplbuf;
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23 bam_header_t *header;
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24 bamFile fp;
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25 int curr_tid, left_pos;
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26 faidx_t *fai;
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27 bcf_callaux_t *bca;
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28
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29 int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
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30 char *ref;
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31 khash_t(kh_rg) *rg_hash;
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32 /* callbacks */
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33 void (*my_destroy)(struct AbstractTview* );
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34 void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
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35 void (*my_mvaddch)(struct AbstractTview*,int,int,int);
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36 void (*my_attron)(struct AbstractTview*,int);
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37 void (*my_attroff)(struct AbstractTview*,int);
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38 void (*my_clear)(struct AbstractTview*);
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39 int (*my_colorpair)(struct AbstractTview*,int);
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40 int (*my_drawaln)(struct AbstractTview*,int,int);
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41 int (*my_loop)(struct AbstractTview*);
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42 int (*my_underline)(struct AbstractTview*);
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43 } tview_t;
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44
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45
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46 char bam_aux_getCEi(bam1_t *b, int i);
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47 char bam_aux_getCSi(bam1_t *b, int i);
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48 char bam_aux_getCQi(bam1_t *b, int i);
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49
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50 #define TV_MIN_ALNROW 2
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51 #define TV_MAX_GOTO 40
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52 #define TV_LOW_MAPQ 10
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53
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54 #define TV_COLOR_MAPQ 0
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55 #define TV_COLOR_BASEQ 1
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56 #define TV_COLOR_NUCL 2
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57 #define TV_COLOR_COL 3
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58 #define TV_COLOR_COLQ 4
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59
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60 #define TV_BASE_NUCL 0
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61 #define TV_BASE_COLOR_SPACE 1
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62
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63 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
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64 int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples);
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65 void base_tv_destroy(tview_t*);
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66 int base_draw_aln(tview_t *tv, int tid, int pos);
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67
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68 typedef struct Tixel
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69 {
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70 int ch;
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71 int attributes;
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72 }tixel_t;
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73
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74 #endif
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75
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