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1 #include <zlib.h>
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2 #include <stdio.h>
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3 #include <ctype.h>
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4 #include <string.h>
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5 #include <stdlib.h>
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6 #include <unistd.h>
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7 #include <assert.h>
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8 #ifdef _WIN32
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9 #include <fcntl.h>
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10 #endif
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11 #include "kstring.h"
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12 #include "bam.h"
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13 #include "sam_header.h"
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14 #include "kseq.h"
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15 #include "khash.h"
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16
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17 KSTREAM_INIT(gzFile, gzread, 16384)
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18 KHASH_MAP_INIT_STR(ref, uint64_t)
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19
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20 void bam_init_header_hash(bam_header_t *header);
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21 void bam_destroy_header_hash(bam_header_t *header);
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22 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
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23
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24 unsigned char bam_nt16_table[256] = {
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25 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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26 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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27 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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28 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
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29 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
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30 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
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31 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
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32 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
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33 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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34 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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35 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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36 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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37 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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38 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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39 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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40 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
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41 };
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42
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43 unsigned short bam_char2flag_table[256] = {
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44 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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45 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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46 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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47 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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48 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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49 BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
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50 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
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51 BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
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52 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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53 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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54 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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55 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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56 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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57 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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58 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
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59 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
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60 };
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61
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62 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
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63
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64 struct __tamFile_t {
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65 gzFile fp;
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66 kstream_t *ks;
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67 kstring_t *str;
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68 uint64_t n_lines;
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69 int is_first;
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70 };
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71
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72 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
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73 {
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74 char **list = 0, *s;
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75 int n = 0, dret, m = 0;
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76 gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
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77 kstream_t *ks;
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78 kstring_t *str;
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79 str = (kstring_t*)calloc(1, sizeof(kstring_t));
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80 ks = ks_init(fp);
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81 while (ks_getuntil(ks, '\n', str, &dret) > 0) {
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82 if (n == m) {
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83 m = m? m << 1 : 16;
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84 list = (char**)realloc(list, m * sizeof(char*));
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85 }
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86 if (str->s[str->l-1] == '\r')
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87 str->s[--str->l] = '\0';
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88 s = list[n++] = (char*)calloc(str->l + 1, 1);
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89 strcpy(s, str->s);
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90 }
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91 ks_destroy(ks);
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92 gzclose(fp);
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93 free(str->s); free(str);
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94 *_n = n;
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95 return list;
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96 }
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97
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98 static bam_header_t *hash2header(const kh_ref_t *hash)
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99 {
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100 bam_header_t *header;
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101 khiter_t k;
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102 header = bam_header_init();
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103 header->n_targets = kh_size(hash);
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104 header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
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105 header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
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106 for (k = kh_begin(hash); k != kh_end(hash); ++k) {
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107 if (kh_exist(hash, k)) {
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108 int i = (int)kh_value(hash, k);
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109 header->target_name[i] = (char*)kh_key(hash, k);
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110 header->target_len[i] = kh_value(hash, k)>>32;
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111 }
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112 }
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113 bam_init_header_hash(header);
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114 return header;
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115 }
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116 bam_header_t *sam_header_read2(const char *fn)
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117 {
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118 bam_header_t *header;
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119 int c, dret, ret, error = 0;
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120 gzFile fp;
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121 kstream_t *ks;
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122 kstring_t *str;
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123 kh_ref_t *hash;
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124 khiter_t k;
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125 if (fn == 0) return 0;
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126 fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
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127 if (fp == 0) return 0;
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128 hash = kh_init(ref);
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129 ks = ks_init(fp);
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130 str = (kstring_t*)calloc(1, sizeof(kstring_t));
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131 while (ks_getuntil(ks, 0, str, &dret) > 0) {
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132 char *s = strdup(str->s);
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133 int len, i;
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134 i = kh_size(hash);
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135 ks_getuntil(ks, 0, str, &dret);
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136 len = atoi(str->s);
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137 k = kh_put(ref, hash, s, &ret);
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138 if (ret == 0) {
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139 fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
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140 error = 1;
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141 }
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142 kh_value(hash, k) = (uint64_t)len<<32 | i;
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143 if (dret != '\n')
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144 while ((c = ks_getc(ks)) != '\n' && c != -1);
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145 }
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146 ks_destroy(ks);
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147 gzclose(fp);
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148 free(str->s); free(str);
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149 fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
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150 if (error) return 0;
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151 header = hash2header(hash);
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152 kh_destroy(ref, hash);
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153 return header;
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154 }
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155 static inline uint8_t *alloc_data(bam1_t *b, int size)
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156 {
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157 if (b->m_data < size) {
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158 b->m_data = size;
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159 kroundup32(b->m_data);
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160 b->data = (uint8_t*)realloc(b->data, b->m_data);
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161 }
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162 return b->data;
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163 }
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164 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
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165 {
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166 fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
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167 abort();
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168 }
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169 static inline void append_text(bam_header_t *header, kstring_t *str)
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170 {
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171 size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
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172 kroundup32(x); kroundup32(y);
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173 if (x < y)
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174 {
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175 header->n_text = y;
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176 header->text = (char*)realloc(header->text, y);
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177 if ( !header->text )
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178 {
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179 fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
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180 abort();
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181 }
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182 }
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183 // Sanity check
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184 if ( header->l_text+str->l+1 >= header->n_text )
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185 {
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186 fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
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187 abort();
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188 }
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189 strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
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190 header->l_text += str->l + 1;
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191 header->text[header->l_text] = 0;
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192 }
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193
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194 int sam_header_parse(bam_header_t *h)
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195 {
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196 char **tmp;
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197 int i;
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198 free(h->target_len); free(h->target_name);
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199 h->n_targets = 0; h->target_len = 0; h->target_name = 0;
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200 if (h->l_text < 3) return 0;
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201 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
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202 tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
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203 if (h->n_targets == 0) return 0;
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204 h->target_name = calloc(h->n_targets, sizeof(void*));
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205 for (i = 0; i < h->n_targets; ++i)
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206 h->target_name[i] = strdup(tmp[i]);
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207 free(tmp);
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208 tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
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209 h->target_len = calloc(h->n_targets, 4);
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210 for (i = 0; i < h->n_targets; ++i)
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211 h->target_len[i] = atoi(tmp[i]);
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212 free(tmp);
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213 return h->n_targets;
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214 }
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215
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216 bam_header_t *sam_header_read(tamFile fp)
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217 {
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218 int ret, dret;
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219 bam_header_t *header = bam_header_init();
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220 kstring_t *str = fp->str;
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221 while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
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222 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
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223 append_text(header, str);
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224 if (dret != '\n') {
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225 ret = ks_getuntil(fp->ks, '\n', str, &dret);
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226 str->s[str->l] = '\n'; // NOT null terminated!!
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227 append_text(header, str);
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228 }
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229 ++fp->n_lines;
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230 }
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231 sam_header_parse(header);
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232 bam_init_header_hash(header);
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233 fp->is_first = 1;
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234 return header;
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235 }
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236
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237 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
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238 {
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239 int ret, doff, doff0, dret, z = 0;
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240 bam1_core_t *c = &b->core;
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241 kstring_t *str = fp->str;
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242 kstream_t *ks = fp->ks;
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243
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244 if (fp->is_first) {
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245 fp->is_first = 0;
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246 ret = str->l;
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247 } else {
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248 do { // special consideration for empty lines
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249 ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
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250 if (ret >= 0) z += str->l + 1;
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251 } while (ret == 0);
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252 }
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253 if (ret < 0) return -1;
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254 ++fp->n_lines;
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255 doff = 0;
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256
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257 { // name
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258 c->l_qname = strlen(str->s) + 1;
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259 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
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260 doff += c->l_qname;
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261 }
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262 { // flag
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263 long flag;
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264 char *s;
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265 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
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266 flag = strtol((char*)str->s, &s, 0);
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267 if (*s) { // not the end of the string
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268 flag = 0;
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269 for (s = str->s; *s; ++s)
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270 flag |= bam_char2flag_table[(int)*s];
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271 }
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272 c->flag = flag;
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273 }
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274 { // tid, pos, qual
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275 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
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276 if (c->tid < 0 && strcmp(str->s, "*")) {
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277 if (header->n_targets == 0) {
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278 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
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279 exit(1);
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280 } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
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281 }
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282 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
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283 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
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284 if (ret < 0) return -2;
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285 }
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286 { // cigar
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287 char *s, *t;
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288 int i, op;
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289 long x;
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290 c->n_cigar = 0;
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291 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
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292 z += str->l + 1;
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293 if (str->s[0] != '*') {
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294 uint32_t *cigar;
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295 for (s = str->s; *s; ++s) {
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296 if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
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297 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
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298 }
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299 b->data = alloc_data(b, doff + c->n_cigar * 4);
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300 cigar = bam1_cigar(b);
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301 for (i = 0, s = str->s; i != c->n_cigar; ++i) {
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302 x = strtol(s, &t, 10);
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303 op = toupper(*t);
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304 if (op == 'M') op = BAM_CMATCH;
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305 else if (op == 'I') op = BAM_CINS;
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306 else if (op == 'D') op = BAM_CDEL;
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307 else if (op == 'N') op = BAM_CREF_SKIP;
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308 else if (op == 'S') op = BAM_CSOFT_CLIP;
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309 else if (op == 'H') op = BAM_CHARD_CLIP;
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310 else if (op == 'P') op = BAM_CPAD;
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311 else if (op == '=') op = BAM_CEQUAL;
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312 else if (op == 'X') op = BAM_CDIFF;
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313 else if (op == 'B') op = BAM_CBACK;
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314 else parse_error(fp->n_lines, "invalid CIGAR operation");
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315 s = t + 1;
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316 cigar[i] = bam_cigar_gen(x, op);
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317 }
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318 if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
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319 c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
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320 doff += c->n_cigar * 4;
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321 } else {
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322 if (!(c->flag&BAM_FUNMAP)) {
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323 fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
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324 c->flag |= BAM_FUNMAP;
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325 }
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326 c->bin = bam_reg2bin(c->pos, c->pos + 1);
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327 }
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328 }
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329 { // mtid, mpos, isize
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330 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
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331 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
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332 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
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333 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
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334 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
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335 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
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336 if (ret < 0) return -4;
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337 }
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338 { // seq and qual
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339 int i;
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340 uint8_t *p = 0;
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341 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
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342 z += str->l + 1;
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343 if (strcmp(str->s, "*")) {
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344 c->l_qseq = strlen(str->s);
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345 if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
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346 fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
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347 (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
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348 parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
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349 }
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350 p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
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351 memset(p, 0, (c->l_qseq+1)/2);
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352 for (i = 0; i < c->l_qseq; ++i)
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353 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
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354 } else c->l_qseq = 0;
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355 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
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356 z += str->l + 1;
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357 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
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358 parse_error(fp->n_lines, "sequence and quality are inconsistent");
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359 p += (c->l_qseq+1)/2;
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360 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
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361 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
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362 doff += c->l_qseq + (c->l_qseq+1)/2;
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363 }
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|
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364 doff0 = doff;
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365 if (dret != '\n' && dret != '\r') { // aux
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366 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
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367 uint8_t *s, type, key[2];
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368 z += str->l + 1;
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369 if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
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370 parse_error(fp->n_lines, "missing colon in auxiliary data");
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371 key[0] = str->s[0]; key[1] = str->s[1];
|
|
|
372 type = str->s[3];
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|
|
373 s = alloc_data(b, doff + 3) + doff;
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374 s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
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|
|
375 if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
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|
|
376 s = alloc_data(b, doff + 2) + doff;
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|
|
377 *s++ = 'A'; *s = str->s[5];
|
|
|
378 doff += 2;
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|
|
379 } else if (type == 'I' || type == 'i') {
|
|
|
380 long long x;
|
|
|
381 s = alloc_data(b, doff + 5) + doff;
|
|
|
382 x = (long long)atoll(str->s + 5);
|
|
|
383 if (x < 0) {
|
|
|
384 if (x >= -127) {
|
|
|
385 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
|
|
|
386 s += 1; doff += 2;
|
|
|
387 } else if (x >= -32767) {
|
|
|
388 *s++ = 's'; *(int16_t*)s = (int16_t)x;
|
|
|
389 s += 2; doff += 3;
|
|
|
390 } else {
|
|
|
391 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
|
|
|
392 s += 4; doff += 5;
|
|
|
393 if (x < -2147483648ll)
|
|
|
394 fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
|
|
|
395 (long long)fp->n_lines, x);
|
|
|
396 }
|
|
|
397 } else {
|
|
|
398 if (x <= 255) {
|
|
|
399 *s++ = 'C'; *s++ = (uint8_t)x;
|
|
|
400 doff += 2;
|
|
|
401 } else if (x <= 65535) {
|
|
|
402 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
|
|
|
403 s += 2; doff += 3;
|
|
|
404 } else {
|
|
|
405 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
|
|
|
406 s += 4; doff += 5;
|
|
|
407 if (x > 4294967295ll)
|
|
|
408 fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
|
|
|
409 (long long)fp->n_lines, x);
|
|
|
410 }
|
|
|
411 }
|
|
|
412 } else if (type == 'f') {
|
|
|
413 s = alloc_data(b, doff + 5) + doff;
|
|
|
414 *s++ = 'f';
|
|
|
415 *(float*)s = (float)atof(str->s + 5);
|
|
|
416 s += 4; doff += 5;
|
|
|
417 } else if (type == 'd') {
|
|
|
418 s = alloc_data(b, doff + 9) + doff;
|
|
|
419 *s++ = 'd';
|
|
|
420 *(float*)s = (float)atof(str->s + 9);
|
|
|
421 s += 8; doff += 9;
|
|
|
422 } else if (type == 'Z' || type == 'H') {
|
|
|
423 int size = 1 + (str->l - 5) + 1;
|
|
|
424 if (type == 'H') { // check whether the hex string is valid
|
|
|
425 int i;
|
|
|
426 if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
|
|
|
427 for (i = 0; i < str->l - 5; ++i) {
|
|
|
428 int c = toupper(str->s[5 + i]);
|
|
|
429 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
|
|
|
430 parse_error(fp->n_lines, "invalid hex character");
|
|
|
431 }
|
|
|
432 }
|
|
|
433 s = alloc_data(b, doff + size) + doff;
|
|
|
434 *s++ = type;
|
|
|
435 memcpy(s, str->s + 5, str->l - 5);
|
|
|
436 s[str->l - 5] = 0;
|
|
|
437 doff += size;
|
|
|
438 } else if (type == 'B') {
|
|
|
439 int32_t n = 0, Bsize, k = 0, size;
|
|
|
440 char *p;
|
|
|
441 if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
|
|
|
442 Bsize = bam_aux_type2size(str->s[5]); // the size of each element
|
|
|
443 for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
|
|
|
444 if (*p == ',') ++n;
|
|
|
445 p = str->s + 7; // now p points to the first number in the array
|
|
|
446 size = 6 + Bsize * n; // total number of bytes allocated to this tag
|
|
|
447 s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
|
|
|
448 *s++ = 'B'; *s++ = str->s[5];
|
|
|
449 memcpy(s, &n, 4); s += 4; // write the number of elements
|
|
|
450 if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
|
|
|
451 else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
|
|
|
452 else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
|
|
|
453 else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
|
|
|
454 else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
|
|
|
455 else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
|
|
|
456 else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtod(p, &p), ++p;
|
|
|
457 else parse_error(fp->n_lines, "unrecognized array type");
|
|
|
458 s += Bsize * n; doff += size;
|
|
|
459 } else parse_error(fp->n_lines, "unrecognized type");
|
|
|
460 if (dret == '\n' || dret == '\r') break;
|
|
|
461 }
|
|
|
462 }
|
|
|
463 b->l_aux = doff - doff0;
|
|
|
464 b->data_len = doff;
|
|
|
465 if (bam_no_B) bam_remove_B(b);
|
|
|
466 return z;
|
|
|
467 }
|
|
|
468
|
|
|
469 tamFile sam_open(const char *fn)
|
|
|
470 {
|
|
|
471 tamFile fp;
|
|
|
472 gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
|
|
|
473 if (gzfp == 0) return 0;
|
|
|
474 fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
|
|
|
475 fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
|
|
|
476 fp->fp = gzfp;
|
|
|
477 fp->ks = ks_init(fp->fp);
|
|
|
478 return fp;
|
|
|
479 }
|
|
|
480
|
|
|
481 void sam_close(tamFile fp)
|
|
|
482 {
|
|
|
483 if (fp) {
|
|
|
484 ks_destroy(fp->ks);
|
|
|
485 gzclose(fp->fp);
|
|
|
486 free(fp->str->s); free(fp->str);
|
|
|
487 free(fp);
|
|
|
488 }
|
|
|
489 }
|
