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1
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1 /*
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2 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
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3 * All rights reserved.
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4 *
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5 * Redistribution and use in source and binary forms, with or without modification,
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6 * are permitted provided that the following conditions are met:
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7 *
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8 * Redistributions of source code must retain the above copyright notice, this list
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9 * of conditions and the following disclaimer.
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10 * - Redistributions in binary form must reproduce the above copyright notice, this
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11 * list of conditions and the following disclaimer in the documentation and/or other
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12 * materials provided with the distribution.
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13 * - Neither the names of the University of Washington, Simon Fraser University,
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14 * nor the names of its contributors may be
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15 * used to endorse or promote products derived from this software without specific
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16 * prior written permission.
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17 *
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18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31 /*
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32 Authors:
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33 Farhad Hormozdiari
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34 Faraz Hach
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35 Can Alkan
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36 Emails:
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37 farhadh AT uw DOT edu
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38 fhach AT cs DOT sfu DOT ca
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39 calkan AT uw DOT edu
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40 */
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41
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42
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43 #include <stdio.h>
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44 #include <stdlib.h>
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45 #include <zlib.h>
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46 #include <string.h>
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47 #include "Common.h"
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48 #include "Output.h"
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49
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50 FILE *_out_fp;
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51 gzFile _out_gzfp;
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52
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53 char buffer[300000];
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54 int bufferSize = 0;
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55
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56
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57 void finalizeGZOutput()
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58 {
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59 gzclose(_out_gzfp);
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60 }
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61
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62 void finalizeTXOutput()
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63 {
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64 fclose(_out_fp);
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65 }
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66
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67
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68 void gzOutputQ(SAM map)
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69 {
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70 gzprintf(_out_gzfp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
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71 map.QNAME,
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72 map.FLAG,
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73 map.RNAME,
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74 map.POS,
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75 map.MAPQ,
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76 map.CIGAR,
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77 map.MRNAME,
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78 map.MPOS,
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79 map.ISIZE,
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80 map.SEQ,
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81 map.QUAL);
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82
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83 int i;
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84
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85 for ( i = 0; i < map.optSize; i++)
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86 {
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87 switch (map.optFields[i].type)
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88 {
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89 case 'A':
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90 gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
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91 break;
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92 case 'i':
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93 gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
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94 break;
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95 case 'f':
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96 gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
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97 break;
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98 case 'Z':
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99 case 'H':
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100 gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
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101 break;
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102 }
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103 }
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104 gzprintf(_out_gzfp, "\n");
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105 }
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106
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107 void outputSAM(FILE *fp, SAM map)
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108 {
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109 fprintf(fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
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110 map.QNAME,
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111 map.FLAG,
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112 map.RNAME,
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113 map.POS,
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114 map.MAPQ,
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115 map.CIGAR,
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116 map.MRNAME,
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117 map.MPOS,
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118 map.ISIZE,
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119 map.SEQ,
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120 map.QUAL);
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121
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122
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123 int i;
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124
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125 for ( i = 0; i < map.optSize; i++)
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126 {
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127 switch (map.optFields[i].type)
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128 {
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129 case 'A':
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130 fprintf(fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
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131 break;
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132 case 'i':
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133 fprintf(fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
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134 break;
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135 case 'f':
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136 fprintf(fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
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137 break;
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138 case 'Z':
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139 case 'H':
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140 fprintf(fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
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141 break;
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142 }
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143 }
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144
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145 fprintf(fp, "\n");
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146
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147 }
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148
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149 void outputQ(SAM map)
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150 {
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151
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152 fprintf(_out_fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
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153 map.QNAME,
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154 map.FLAG,
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155 map.RNAME,
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156 map.POS,
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157 map.MAPQ,
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158 map.CIGAR,
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159 map.MRNAME,
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160 map.MPOS,
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161 map.ISIZE,
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162 map.SEQ,
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163 map.QUAL);
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164
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165
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166 int i;
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167
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168 for ( i = 0; i < map.optSize; i++)
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169 {
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170 switch (map.optFields[i].type)
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171 {
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172 case 'A':
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173 fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
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174 break;
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175 case 'i':
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176 fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
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177 break;
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178 case 'f':
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179 fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
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180 break;
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181 case 'Z':
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182 case 'H':
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183 fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
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184 break;
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185 }
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186 }
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187
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188 fprintf(_out_fp, "\n");
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189 }
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190
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191 int initOutput ( char *fileName, int compressed)
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192 {
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193 if (compressed)
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194 {
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195 char newFileName[strlen(fileName)+4];
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196 sprintf(newFileName, "%s.gz", fileName);
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197
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198 _out_gzfp = fileOpenGZ(newFileName, "w1f");
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199 if (_out_gzfp == Z_NULL)
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200 {
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201 return 0;
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202 }
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203
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204 finalizeOutput = &finalizeGZOutput;
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205
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206 output = &gzOutputQ;
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207 }
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208 else
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209 {
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210 _out_fp = fileOpen(fileName, "w");
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211 if (_out_fp == NULL)
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212 {
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213 return 0;
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214 }
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215
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216 finalizeOutput = &finalizeTXOutput;
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217 output = &outputQ;
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218 }
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219 buffer[0] = '\0';
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220 return 1;
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221 }
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222
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223 FILE* getOutputFILE()
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224 {
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225 if(_out_fp != NULL)
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226 return _out_fp;
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227 else if(_out_gzfp != NULL)
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228 return _out_gzfp;
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229 else
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230 return NULL;
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231 }
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