Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/srf.h @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 #ifndef _SRF_H_ |
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2 #define _SRF_H_ |
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3 |
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4 #include "io_lib/hash_table.h" |
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5 #include "io_lib/ztr.h" |
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6 #include "io_lib/mFILE.h" |
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7 |
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8 #define SRF_MAGIC "SSRF" |
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9 #define SRF_VERSION "1.3" |
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10 |
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11 #define SRFB_CONTAINER 'S' |
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12 #define SRFB_XML 'X' |
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13 #define SRFB_TRACE_HEADER 'H' |
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14 #define SRFB_TRACE_BODY 'R' |
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15 #define SRFB_INDEX 'I' |
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16 |
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17 /* Lack of index => 8 zero bytes at end of file to indicate zero length */ |
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18 #define SRFB_NULL_INDEX '\0' |
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19 |
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20 /*--- Public structures */ |
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21 |
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22 /* Container header - several per file */ |
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23 typedef struct { |
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24 int block_type; |
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25 char version[256]; |
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26 char container_type; |
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27 char base_caller[256]; |
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28 char base_caller_version[256]; |
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29 } srf_cont_hdr_t; |
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30 |
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31 /* Trace header - several per container */ |
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32 typedef struct { |
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33 int block_type; |
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34 char read_prefix_type; |
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35 char id_prefix[256]; |
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36 uint32_t trace_hdr_size; |
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37 unsigned char *trace_hdr; |
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38 } srf_trace_hdr_t; |
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39 |
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40 /* Trace body - several per trace header */ |
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41 typedef struct { |
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42 int block_type; |
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43 int read_id_length; |
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44 char read_id[256]; |
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45 unsigned char flags; |
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46 uint32_t trace_size; |
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47 unsigned char *trace; |
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48 } srf_trace_body_t; |
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49 |
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50 /* XML - NCBI TraceInfo data block */ |
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51 typedef struct { |
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52 uint32_t xml_len; |
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53 char *xml; |
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54 } srf_xml_t; |
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55 |
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56 #define SRF_READ_FLAG_BAD_MASK (1<<0) |
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57 #define SRF_READ_FLAG_WITHDRAWN_MASK (1<<1) |
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58 #define SRF_READ_FLAG_USER_MASK (7<<5) |
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59 |
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60 /* Indexing */ |
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61 typedef struct { |
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62 char magic[4]; |
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63 char version[4]; |
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64 uint64_t size; |
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65 uint32_t n_container; |
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66 uint32_t n_data_block_hdr; |
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67 uint64_t n_buckets; |
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68 int8_t index_type; |
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69 int8_t dbh_pos_stored_sep; |
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70 char dbh_file[256]; |
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71 char cont_file[256]; |
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72 int index_hdr_sz; /* size of the above data on disk */ |
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73 } srf_index_hdr_t; |
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74 |
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75 /* In-memory index itself */ |
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76 #define SRF_INDEX_NAME_BLOCK_SIZE 10000000 |
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77 |
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78 typedef struct { |
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79 size_t used; |
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80 size_t space; |
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81 char *names; |
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82 } srf_name_block_t; |
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83 |
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84 typedef struct { |
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85 char ch_file[PATH_MAX+1]; |
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86 char th_file[PATH_MAX+1]; |
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87 Array ch_pos; |
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88 Array th_pos; |
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89 Array name_blocks; |
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90 int dbh_pos_stored_sep; |
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91 HashTable *db_hash; |
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92 } srf_index_t; |
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93 |
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94 /* Master SRF object */ |
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95 typedef struct { |
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96 FILE *fp; |
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97 |
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98 /* Cached copies of each of the most recent chunk types loaded */ |
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99 srf_cont_hdr_t ch; |
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100 srf_trace_hdr_t th; |
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101 srf_trace_body_t tb; |
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102 srf_xml_t xml; |
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103 srf_index_hdr_t hdr; |
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104 |
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105 /* Private: cached data for use by srf_next_ztr */ |
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106 ztr_t *ztr; |
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107 mFILE *mf; |
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108 long mf_pos, mf_end; |
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109 } srf_t; |
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110 |
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111 #define SRF_INDEX_MAGIC "Ihsh" |
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112 #define SRF_INDEX_VERSION "1.01" |
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113 |
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114 |
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115 /*--- Initialisation */ |
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116 srf_t *srf_create(FILE *fp); |
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117 srf_t *srf_open(char *fn, char *mode); |
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118 void srf_destroy(srf_t *srf, int auto_close); |
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119 |
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120 /*--- Base type I/O methods */ |
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121 |
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122 int srf_write_pstring(srf_t *srf, char *str); |
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123 int srf_write_pstringb(srf_t *srf, char *str, int length); |
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124 int srf_read_pstring(srf_t *srf, char *str); |
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125 |
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126 int srf_read_uint32(srf_t *srf, uint32_t *val); |
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127 int srf_write_uint32(srf_t *srf, uint32_t val); |
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128 |
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129 int srf_read_uint64(srf_t *srf, uint64_t *val); |
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130 int srf_write_uint64(srf_t *srf, uint64_t val); |
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131 |
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132 |
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133 /*--- Mid level I/O - srf block */ |
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134 srf_cont_hdr_t *srf_construct_cont_hdr(srf_cont_hdr_t *ch, |
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135 char *bc, |
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136 char *bc_version); |
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137 void srf_destroy_cont_hdr(srf_cont_hdr_t *ch); |
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138 int srf_read_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch); |
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139 int srf_write_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch); |
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140 |
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141 int srf_read_xml(srf_t *srf, srf_xml_t *xml); |
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142 int srf_write_xml(srf_t *srf, srf_xml_t *xml); |
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143 |
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144 srf_trace_hdr_t *srf_construct_trace_hdr(srf_trace_hdr_t *th, |
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145 char *prefix, |
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146 unsigned char *header, |
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147 uint32_t header_sz); |
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148 void srf_destroy_trace_hdr(srf_trace_hdr_t *th); |
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149 int srf_read_trace_hdr(srf_t *srf, srf_trace_hdr_t *th); |
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150 int srf_write_trace_hdr(srf_t *srf, srf_trace_hdr_t *th); |
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151 |
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152 srf_trace_body_t *srf_construct_trace_body(srf_trace_body_t *th, |
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153 char *suffix, |
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154 int suffix_len, |
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155 unsigned char *body, |
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156 uint32_t body_size, |
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157 unsigned char flags); |
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158 void srf_destroy_trace_body(srf_trace_body_t *th); |
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159 int srf_write_trace_body(srf_t *srf, srf_trace_body_t *th); |
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160 int srf_read_trace_body(srf_t *srf, srf_trace_body_t *th, int no_trace); |
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161 |
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162 int srf_read_index_hdr(srf_t *srf, srf_index_hdr_t *hdr, int no_seek); |
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163 int srf_write_index_hdr(srf_t *srf, srf_index_hdr_t *hdr); |
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164 srf_index_t *srf_index_create(char *ch_file, char *th_file, int dbh_sep); |
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165 void srf_index_destroy(srf_index_t *idx); |
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166 void srf_index_stats(srf_index_t *idx, FILE *fp); |
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167 int srf_index_add_cont_hdr(srf_index_t *idx, uint64_t pos); |
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168 int srf_index_add_trace_hdr(srf_index_t *idx, uint64_t pos); |
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169 int srf_index_add_trace_body(srf_index_t *idx, char *name, uint64_t pos); |
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170 int srf_index_write(srf_t *srf, srf_index_t *idx); |
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171 |
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172 /*--- Higher level I/O functions */ |
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173 mFILE *srf_next_trace(srf_t *srf, char *name); |
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174 ztr_t *srf_next_ztr_flags(srf_t *srf, char *name, int filter_mask, int *flags); |
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175 ztr_t *srf_next_ztr(srf_t *srf, char *name, int filter_mask); |
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176 |
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177 ztr_t *partial_decode_ztr(srf_t *srf, mFILE *mf, ztr_t *z); |
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178 ztr_t *ztr_dup(ztr_t *src); |
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179 |
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180 int srf_next_block_type(srf_t *srf); /* peek ahead */ |
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181 int srf_next_block_details(srf_t *srf, uint64_t *pos, char *name); |
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182 |
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183 int srf_find_trace(srf_t *srf, char *trace, |
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184 uint64_t *cpos, uint64_t *hpos, uint64_t *dpos); |
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185 |
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186 int construct_trace_name(char *fmt, |
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187 unsigned char *suffix, int suffix_len, |
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188 char *name, int name_len); |
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189 |
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190 #endif /* _SRF_H_ */ |