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1 #undef _HAVE_CURSES
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2
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3 #if _CURSES_LIB == 0
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4 #elif _CURSES_LIB == 1
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5 #include <curses.h>
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6 #ifndef NCURSES_VERSION
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7 #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
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8 #else
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9 #define _HAVE_CURSES
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10 #endif
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11 #elif _CURSES_LIB == 2
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12 #include <xcurses.h>
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13 #define _HAVE_CURSES
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14 #else
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15 #warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
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16 #endif
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17
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18 #ifdef _HAVE_CURSES
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19 #include <ctype.h>
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20 #include <assert.h>
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21 #include <string.h>
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22 #include "bam.h"
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23 #include "faidx.h"
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24 #include "bam_maqcns.h"
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25
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26 char bam_aux_getCEi(bam1_t *b, int i);
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27 char bam_aux_getCSi(bam1_t *b, int i);
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28 char bam_aux_getCQi(bam1_t *b, int i);
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29
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30 #define TV_MIN_ALNROW 2
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31 #define TV_MAX_GOTO 40
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32 #define TV_LOW_MAPQ 10
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33
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34 #define TV_COLOR_MAPQ 0
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35 #define TV_COLOR_BASEQ 1
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36 #define TV_COLOR_NUCL 2
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37 #define TV_COLOR_COL 3
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38 #define TV_COLOR_COLQ 4
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39
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40 #define TV_BASE_NUCL 0
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41 #define TV_BASE_COLOR_SPACE 1
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42
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43 typedef struct {
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44 int mrow, mcol;
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45 WINDOW *wgoto, *whelp;
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46
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47 bam_index_t *idx;
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48 bam_lplbuf_t *lplbuf;
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49 bam_header_t *header;
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50 bamFile fp;
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51 int curr_tid, left_pos;
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52 faidx_t *fai;
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53 bam_maqcns_t *bmc;
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54
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55 int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
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56 char *ref;
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57 } tview_t;
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58
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59 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
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60 {
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61 tview_t *tv = (tview_t*)data;
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62 int i, j, c, rb, attr, max_ins = 0;
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63 uint32_t call = 0;
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64 if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
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65 // print referece
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66 rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
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67 for (i = tv->last_pos + 1; i < pos; ++i) {
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68 if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
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69 c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
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70 mvaddch(1, tv->ccol++, c);
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71 }
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72 if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
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73 // print consensus
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74 call = bam_maqcns_call(n, pl, tv->bmc);
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75 attr = A_UNDERLINE;
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76 c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
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77 i = (call>>8&0xff)/10+1;
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78 if (i > 4) i = 4;
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79 attr |= COLOR_PAIR(i);
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80 if (c == toupper(rb)) c = '.';
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81 attron(attr);
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82 mvaddch(2, tv->ccol, c);
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83 attroff(attr);
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84 if(tv->ins) {
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85 // calculate maximum insert
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86 for (i = 0; i < n; ++i) {
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87 const bam_pileup1_t *p = pl + i;
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88 if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
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89 }
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90 }
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91 // core loop
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92 for (j = 0; j <= max_ins; ++j) {
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93 for (i = 0; i < n; ++i) {
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94 const bam_pileup1_t *p = pl + i;
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95 int row = TV_MIN_ALNROW + p->level - tv->row_shift;
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96 if (j == 0) {
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97 if (!p->is_del) {
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98 if (tv->base_for == TV_BASE_COLOR_SPACE &&
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99 (c = bam_aux_getCSi(p->b, p->qpos))) {
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100 c = bam_aux_getCSi(p->b, p->qpos);
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101 // assume that if we found one color, we will be able to get the color error
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102 if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
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103 } else {
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104 if (tv->show_name) {
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105 char *name = bam1_qname(p->b);
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106 c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
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107 } else {
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108 c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
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109 if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
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110 }
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111 }
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112 } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
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113 } else { // padding
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114 if (j > p->indel) c = '*';
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115 else { // insertion
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116 if (tv->base_for == TV_BASE_NUCL) {
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117 if (tv->show_name) {
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118 char *name = bam1_qname(p->b);
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119 c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
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120 } else {
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121 c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
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122 if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
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123 }
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124 } else {
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125 c = bam_aux_getCSi(p->b, p->qpos + j);
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126 if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
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127 }
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128 }
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129 }
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130 if (row > TV_MIN_ALNROW && row < tv->mrow) {
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131 int x;
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132 attr = 0;
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133 if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
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134 || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
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135 if (tv->color_for == TV_COLOR_BASEQ) {
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136 x = bam1_qual(p->b)[p->qpos]/10 + 1;
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137 if (x > 4) x = 4;
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138 attr |= COLOR_PAIR(x);
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139 } else if (tv->color_for == TV_COLOR_MAPQ) {
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140 x = p->b->core.qual/10 + 1;
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141 if (x > 4) x = 4;
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142 attr |= COLOR_PAIR(x);
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143 } else if (tv->color_for == TV_COLOR_NUCL) {
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144 x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
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145 attr |= COLOR_PAIR(x);
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146 } else if(tv->color_for == TV_COLOR_COL) {
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147 x = 0;
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148 switch(bam_aux_getCSi(p->b, p->qpos)) {
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149 case '0': x = 0; break;
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150 case '1': x = 1; break;
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151 case '2': x = 2; break;
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152 case '3': x = 3; break;
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153 case '4': x = 4; break;
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154 default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
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155 }
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156 x+=5;
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157 attr |= COLOR_PAIR(x);
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158 } else if(tv->color_for == TV_COLOR_COLQ) {
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159 x = bam_aux_getCQi(p->b, p->qpos);
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160 if(0 == x) x = bam1_qual(p->b)[p->qpos];
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161 x = x/10 + 1;
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162 if (x > 4) x = 4;
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163 attr |= COLOR_PAIR(x);
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164 }
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165 attron(attr);
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166 mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
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167 attroff(attr);
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168 }
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169 }
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170 c = j? '*' : rb;
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171 if (c == '*') {
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172 attr = COLOR_PAIR(8);
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173 attron(attr);
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174 mvaddch(1, tv->ccol++, c);
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175 attroff(attr);
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176 } else mvaddch(1, tv->ccol++, c);
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177 }
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178 tv->last_pos = pos;
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179 return 0;
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180 }
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181
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182 tview_t *tv_init(const char *fn, const char *fn_fa)
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183 {
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184 tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
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185 tv->is_dot = 1;
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186 tv->fp = bam_open(fn, "r");
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187 bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
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188 assert(tv->fp);
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189 tv->header = bam_header_read(tv->fp);
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190 tv->idx = bam_index_load(fn);
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191 if (tv->idx == 0) exit(1);
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192 tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
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193 if (fn_fa) tv->fai = fai_load(fn_fa);
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194 tv->bmc = bam_maqcns_init();
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195 tv->ins = 1;
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196 bam_maqcns_prepare(tv->bmc);
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197
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198 initscr();
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199 keypad(stdscr, TRUE);
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200 clear();
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201 noecho();
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202 cbreak();
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203 tv->mrow = 24; tv->mcol = 80;
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204 getmaxyx(stdscr, tv->mrow, tv->mcol);
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205 tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
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206 tv->whelp = newwin(29, 40, 5, 5);
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207 tv->color_for = TV_COLOR_MAPQ;
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208 start_color();
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209 init_pair(1, COLOR_BLUE, COLOR_BLACK);
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210 init_pair(2, COLOR_GREEN, COLOR_BLACK);
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211 init_pair(3, COLOR_YELLOW, COLOR_BLACK);
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212 init_pair(4, COLOR_WHITE, COLOR_BLACK);
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213 init_pair(5, COLOR_GREEN, COLOR_BLACK);
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214 init_pair(6, COLOR_CYAN, COLOR_BLACK);
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215 init_pair(7, COLOR_YELLOW, COLOR_BLACK);
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216 init_pair(8, COLOR_RED, COLOR_BLACK);
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217 init_pair(9, COLOR_BLUE, COLOR_BLACK);
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218 return tv;
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219 }
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220
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221 void tv_destroy(tview_t *tv)
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222 {
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223 delwin(tv->wgoto); delwin(tv->whelp);
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224 endwin();
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225
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226 bam_lplbuf_destroy(tv->lplbuf);
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227 bam_maqcns_destroy(tv->bmc);
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228 bam_index_destroy(tv->idx);
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229 if (tv->fai) fai_destroy(tv->fai);
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230 free(tv->ref);
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231 bam_header_destroy(tv->header);
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232 bam_close(tv->fp);
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233 free(tv);
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234 }
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235
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236 int tv_fetch_func(const bam1_t *b, void *data)
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237 {
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238 tview_t *tv = (tview_t*)data;
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239 if (tv->no_skip) {
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240 uint32_t *cigar = bam1_cigar(b); // this is cheating...
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241 int i;
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242 for (i = 0; i <b->core.n_cigar; ++i) {
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243 if ((cigar[i]&0xf) == BAM_CREF_SKIP)
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244 cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
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245 }
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246 }
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247 bam_lplbuf_push(b, tv->lplbuf);
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248 return 0;
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249 }
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250
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251 int tv_draw_aln(tview_t *tv, int tid, int pos)
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252 {
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253 // reset
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254 clear();
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255 tv->curr_tid = tid; tv->left_pos = pos;
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256 tv->last_pos = tv->left_pos - 1;
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257 tv->ccol = 0;
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258 // print ref and consensus
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259 if (tv->fai) {
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260 char *str;
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261 if (tv->ref) free(tv->ref);
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262 str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
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263 sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
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264 tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
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265 free(str);
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266 }
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267 // draw aln
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268 bam_lplbuf_reset(tv->lplbuf);
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269 bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
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270 bam_lplbuf_push(0, tv->lplbuf);
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271
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272 while (tv->ccol < tv->mcol) {
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273 int pos = tv->last_pos + 1;
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274 if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
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275 mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
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276 ++tv->last_pos;
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277 }
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278 return 0;
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279 }
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280
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281 static void tv_win_goto(tview_t *tv, int *tid, int *pos)
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282 {
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283 char str[256], *p;
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284 int i, l = 0;
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285 wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
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286 mvwprintw(tv->wgoto, 1, 2, "Goto: ");
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287 for (;;) {
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288 int c = wgetch(tv->wgoto);
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289 wrefresh(tv->wgoto);
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290 if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
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291 --l;
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292 } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
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293 int _tid = -1, _beg, _end;
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294 if (str[0] == '=') {
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295 _beg = strtol(str+1, &p, 10) - 1;
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296 if (_beg > 0) {
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297 *pos = _beg;
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298 return;
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299 }
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300 } else {
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301 bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
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302 if (_tid >= 0) {
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303 *tid = _tid; *pos = _beg;
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304 return;
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305 }
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306 }
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307 } else if (isgraph(c)) {
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308 if (l < TV_MAX_GOTO) str[l++] = c;
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309 } else if (c == '\027') l = 0;
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310 else if (c == '\033') return;
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311 str[l] = '\0';
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312 for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
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313 mvwprintw(tv->wgoto, 1, 8, "%s", str);
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314 }
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315 }
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316
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317 static void tv_win_help(tview_t *tv) {
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318 int r = 1;
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319 WINDOW *win = tv->whelp;
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320 wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
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321 mvwprintw(win, r++, 2, " -=- Help -=- ");
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322 r++;
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323 mvwprintw(win, r++, 2, "? This window");
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324 mvwprintw(win, r++, 2, "Arrows Small scroll movement");
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325 mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
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326 mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
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327 mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
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328 mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
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329 mvwprintw(win, r++, 2, "space Scroll one screen");
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330 mvwprintw(win, r++, 2, "backspace Scroll back one screen");
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331 mvwprintw(win, r++, 2, "g Go to specific location");
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332 mvwprintw(win, r++, 2, "m Color for mapping qual");
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333 mvwprintw(win, r++, 2, "n Color for nucleotide");
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334 mvwprintw(win, r++, 2, "b Color for base quality");
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335 mvwprintw(win, r++, 2, "c Color for cs color");
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336 mvwprintw(win, r++, 2, "z Color for cs qual");
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337 mvwprintw(win, r++, 2, ". Toggle on/off dot view");
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338 mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
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339 mvwprintw(win, r++, 2, "r Toggle on/off rd name");
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340 mvwprintw(win, r++, 2, "N Turn on nt view");
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341 mvwprintw(win, r++, 2, "C Turn on cs view");
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342 mvwprintw(win, r++, 2, "i Toggle on/off ins");
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343 mvwprintw(win, r++, 2, "q Exit");
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344 r++;
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345 mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
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346 mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
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347 mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
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348 wrefresh(win);
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349 wgetch(win);
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350 }
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351
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352 void tv_loop(tview_t *tv)
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353 {
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354 int tid, pos;
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355 tid = tv->curr_tid; pos = tv->left_pos;
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356 while (1) {
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357 int c = getch();
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358 switch (c) {
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359 case '?': tv_win_help(tv); break;
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360 case '\033':
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361 case 'q': goto end_loop;
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362 case '/':
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|
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363 case 'g': tv_win_goto(tv, &tid, &pos); break;
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364 case 'm': tv->color_for = TV_COLOR_MAPQ; break;
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365 case 'b': tv->color_for = TV_COLOR_BASEQ; break;
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366 case 'n': tv->color_for = TV_COLOR_NUCL; break;
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|
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367 case 'c': tv->color_for = TV_COLOR_COL; break;
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368 case 'z': tv->color_for = TV_COLOR_COLQ; break;
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369 case 's': tv->no_skip = !tv->no_skip; break;
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370 case 'r': tv->show_name = !tv->show_name; break;
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|
|
371 case KEY_LEFT:
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|
|
372 case 'h': --pos; break;
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|
|
373 case KEY_RIGHT:
|
|
|
374 case 'l': ++pos; break;
|
|
|
375 case KEY_SLEFT:
|
|
|
376 case 'H': pos -= 20; break;
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|
|
377 case KEY_SRIGHT:
|
|
|
378 case 'L': pos += 20; break;
|
|
|
379 case '.': tv->is_dot = !tv->is_dot; break;
|
|
|
380 case 'N': tv->base_for = TV_BASE_NUCL; break;
|
|
|
381 case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
|
|
|
382 case 'i': tv->ins = !tv->ins; break;
|
|
|
383 case '\010': pos -= 1000; break;
|
|
|
384 case '\014': pos += 1000; break;
|
|
|
385 case ' ': pos += tv->mcol; break;
|
|
|
386 case KEY_UP:
|
|
|
387 case 'j': --tv->row_shift; break;
|
|
|
388 case KEY_DOWN:
|
|
|
389 case 'k': ++tv->row_shift; break;
|
|
|
390 case KEY_BACKSPACE:
|
|
|
391 case '\177': pos -= tv->mcol; break;
|
|
|
392 case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
|
|
|
393 default: continue;
|
|
|
394 }
|
|
|
395 if (pos < 0) pos = 0;
|
|
|
396 if (tv->row_shift < 0) tv->row_shift = 0;
|
|
|
397 tv_draw_aln(tv, tid, pos);
|
|
|
398 }
|
|
|
399 end_loop:
|
|
|
400 return;
|
|
|
401 }
|
|
|
402
|
|
|
403 int bam_tview_main(int argc, char *argv[])
|
|
|
404 {
|
|
|
405 tview_t *tv;
|
|
|
406 if (argc == 1) {
|
|
|
407 fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
|
|
|
408 return 1;
|
|
|
409 }
|
|
|
410 tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
|
|
|
411 tv_draw_aln(tv, 0, 0);
|
|
|
412 tv_loop(tv);
|
|
|
413 tv_destroy(tv);
|
|
|
414 return 0;
|
|
|
415 }
|
|
|
416 #else // #ifdef _HAVE_CURSES
|
|
|
417 #include <stdio.h>
|
|
|
418 #warning "No curses library is available; tview is disabled."
|
|
|
419 int bam_tview_main(int argc, char *argv[])
|
|
|
420 {
|
|
|
421 fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
|
|
|
422 return 1;
|
|
|
423 }
|
|
|
424 #endif // #ifdef _HAVE_CURSES
|
