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1 /*
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2 Copyright (C) 2014 Genome Research Ltd.
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3
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4 Author: Petr Danecek <pd3@sanger.ac.uk>
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5
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6 Permission is hereby granted, free of charge, to any person obtaining a copy
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7 of this software and associated documentation files (the "Software"), to deal
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8 in the Software without restriction, including without limitation the rights
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9 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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10 copies of the Software, and to permit persons to whom the Software is
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11 furnished to do so, subject to the following conditions:
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12
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13 The above copyright notice and this permission notice shall be included in
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14 all copies or substantial portions of the Software.
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15
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16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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17 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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18 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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19 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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20 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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21 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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22 THE SOFTWARE.
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23 */
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24
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25 #include "htslib/hts.h"
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26 #include "htslib/kstring.h"
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27 #include "htslib/kseq.h"
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28 #include "htslib/khash_str2int.h"
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29 #include "htslib/regidx.h"
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30
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31 #define LIDX_SHIFT 13 // number of insignificant index bits
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32
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33 // List of regions for one chromosome
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34 typedef struct
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35 {
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36 int *idx, nidx;
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37 int nregs, mregs; // n:used, m:alloced
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38 reg_t *regs;
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39 void *payload;
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40 }
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41 reglist_t;
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42
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43 // Container of all sequences
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44 struct _regidx_t
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45 {
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46 int nseq, mseq; // n:used, m:alloced
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47 reglist_t *seq; // regions for each sequence
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48 void *seq2regs; // hash for fast lookup from chr name to regions
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49 char **seq_names;
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50 regidx_free_f free; // function to free any data allocated by regidx_parse_f
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51 regidx_parse_f parse; // parse one input line
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52 void *usr; // user data to pass to regidx_parse_f
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53
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54 // temporary data for index initialization
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55 kstring_t str;
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56 int rid_prev, start_prev, end_prev;
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57 int payload_size;
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58 void *payload;
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59 };
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60
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61 int regidx_seq_nregs(regidx_t *idx, const char *seq)
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62 {
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63 int iseq;
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64 if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence
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65 return idx->seq[iseq].nregs;
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66 }
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67
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68 int regidx_nregs(regidx_t *idx)
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69 {
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70 int i, nregs = 0;
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71 for (i=0; i<idx->nseq; i++) nregs += idx->seq[i].nregs;
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72 return nregs;
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73 }
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74
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75 char **regidx_seq_names(regidx_t *idx, int *n)
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76 {
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77 *n = idx->nseq;
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78 return idx->seq_names;
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79 }
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80
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81 int _regidx_build_index(regidx_t *idx)
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82 {
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83 int iseq;
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84 for (iseq=0; iseq<idx->nseq; iseq++)
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85 {
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86 reglist_t *list = &idx->seq[iseq];
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87 int j,k, imax = 0; // max index bin
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88 for (j=0; j<list->nregs; j++)
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89 {
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90 int ibeg = list->regs[j].start >> LIDX_SHIFT;
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91 int iend = list->regs[j].end >> LIDX_SHIFT;
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92 if ( imax < iend + 1 )
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93 {
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94 int old_imax = imax;
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95 imax = iend + 1;
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96 kroundup32(imax);
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97 list->idx = (int*) realloc(list->idx, imax*sizeof(int));
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98 for (k=old_imax; k<imax; k++) list->idx[k] = -1;
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99 }
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100 if ( ibeg==iend )
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101 {
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102 if ( list->idx[ibeg]<0 ) list->idx[ibeg] = j;
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103 }
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104 else
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105 {
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106 for (k=ibeg; k<=iend; k++)
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107 if ( list->idx[k]<0 ) list->idx[k] = j;
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108 }
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109 list->nidx = iend + 1;
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110 }
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111 }
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112 return 0;
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113 }
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114
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115 int regidx_insert(regidx_t *idx, char *line)
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116 {
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117 if ( !line )
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118 return _regidx_build_index(idx);
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119
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120 char *chr_from, *chr_to;
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121 reg_t reg;
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122 int ret = idx->parse(line,&chr_from,&chr_to,®,idx->payload,idx->usr);
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123 if ( ret==-2 ) return -1; // error
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124 if ( ret==-1 ) return 0; // skip the line
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125
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126 int rid;
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127 idx->str.l = 0;
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128 kputsn(chr_from, chr_to-chr_from+1, &idx->str);
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129 if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 )
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130 {
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131 idx->nseq++;
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132 int m_prev = idx->mseq;
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133 hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
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134 hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
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135 idx->seq_names[idx->nseq-1] = strdup(idx->str.s);
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136 rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]);
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137 }
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138
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139 reglist_t *list = &idx->seq[rid];
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140 list->nregs++;
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141 int m_prev = list->mregs;
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142 hts_expand(reg_t,list->nregs,list->mregs,list->regs);
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143 list->regs[list->nregs-1] = reg;
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144 if ( idx->payload_size )
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145 {
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146 if ( m_prev < list->mregs ) list->payload = realloc(list->payload,idx->payload_size*list->mregs);
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147 memcpy(list->payload + idx->payload_size*(list->nregs-1), idx->payload, idx->payload_size);
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148 }
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149
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150 if ( idx->rid_prev==rid )
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151 {
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152 if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
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153 {
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154 fprintf(stderr,"The regions are not sorted: %s:%d-%d is before %s:%d-%d\n",
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155 idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1);
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156 return -1;
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157 }
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158 }
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159 idx->rid_prev = rid;
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160 idx->start_prev = reg.start;
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161 idx->end_prev = reg.end;
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162 return 0;
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163 }
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164
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165 regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
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166 {
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167 if ( !parser )
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168 {
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169 if ( !fname ) parser = regidx_parse_tab;
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170 else
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171 {
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172 int len = strlen(fname);
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173 if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
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174 parser = regidx_parse_bed;
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175 else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) )
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176 parser = regidx_parse_bed;
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177 else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
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178 parser = regidx_parse_bed;
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179 else
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180 parser = regidx_parse_tab;
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181 }
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182 }
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183
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184 regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
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185 idx->free = free_f;
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186 idx->parse = parser;
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187 idx->usr = usr_dat;
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188 idx->seq2regs = khash_str2int_init();
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189 idx->rid_prev = -1;
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190 idx->start_prev = -1;
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191 idx->end_prev = -1;
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192 idx->payload_size = payload_size;
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193 if ( payload_size ) idx->payload = malloc(payload_size);
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194
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195 if ( !fname ) return idx;
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196
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197 kstring_t str = {0,0,0};
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198
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199 htsFile *fp = hts_open(fname,"r");
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200 if ( !fp ) goto error;
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201
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202 while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
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203 {
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204 if ( regidx_insert(idx, str.s) ) goto error;
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205 }
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206 regidx_insert(idx, NULL);
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207
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208 free(str.s);
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209 hts_close(fp);
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210 return idx;
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211
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212 error:
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213 free(str.s);
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214 if ( fp ) hts_close(fp);
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215 regidx_destroy(idx);
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216 return NULL;
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217 }
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218
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219 void regidx_destroy(regidx_t *idx)
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220 {
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221 int i, j;
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222 for (i=0; i<idx->nseq; i++)
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223 {
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224 reglist_t *list = &idx->seq[i];
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225 if ( idx->free )
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226 {
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227 for (j=0; j<list->nregs; j++)
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228 idx->free(list->payload + idx->payload_size*j);
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229 }
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230 free(list->payload);
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231 free(list->regs);
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232 free(list->idx);
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233 }
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234 free(idx->seq_names);
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235 free(idx->seq);
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236 free(idx->str.s);
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237 free(idx->payload);
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238 khash_str2int_destroy_free(idx->seq2regs);
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239 free(idx);
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240 }
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241
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242 int regidx_overlap(regidx_t *idx, const char *chr, uint32_t from, uint32_t to, regitr_t *itr)
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243 {
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244 if ( itr ) itr->i = itr->n = 0;
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245
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246 int iseq;
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247 if ( khash_str2int_get(idx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence
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248
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249 reglist_t *list = &idx->seq[iseq];
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250 if ( !list->nregs ) return 0;
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251
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252 int i, ibeg = from>>LIDX_SHIFT;
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253 int ireg = ibeg < list->nidx ? list->idx[ibeg] : list->idx[ list->nidx - 1 ];
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254 if ( ireg < 0 )
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255 {
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256 // linear search; if slow, replace with binary search
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257 if ( ibeg > list->nidx ) ibeg = list->nidx;
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258 for (i=ibeg - 1; i>=0; i--)
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259 if ( list->idx[i] >=0 ) break;
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260 ireg = i>=0 ? list->idx[i] : 0;
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261 }
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262 for (i=ireg; i<list->nregs; i++)
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263 {
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264 if ( list->regs[i].start > to ) return 0; // no match
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265 if ( list->regs[i].end >= from && list->regs[i].start <= to ) break; // found
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266 }
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267
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268 if ( i>=list->nregs ) return 0; // no match
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269
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270 if ( !itr ) return 1;
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271
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272 itr->i = 0;
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273 itr->n = list->nregs - i;
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274 itr->reg = &idx->seq[iseq].regs[i];
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275 if ( idx->payload_size )
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276 itr->payload = idx->seq[iseq].payload + i*idx->payload_size;
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277 else
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278 itr->payload = NULL;
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279
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280 return 1;
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281 }
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282
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283 int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
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284 {
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285 char *ss = (char*) line;
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286 while ( *ss && isspace(*ss) ) ss++;
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287 if ( !*ss ) return -1; // skip blank lines
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288 if ( *ss=='#' ) return -1; // skip comments
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289
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290 char *se = ss;
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291 while ( *se && !isspace(*se) ) se++;
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292 if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
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293
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294 *chr_beg = ss;
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295 *chr_end = se-1;
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296
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297 ss = se+1;
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298 reg->start = strtol(ss, &se, 10);
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299 if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
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300
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301 ss = se+1;
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302 reg->end = strtol(ss, &se, 10) - 1;
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303 if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
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304
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305 return 0;
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306 }
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307
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308 int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
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309 {
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310 char *ss = (char*) line;
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311 while ( *ss && isspace(*ss) ) ss++;
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312 if ( !*ss ) return -1; // skip blank lines
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313 if ( *ss=='#' ) return -1; // skip comments
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314
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315 char *se = ss;
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316 while ( *se && !isspace(*se) ) se++;
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317 if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
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318
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319 *chr_beg = ss;
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320 *chr_end = se-1;
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321
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322 ss = se+1;
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323 reg->start = strtol(ss, &se, 10) - 1;
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324 if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
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325
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326 if ( !se[0] || !se[1] )
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327 reg->end = reg->start;
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328 else
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329 {
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330 ss = se+1;
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331 reg->end = strtol(ss, &se, 10);
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332 if ( ss==se ) reg->end = reg->start;
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333 else reg->end--;
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334 }
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335
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336 return 0;
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337 }
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338
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