Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/scf.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 /* |
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2 * Copyright (c) Medical Research Council 1994. All rights reserved. |
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3 * |
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4 * Permission to use, copy, modify and distribute this software and its |
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5 * documentation for any purpose is hereby granted without fee, provided that |
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6 * this copyright and notice appears in all copies. |
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7 * |
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8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, |
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9 * as part of the Staden Package at the MRC Laboratory of Molecular |
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10 * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. |
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11 * |
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12 * MRC disclaims all warranties with regard to this software. |
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13 */ |
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14 |
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15 /* |
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16 * File: scf.h |
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17 * Version: 3.00 |
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18 * |
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19 * Description: file structure definitions for SCF file |
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20 * |
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21 * Created: 19 November 1992 |
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22 * |
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23 */ |
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24 |
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25 #ifndef _SCF_H_ |
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26 #define _SCF_H_ |
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27 |
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28 #include <stdio.h> |
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29 #include <sys/types.h> |
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30 |
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31 #include "io_lib/mFILE.h" |
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32 #include "io_lib/os.h" |
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33 |
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34 #ifdef __cplusplus |
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35 extern "C" { |
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36 #endif |
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37 |
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38 /* |
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39 *----------------------------------------------------------------------------- |
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40 * Macros |
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41 *----------------------------------------------------------------------------- |
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42 */ |
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43 |
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44 /* The SCF magic number */ |
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45 #define SCF_MAGIC (((((uint_4)'.'<<8)+(uint_4)'s'<<8)+(uint_4)'c'<<8)+(uint_4)'f') |
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46 |
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47 /* prior to this was a different format */ |
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48 #define SCF_VERSION_OLDEST 2.00 |
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49 #define SCF_VERSION_OLD 2.02 |
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50 |
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51 /* The current SCF format level */ |
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52 #define SCF_VERSION 3.00 |
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53 |
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54 /* Uncertainty code sets supported */ |
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55 #define CSET_DEFAULT 0 /* {A,C,G,T,-} */ |
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56 #define CSET_STADEN 1 |
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57 #define CSET_NC_IUB 2 /* Pharmacia A.L.F. */ |
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58 #define CSET_ALF 3 /* extended NC_IUB */ |
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59 #define CSET_ABI 4 /* {A,C,G,T,N} */ |
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60 #define CSET_IBI 5 /* IBI/Pustell */ |
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61 #define CSET_DNASTAR 6 /* DNA* */ |
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62 #define CSET_DNASIS 7 |
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63 #define CSET_PCGENE 8 /* IG/PC-Gene */ |
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64 #define CSET_GENIE 9 /* MicroGenie */ |
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65 |
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66 /* define samples to delta_delta values */ |
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67 #define DELTA_IT 1 |
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68 |
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69 /* What components to read */ |
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70 #define READ_BASES (1<<0) |
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71 #define READ_SAMPLES (1<<1) |
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72 #define READ_COMMENTS (1<<2) |
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73 #define READ_ALL (READ_BASES | READ_SAMPLES | READ_COMMENTS) |
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74 |
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75 /* |
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76 *----------------------------------------------------------------------------- |
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77 * Structures and typedefs |
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78 *----------------------------------------------------------------------------- |
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79 */ |
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80 |
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81 /* |
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82 * Type definition for the Header structure |
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83 */ |
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84 typedef struct { |
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85 uint_4 magic_number; /* SCF_MAGIC */ |
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86 uint_4 samples; /* Number of elements in Samples matrix */ |
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87 uint_4 samples_offset; /* Byte offset from start of file */ |
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88 uint_4 bases; /* Number of bases in Bases matrix */ |
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89 uint_4 bases_left_clip; /* OBSOLETE: No. bases in left clip (vector) */ |
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90 uint_4 bases_right_clip; /* OBSOLETE: No. bases in right clip (qual) */ |
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91 uint_4 bases_offset; /* Byte offset from start of file */ |
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92 uint_4 comments_size; /* Number of bytes in Comment section */ |
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93 uint_4 comments_offset; /* Byte offset from start of file */ |
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94 char version[4]; /* "version.revision" */ |
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95 uint_4 sample_size; /* precision of samples (in bytes) */ |
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96 uint_4 code_set; /* uncertainty codes used */ |
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97 uint_4 private_size; /* size of private data, 0 if none */ |
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98 uint_4 private_offset; /* Byte offset from start of file */ |
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99 uint_4 spare[18]; /* Unused */ |
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100 } Header; |
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101 |
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102 /* |
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103 * Header.sample_size == 1. |
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104 */ |
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105 typedef struct { |
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106 uint_1 sample_A; /* Sample for A trace */ |
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107 uint_1 sample_C; /* Sample for C trace */ |
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108 uint_1 sample_G; /* Sample for G trace */ |
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109 uint_1 sample_T; /* Sample for T trace */ |
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110 } Samples1; |
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111 |
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112 /* |
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113 * Header.sample_size == 2. |
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114 */ |
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115 typedef struct { |
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116 uint_2 sample_A; /* Sample for A trace */ |
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117 uint_2 sample_C; /* Sample for C trace */ |
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118 uint_2 sample_G; /* Sample for G trace */ |
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119 uint_2 sample_T; /* Sample for T trace */ |
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120 } Samples2; |
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121 |
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122 /* |
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123 * Type definition for the sequence data |
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124 */ |
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125 typedef struct { |
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126 uint_4 peak_index; /* Index into Samples matrix for base position */ |
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127 uint_1 prob_A; /* Probability of it being an A */ |
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128 uint_1 prob_C; /* Probability of it being an C */ |
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129 uint_1 prob_G; /* Probability of it being an G */ |
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130 uint_1 prob_T; /* Probability of it being an T */ |
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131 char base; /* Base called */ |
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132 uint_1 spare[3]; /* Spare */ |
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133 } Bases; |
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134 |
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135 |
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136 /* |
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137 * Type definition for the comments |
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138 */ |
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139 typedef char Comments; /* Zero terminated list of \n separated entries */ |
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140 |
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141 |
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142 /* |
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143 * All of the above structs in a single scf format. |
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144 */ |
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145 typedef struct { |
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146 Header header; |
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147 union Samples { |
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148 Samples1 *samples1; |
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149 Samples2 *samples2; |
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150 } samples; |
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151 Bases *bases; |
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152 Comments *comments; |
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153 char *private_data; |
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154 } Scf; |
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155 |
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156 /* |
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157 *----------------------------------------------------------------------------- |
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158 * Function prototypes |
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159 *----------------------------------------------------------------------------- |
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160 */ |
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161 |
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162 /* |
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163 * Reading SCF Files |
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164 * ----------------- |
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165 */ |
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166 |
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167 /* |
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168 * Read the Header struct. |
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169 * Returns: |
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170 * 0 - success |
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171 * -1 - failure |
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172 */ |
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173 int read_scf_header(mFILE *fp, Header *h); |
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174 |
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175 /* |
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176 * Read a single 8bit sample |
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177 * Returns: |
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178 * 0 - success |
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179 * -1 - failure |
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180 */ |
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181 int read_scf_sample1(mFILE *fp, Samples1 *s); |
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182 |
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183 /* |
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184 * Read several 8bit samples |
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185 * Returns: |
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186 * 0 - success |
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187 * -1 - failure |
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188 */ |
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189 int read_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples); |
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190 |
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191 /* |
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192 * Read several 8bit samples in delta_delta format |
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193 * Returns: |
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194 * 0 - success |
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195 * -1 - failure |
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196 */ |
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197 int read_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples); |
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198 |
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199 /* |
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200 * Read a single 16bit sample |
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201 * Returns: |
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202 * 0 - success |
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203 * -1 - failure |
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204 */ |
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205 int read_scf_sample2(mFILE *fp, Samples2 *s); |
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206 |
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207 /* |
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208 * Read several 16bit samples |
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209 * Returns: |
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210 * 0 - success |
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211 * -1 - failure |
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212 */ |
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213 int read_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples); |
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214 |
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215 /* |
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216 * Read several 16bit samples in delta_delta format |
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217 * Returns: |
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218 * 0 - success |
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219 * -1 - failure |
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220 */ |
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221 int read_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples); |
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222 |
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223 /* |
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224 * Read a single Bases structure |
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225 * Returns: |
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226 * 0 - success |
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227 * -1 - failure |
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228 */ |
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229 int read_scf_base(mFILE *fp, Bases *b); |
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230 |
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231 /* |
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232 * Read several Bases structures consecutively |
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233 * Returns: |
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234 * 0 - success |
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235 * -1 - failure |
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236 */ |
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237 int read_scf_bases(mFILE *fp, Bases *b, size_t num_bases); |
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238 |
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239 /* |
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240 * Read Bases, peak_indexes and probs |
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241 * Returns: |
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242 * 0 - success |
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243 * -1 - failure |
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244 */ |
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245 int read_scf_bases3(mFILE *fp, Bases *b, size_t num_bases); |
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246 |
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247 /* |
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248 * Read the SCF Comments. |
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249 * Returns: |
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250 * 0 - success |
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251 * -1 - failure |
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252 */ |
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253 int read_scf_comment(mFILE *fp, Comments *c, size_t l); |
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254 |
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255 /* |
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256 * Reads a whole SCF file into a Scf structure. This memory for this |
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257 * structure is allocated by this routine. To free this memory use |
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258 * scf_deallocate(). |
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259 * Returns: |
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260 * Scf * - Success, the Scf structure read. |
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261 * NULL - Failure. |
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262 * On failure NULL is returned, otherwise the Scf struct. |
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263 */ |
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264 Scf *read_scf(char *fn); |
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265 Scf *fread_scf(FILE *fp); |
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266 Scf *mfread_scf(mFILE *fp); |
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267 |
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268 |
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269 /* |
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270 * Writing SCF Files |
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271 * ----------------- |
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272 */ |
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273 |
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274 /* |
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275 * Write the Header struct. |
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276 * Returns: |
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277 * 0 - success |
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278 * -1 - failure |
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279 */ |
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280 int write_scf_header(mFILE *fp, Header *h); |
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281 |
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282 /* |
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283 * Write a single 8bit sample |
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284 * Returns: |
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285 * 0 - success |
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286 * -1 - failure |
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287 */ |
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288 int write_scf_sample1(mFILE *fp, Samples1 *s); |
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289 |
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290 /* |
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291 * Write several 8bit samples |
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292 * Returns: |
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293 * 0 - success |
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294 * -1 - failure |
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295 */ |
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296 int write_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples); |
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297 |
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298 /* |
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299 * Write several 8bit samples in delta_delta format |
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300 * Returns: |
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301 * 0 - success |
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302 * -1 - failure |
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303 */ |
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304 int write_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples); |
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305 |
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306 /* |
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307 * Write 16bit samples |
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308 * Returns: |
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309 * 0 - success |
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310 * -1 - failure |
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311 */ |
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312 int write_scf_sample2(mFILE *fp, Samples2 *s); |
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313 |
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314 /* |
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315 * Write several 16bit samples |
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316 * Returns: |
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317 * 0 - success |
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318 * -1 - failure |
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319 */ |
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320 int write_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples); |
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321 |
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322 /* |
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323 * Write several 16bit samples in delta_delta format |
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324 * Returns: |
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325 * 0 - success |
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326 * -1 - failure |
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327 */ |
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328 int write_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples); |
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329 |
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330 /* |
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331 * Write the Bases structure |
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332 * Returns: |
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333 * 0 - success |
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334 * -1 - failure |
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335 */ |
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336 int write_scf_base(mFILE *fp, Bases *b); |
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337 |
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338 /* |
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339 * Write the several Bases structures consecutively |
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340 * Returns: |
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341 * 0 - success |
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342 * -1 - failure |
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343 */ |
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344 int write_scf_bases(mFILE *fp, Bases *b, size_t num_bases); |
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345 |
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346 /* |
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347 * Write the bases, then peak indexes, then probs |
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348 * Returns: |
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349 * 0 - success |
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350 * -1 - failure |
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351 */ |
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352 int write_scf_bases3(mFILE *fp, Bases *b, size_t num_bases); |
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353 |
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354 /* |
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355 * Write the SCF Comments. |
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356 * Returns: |
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357 * 0 - success |
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358 * -1 - failure |
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359 */ |
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360 int write_scf_comment(mFILE *fp, Comments *c, size_t l); |
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361 |
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362 |
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363 /* |
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364 * Writes a whole Scf structure to filename "fn". |
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365 * This initialises several fields in the Header struct for you. These are: |
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366 * samples_offset |
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367 * bases_offset |
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368 * comments_offset |
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369 * magic_number |
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370 * |
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371 * All other fields are assumed to be correctly set. |
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372 * |
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373 * Returns: |
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374 * 0 for success |
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375 * -1 for failure |
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376 */ |
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377 int write_scf(Scf *scf, char *fn); |
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378 int fwrite_scf(Scf *scf, FILE *fp); |
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379 int mfwrite_scf(Scf *scf, mFILE *fp); |
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380 |
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381 /* |
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382 * Request which (major) version of scf to use when writing. |
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383 * Defaults to the latest. Currently suitable fields are |
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384 * 2 and 3. |
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385 * |
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386 * Returns 0 for success, -1 for failure. |
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387 */ |
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388 int set_scf_version(int version); |
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389 |
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390 |
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391 /* |
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392 * Miscellaneous SCF utilities |
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393 * --------------------------- |
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394 */ |
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395 |
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396 /* |
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397 * Converts an SCF version string (eg "2.00") to a float |
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398 */ |
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399 float scf_version_str2float(char version[]); |
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400 |
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401 /* |
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402 * Converts an SCF version float (eg 2.00) to a string |
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403 * Returns: |
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404 * A statically allocated 5 character string. |
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405 */ |
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406 char *scf_version_float2str(float f); |
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407 |
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408 /* |
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409 * Allocates memory for the scf elements based upon arguments passed. |
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410 * Returns; |
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411 * Scf * - Success. The scf structure and it's samples, bases, |
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412 * and comments fields have been allocated. |
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413 * NULL - Failure. |
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414 */ |
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415 Scf *scf_allocate(int num_samples, int sample_size, int num_bases, |
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416 int comment_size, int private_size); |
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417 |
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418 /* |
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419 * Frees memory allocated by scf_allocate. |
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420 */ |
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421 void scf_deallocate(Scf *scf); |
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422 |
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423 /* |
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424 * Checks to see if the file with name "fn" is in SCF format. |
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425 * Returns: |
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426 * 1 - is in SCF format |
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427 * 0 - is not in SCF format |
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428 * -1 - failure |
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429 */ |
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430 int is_scf(char *fn); |
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431 |
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432 /* |
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433 * Change sample points to delta_delta values for uint1 |
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434 */ |
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435 void scf_delta_samples1 ( int1 samples[], int num_samples, int job); |
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436 |
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437 /* |
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438 * Change sample points to delta_delta values for uint2 |
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439 */ |
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440 void scf_delta_samples2 ( uint2 samples[], int num_samples, int job); |
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441 |
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442 #ifdef __cplusplus |
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443 } |
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444 #endif |
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445 |
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446 #endif /*_SCF_H_*/ |
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447 |