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1 #include <assert.h>
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2 #include "bam_tview.h"
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3
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4 int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
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5 {
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6 assert(tv!=NULL);
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7 assert(fn!=NULL);
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8 tv->mrow = 24; tv->mcol = 80;
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9 tv->color_for = TV_COLOR_MAPQ;
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10 tv->is_dot = 1;
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11
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12 tv->fp = bam_open(fn, "r");
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13 if(tv->fp==0)
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14 {
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15 fprintf(stderr,"bam_open %s. %s\n", fn,fn_fa);
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16 exit(EXIT_FAILURE);
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17 }
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18 bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
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19 assert(tv->fp);
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20
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21 tv->header = bam_header_read(tv->fp);
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22 if(tv->header==0)
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23 {
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24 fprintf(stderr,"Cannot read '%s'.\n", fn);
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25 exit(EXIT_FAILURE);
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26 }
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27 tv->idx = bam_index_load(fn);
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28 if (tv->idx == 0)
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29 {
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30 fprintf(stderr,"Cannot read index for '%s'.\n", fn);
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31 exit(EXIT_FAILURE);
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32 }
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33 tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
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34 if (fn_fa) tv->fai = fai_load(fn_fa);
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35 tv->bca = bcf_call_init(0.83, 13);
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36 tv->ins = 1;
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37
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38 if ( samples )
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39 {
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40 if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
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41 void *iter = tv->header->dict;
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42 const char *key, *val;
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43 int n = 0;
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44 tv->rg_hash = kh_init(kh_rg);
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45 while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
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46 {
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47 if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
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48 {
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49 khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
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50 if ( k != kh_end(tv->rg_hash) ) continue;
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51 int ret;
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52 k = kh_put(kh_rg, tv->rg_hash, key, &ret);
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53 kh_value(tv->rg_hash, k) = val;
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54 n++;
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55 }
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56 }
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57 if ( !n )
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58 {
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59 fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
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60 exit(EXIT_FAILURE);
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61 }
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62 }
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63
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64 return 0;
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65 }
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66
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67
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68 void base_tv_destroy(tview_t* tv)
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69 {
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70 bam_lplbuf_destroy(tv->lplbuf);
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71 bcf_call_destroy(tv->bca);
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72 bam_index_destroy(tv->idx);
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73 if (tv->fai) fai_destroy(tv->fai);
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74 free(tv->ref);
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75 bam_header_destroy(tv->header);
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76 bam_close(tv->fp);
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77 }
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78
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79
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80 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
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81 {
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82 extern unsigned char bam_nt16_table[256];
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83 tview_t *tv = (tview_t*)data;
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84 int i, j, c, rb, attr, max_ins = 0;
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85 uint32_t call = 0;
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86 if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
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87 // print referece
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88 rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
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89 for (i = tv->last_pos + 1; i < pos; ++i) {
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90 if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
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91 c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
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92 tv->my_mvaddch(tv,1, tv->ccol++, c);
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93 }
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94 if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
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95 { // call consensus
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96 bcf_callret1_t bcr;
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97 int qsum[4], a1, a2, tmp;
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98 double p[3], prior = 30;
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99 bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
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100 for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
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101 for (i = 1; i < 4; ++i) // insertion sort
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102 for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
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103 tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
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104 a1 = qsum[0]&3; a2 = qsum[1]&3;
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105 p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
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106 if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
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107 if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
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108 if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
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109 else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
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110 else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
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111 }
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112 attr = tv->my_underline(tv);
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113 c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
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114 i = (call&0xffff)/10+1;
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115 if (i > 4) i = 4;
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116 attr |= tv->my_colorpair(tv,i);
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117 if (c == toupper(rb)) c = '.';
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118 tv->my_attron(tv,attr);
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119 tv->my_mvaddch(tv,2, tv->ccol, c);
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120 tv->my_attroff(tv,attr);
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121 if(tv->ins) {
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122 // calculate maximum insert
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123 for (i = 0; i < n; ++i) {
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124 const bam_pileup1_t *p = pl + i;
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125 if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
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126 }
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127 }
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128 // core loop
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129 for (j = 0; j <= max_ins; ++j) {
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130 for (i = 0; i < n; ++i) {
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131 const bam_pileup1_t *p = pl + i;
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132 int row = TV_MIN_ALNROW + p->level - tv->row_shift;
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133 if (j == 0) {
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134 if (!p->is_del) {
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135 if (tv->base_for == TV_BASE_COLOR_SPACE &&
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136 (c = bam_aux_getCSi(p->b, p->qpos))) {
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137 // assume that if we found one color, we will be able to get the color error
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138 if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
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139 } else {
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140 if (tv->show_name) {
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141 char *name = bam1_qname(p->b);
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142 c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
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143 } else {
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144 c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
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145 if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
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146 }
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147 }
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148 } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
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149 } else { // padding
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150 if (j > p->indel) c = '*';
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151 else { // insertion
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152 if (tv->base_for == TV_BASE_NUCL) {
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153 if (tv->show_name) {
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154 char *name = bam1_qname(p->b);
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155 c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
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156 } else {
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157 c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
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158 if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
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159 }
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160 } else {
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161 c = bam_aux_getCSi(p->b, p->qpos + j);
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162 if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
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163 }
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164 }
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165 }
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166 if (row > TV_MIN_ALNROW && row < tv->mrow) {
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167 int x;
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168 attr = 0;
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169 if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
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170 || (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
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171 if (tv->color_for == TV_COLOR_BASEQ) {
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172 x = bam1_qual(p->b)[p->qpos]/10 + 1;
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173 if (x > 4) x = 4;
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174 attr |= tv->my_colorpair(tv,x);
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175 } else if (tv->color_for == TV_COLOR_MAPQ) {
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176 x = p->b->core.qual/10 + 1;
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177 if (x > 4) x = 4;
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178 attr |= tv->my_colorpair(tv,x);
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179 } else if (tv->color_for == TV_COLOR_NUCL) {
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180 x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
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181 attr |= tv->my_colorpair(tv,x);
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182 } else if(tv->color_for == TV_COLOR_COL) {
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183 x = 0;
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184 switch(bam_aux_getCSi(p->b, p->qpos)) {
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185 case '0': x = 0; break;
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186 case '1': x = 1; break;
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187 case '2': x = 2; break;
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188 case '3': x = 3; break;
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189 case '4': x = 4; break;
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190 default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
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191 }
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192 x+=5;
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193 attr |= tv->my_colorpair(tv,x);
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194 } else if(tv->color_for == TV_COLOR_COLQ) {
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195 x = bam_aux_getCQi(p->b, p->qpos);
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196 if(0 == x) x = bam1_qual(p->b)[p->qpos];
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197 x = x/10 + 1;
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198 if (x > 4) x = 4;
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199 attr |= tv->my_colorpair(tv,x);
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200 }
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201 tv->my_attron(tv,attr);
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202 tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
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203 tv->my_attroff(tv,attr);
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204 }
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205 }
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206 c = j? '*' : rb;
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207 if (c == '*') {
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208 attr = tv->my_colorpair(tv,8);
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209 tv->my_attron(tv,attr);
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210 tv->my_mvaddch(tv,1, tv->ccol++, c);
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211 tv->my_attroff(tv,attr);
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212 } else tv->my_mvaddch(tv,1, tv->ccol++, c);
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213 }
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214 tv->last_pos = pos;
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215 return 0;
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216 }
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217
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218
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219
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220
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221 int tv_fetch_func(const bam1_t *b, void *data)
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222 {
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223 tview_t *tv = (tview_t*)data;
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224 if ( tv->rg_hash )
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225 {
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226 const uint8_t *rg = bam_aux_get(b, "RG");
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227 if ( !rg ) return 0;
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228 khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
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229 if ( k == kh_end(tv->rg_hash) ) return 0;
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230 }
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231 if (tv->no_skip) {
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232 uint32_t *cigar = bam1_cigar(b); // this is cheating...
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233 int i;
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234 for (i = 0; i <b->core.n_cigar; ++i) {
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235 if ((cigar[i]&0xf) == BAM_CREF_SKIP)
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236 cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
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237 }
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238 }
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239 bam_lplbuf_push(b, tv->lplbuf);
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240 return 0;
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241 }
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242
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243 int base_draw_aln(tview_t *tv, int tid, int pos)
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244 {
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245 assert(tv!=NULL);
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246 // reset
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247 tv->my_clear(tv);
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248 tv->curr_tid = tid; tv->left_pos = pos;
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249 tv->last_pos = tv->left_pos - 1;
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250 tv->ccol = 0;
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251 // print ref and consensus
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252 if (tv->fai) {
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253 char *str;
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254 if (tv->ref) free(tv->ref);
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255 assert(tv->curr_tid>=0);
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256
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257 str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
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258 assert(str!=NULL);
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259 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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260 tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
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261 free(str);
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262 }
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263 // draw aln
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264 bam_lplbuf_reset(tv->lplbuf);
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265 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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266 bam_lplbuf_push(0, tv->lplbuf);
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267
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268 while (tv->ccol < tv->mcol) {
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269 int pos = tv->last_pos + 1;
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270 if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
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271 tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
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272 ++tv->last_pos;
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273 }
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274 return 0;
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275 }
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276
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277
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278
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279
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280 static void error(const char *format, ...)
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281 {
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282 if ( !format )
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283 {
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284 fprintf(stderr, "\n");
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285 fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
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286 fprintf(stderr, "Options:\n");
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287 fprintf(stderr, " -d display output as (H)tml or (C)urses or (T)ext \n");
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288 fprintf(stderr, " -p chr:pos go directly to this position\n");
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289 fprintf(stderr, " -s STR display only reads from this sample or group\n");
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290 fprintf(stderr, "\n\n");
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291 }
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292 else
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293 {
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294 va_list ap;
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295 va_start(ap, format);
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296 vfprintf(stderr, format, ap);
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297 va_end(ap);
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298 }
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299 exit(-1);
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300 }
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301
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302 enum dipsay_mode {display_ncurses,display_html,display_text};
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303 extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
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304 extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
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305 extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
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306
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307 int bam_tview_main(int argc, char *argv[])
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308 {
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309 int view_mode=display_ncurses;
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310 tview_t* tv=NULL;
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311 char *samples=NULL, *position=NULL;
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312 int c;
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313 while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
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314 switch (c) {
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315 case 's': samples=optarg; break;
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316 case 'p': position=optarg; break;
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317 case 'd':
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318 {
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319 switch(optarg[0])
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320 {
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321 case 'H': case 'h': view_mode=display_html;break;
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322 case 'T': case 't': view_mode=display_text;break;
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323 case 'C': case 'c': view_mode=display_ncurses;break;
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324 default: view_mode=display_ncurses;break;
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325 }
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326 break;
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327 }
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328 default: error(NULL);
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329 }
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330 }
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331 if (argc==optind) error(NULL);
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332
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333 switch(view_mode)
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334 {
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335 case display_ncurses:
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336 {
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337 tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
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338 break;
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339 }
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340 case display_text:
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341 {
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342 tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
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343 break;
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|
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344 }
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345 case display_html:
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346 {
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347 tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
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348 break;
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|
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349 }
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350 }
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351 if(tv==NULL)
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352 {
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353 error("cannot create view");
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354 return EXIT_FAILURE;
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|
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355 }
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356
|
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357 if ( position )
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|
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358 {
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359 int _tid = -1, _beg, _end;
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360 bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
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361 if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
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|
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362 }
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363 tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
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364 tv->my_loop(tv);
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|
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365 tv->my_destroy(tv);
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|
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366
|
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367 return EXIT_SUCCESS;
|
|
|
368 }
|
