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1 #include <stdlib.h>
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2 #include <string.h>
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3 #include <stdio.h>
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4 #include <unistd.h>
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5 #include <math.h>
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6 #include "sam_header.h"
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7 #include "sam.h"
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8 #include "faidx.h"
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9 #include "kstring.h"
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10 #include "khash.h"
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11 KHASH_SET_INIT_STR(rg)
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12
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13 // When counting records instead of printing them,
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14 // data passed to the bam_fetch callback is encapsulated in this struct.
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15 typedef struct {
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16 bam_header_t *header;
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17 int *count;
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18 } count_func_data_t;
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19
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20 typedef khash_t(rg) *rghash_t;
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21
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22 static rghash_t g_rghash = 0;
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23 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
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24 static char *g_library, *g_rg;
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25 static int g_sol2sanger_tbl[128];
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26 static void *g_bed;
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27
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28 void *bed_read(const char *fn);
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29 void bed_destroy(void *_h);
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30 int bed_overlap(const void *_h, const char *chr, int beg, int end);
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31
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32 static void sol2sanger(bam1_t *b)
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33 {
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34 int l;
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35 uint8_t *qual = bam1_qual(b);
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36 if (g_sol2sanger_tbl[30] == 0) {
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37 for (l = 0; l != 128; ++l) {
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38 g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
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39 if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
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40 }
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41 }
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42 for (l = 0; l < b->core.l_qseq; ++l) {
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43 int q = qual[l];
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44 if (q > 127) q = 127;
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45 qual[l] = g_sol2sanger_tbl[q];
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46 }
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47 }
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48
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49 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
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50 {
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51 if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
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52 return 1;
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53 if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
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54 return 1;
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55 if (g_rg || g_rghash) {
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56 uint8_t *s = bam_aux_get(b, "RG");
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57 if (s) {
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58 if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
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59 if (g_rghash) {
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60 khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
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61 return (k != kh_end(g_rghash))? 0 : 1;
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62 }
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63 }
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64 }
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65 if (g_library) {
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66 const char *p = bam_get_library((bam_header_t*)h, b);
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67 return (p && strcmp(p, g_library) == 0)? 0 : 1;
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68 }
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69 return 0;
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70 }
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71
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72 static char *drop_rg(char *hdtxt, rghash_t h, int *len)
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73 {
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74 char *p = hdtxt, *q, *r, *s;
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75 kstring_t str;
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76 memset(&str, 0, sizeof(kstring_t));
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77 while (1) {
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78 int toprint = 0;
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79 q = strchr(p, '\n');
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80 if (q == 0) q = p + strlen(p);
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81 if (q - p < 3) break; // the line is too short; then stop
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82 if (strncmp(p, "@RG\t", 4) == 0) {
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83 int c;
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84 khint_t k;
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85 if ((r = strstr(p, "\tID:")) != 0) {
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86 r += 4;
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87 for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
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88 c = *s; *s = '\0';
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89 k = kh_get(rg, h, r);
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90 *s = c;
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91 if (k != kh_end(h)) toprint = 1;
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92 }
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93 } else toprint = 1;
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94 if (toprint) {
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95 kputsn(p, q - p, &str); kputc('\n', &str);
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96 }
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97 p = q + 1;
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98 }
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99 *len = str.l;
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100 return str.s;
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101 }
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102
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103 // callback function for bam_fetch() that prints nonskipped records
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104 static int view_func(const bam1_t *b, void *data)
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105 {
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106 if (!__g_skip_aln(((samfile_t*)data)->header, b))
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107 samwrite((samfile_t*)data, b);
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108 return 0;
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109 }
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110
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111 // callback function for bam_fetch() that counts nonskipped records
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112 static int count_func(const bam1_t *b, void *data)
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113 {
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114 if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
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115 (*((count_func_data_t*)data)->count)++;
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116 }
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117 return 0;
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118 }
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119
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120 static int usage(int is_long_help);
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121
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122 int main_samview(int argc, char *argv[])
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123 {
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124 int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
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125 int of_type = BAM_OFDEC, is_long_help = 0;
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126 int count = 0;
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127 samfile_t *in = 0, *out = 0;
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128 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
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129
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130 /* parse command-line options */
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131 strcpy(in_mode, "r"); strcpy(out_mode, "w");
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132 while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
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133 switch (c) {
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134 case 'c': is_count = 1; break;
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135 case 'C': slx2sngr = 1; break;
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136 case 'S': is_bamin = 0; break;
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137 case 'b': is_bamout = 1; break;
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138 case 't': fn_list = strdup(optarg); is_bamin = 0; break;
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139 case 'h': is_header = 1; break;
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140 case 'H': is_header_only = 1; break;
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141 case 'o': fn_out = strdup(optarg); break;
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142 case 'f': g_flag_on = strtol(optarg, 0, 0); break;
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143 case 'F': g_flag_off = strtol(optarg, 0, 0); break;
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144 case 'q': g_min_mapQ = atoi(optarg); break;
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145 case 'u': compress_level = 0; break;
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146 case '1': compress_level = 1; break;
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147 case 'l': g_library = strdup(optarg); break;
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148 case 'L': g_bed = bed_read(optarg); break;
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149 case 'r': g_rg = strdup(optarg); break;
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150 case 'R': fn_rg = strdup(optarg); break;
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151 case 'x': of_type = BAM_OFHEX; break;
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152 case 'X': of_type = BAM_OFSTR; break;
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153 case '?': is_long_help = 1; break;
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154 case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
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155 default: return usage(is_long_help);
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156 }
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157 }
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158 if (compress_level >= 0) is_bamout = 1;
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159 if (is_header_only) is_header = 1;
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160 if (is_bamout) strcat(out_mode, "b");
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161 else {
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162 if (of_type == BAM_OFHEX) strcat(out_mode, "x");
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163 else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
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164 }
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165 if (is_bamin) strcat(in_mode, "b");
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166 if (is_header) strcat(out_mode, "h");
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167 if (compress_level >= 0) {
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168 char tmp[2];
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169 tmp[0] = compress_level + '0'; tmp[1] = '\0';
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170 strcat(out_mode, tmp);
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171 }
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172 if (argc == optind) return usage(is_long_help); // potential memory leak...
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173
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174 // read the list of read groups
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175 if (fn_rg) {
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176 FILE *fp_rg;
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177 char buf[1024];
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178 int ret;
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179 g_rghash = kh_init(rg);
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180 fp_rg = fopen(fn_rg, "r");
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181 while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
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182 kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
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183 fclose(fp_rg);
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184 }
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185
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186 // generate the fn_list if necessary
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187 if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
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188 // open file handlers
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189 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
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190 fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
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191 ret = 1;
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192 goto view_end;
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193 }
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194 if (in->header == 0) {
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195 fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
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196 ret = 1;
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197 goto view_end;
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198 }
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199 if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
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200 char *tmp;
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201 int l;
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202 tmp = drop_rg(in->header->text, g_rghash, &l);
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203 free(in->header->text);
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204 in->header->text = tmp;
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205 in->header->l_text = l;
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206 }
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207 if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
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208 fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
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209 ret = 1;
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210 goto view_end;
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211 }
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212 if (is_header_only) goto view_end; // no need to print alignments
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213
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214 if (argc == optind + 1) { // convert/print the entire file
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215 bam1_t *b = bam_init1();
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216 int r;
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217 while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
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218 if (!__g_skip_aln(in->header, b)) {
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219 if (slx2sngr) sol2sanger(b);
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220 if (!is_count) samwrite(out, b); // write the alignment to `out'
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221 count++;
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222 }
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223 }
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224 if (r < -1) {
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225 fprintf(stderr, "[main_samview] truncated file.\n");
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226 ret = 1;
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227 }
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228 bam_destroy1(b);
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229 } else { // retrieve alignments in specified regions
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230 int i;
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231 bam_index_t *idx = 0;
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232 if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
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233 if (idx == 0) { // index is unavailable
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234 fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
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235 ret = 1;
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236 goto view_end;
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237 }
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238 for (i = optind + 1; i < argc; ++i) {
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239 int tid, beg, end, result;
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240 bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
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241 if (tid < 0) { // reference name is not found
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242 fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
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243 continue;
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244 }
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245 // fetch alignments
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246 if (is_count) {
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247 count_func_data_t count_data = { in->header, &count };
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248 result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
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249 } else
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250 result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
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251 if (result < 0) {
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252 fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
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253 ret = 1;
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254 break;
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255 }
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256 }
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257 bam_index_destroy(idx); // destroy the BAM index
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258 }
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259
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260 view_end:
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261 if (is_count && ret == 0) {
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262 printf("%d\n", count);
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263 }
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264 // close files, free and return
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265 free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
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266 if (g_bed) bed_destroy(g_bed);
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267 if (g_rghash) {
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268 khint_t k;
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269 for (k = 0; k < kh_end(g_rghash); ++k)
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270 if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
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271 kh_destroy(rg, g_rghash);
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272 }
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273 samclose(in);
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274 if (!is_count)
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275 samclose(out);
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276 return ret;
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277 }
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278
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279 static int usage(int is_long_help)
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280 {
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281 fprintf(stderr, "\n");
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282 fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
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283 fprintf(stderr, "Options: -b output BAM\n");
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284 fprintf(stderr, " -h print header for the SAM output\n");
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285 fprintf(stderr, " -H print header only (no alignments)\n");
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286 fprintf(stderr, " -S input is SAM\n");
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287 fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
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288 fprintf(stderr, " -1 fast compression (force -b)\n");
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289 fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n");
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290 fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
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291 fprintf(stderr, " -c print only the count of matching records\n");
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292 fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
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293 fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
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294 fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
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295 fprintf(stderr, " -o FILE output file name [stdout]\n");
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296 fprintf(stderr, " -R FILE list of read groups to be outputted [null]\n");
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297 fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
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298 fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
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299 fprintf(stderr, " -q INT minimum mapping quality [0]\n");
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300 fprintf(stderr, " -l STR only output reads in library STR [null]\n");
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301 fprintf(stderr, " -r STR only output reads in read group STR [null]\n");
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302 fprintf(stderr, " -? longer help\n");
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303 fprintf(stderr, "\n");
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304 if (is_long_help)
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305 fprintf(stderr, "Notes:\n\
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306 \n\
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307 1. By default, this command assumes the file on the command line is in\n\
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308 the BAM format and it prints the alignments in SAM. If `-t' is\n\
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309 applied, the input file is assumed to be in the SAM format. The\n\
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310 file supplied with `-t' is SPACE/TAB delimited with the first two\n\
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311 fields of each line consisting of the reference name and the\n\
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312 corresponding sequence length. The `.fai' file generated by `faidx'\n\
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313 can be used here. This file may be empty if reads are unaligned.\n\
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314 \n\
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315 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
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316 \n\
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317 3. BAM->SAM conversion: `samtools view in.bam'.\n\
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318 \n\
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319 4. A region should be presented in one of the following formats:\n\
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320 `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
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321 specified, the input alignment file must be an indexed BAM file.\n\
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322 \n\
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323 5. Option `-u' is preferred over `-b' when the output is piped to\n\
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324 another samtools command.\n\
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325 \n\
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326 6. In a string FLAG, each character represents one bit with\n\
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327 p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
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328 U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
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329 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
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330 f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
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331 `-X' are samtools-C specific. Picard and older samtools do not\n\
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332 support HEX or string flags.\n\
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333 \n");
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334 return 1;
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335 }
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336
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337 int main_import(int argc, char *argv[])
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338 {
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339 int argc2, ret;
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340 char **argv2;
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341 if (argc != 4) {
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342 fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
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343 return 1;
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344 }
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345 argc2 = 6;
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346 argv2 = calloc(6, sizeof(char*));
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347 argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
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348 ret = main_samview(argc2, argv2);
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349 free(argv2);
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350 return ret;
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351 }
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