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1 /*
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2 * Copyright (c) <2008 - 2009>, 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 name of the <ORGANIZATION> nor the names of its contributors may be
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14 * used to endorse or promote products derived from this software without specific
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15 * prior written permission.
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16 *
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17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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28 */
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29
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30 /*
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31 * Author : Faraz Hach
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32 * Email : fhach AT cs DOT sfu
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33 * Last Update : 2009-12-08
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34 */
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35
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36
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37 #include <stdio.h>
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38 #include <stdlib.h>
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39 #include <zlib.h>
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40 #include <string.h>
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41 #include "Common.h"
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42 #include "Output.h"
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43
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44 FILE *_out_fp;
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45 gzFile _out_gzfp;
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46
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47
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48
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49 void finalizeGZOutput()
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50 {
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51 gzclose(_out_gzfp);
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52 }
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53
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54 void finalizeTXOutput()
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55 {
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56 fclose(_out_fp);
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57 }
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58
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59
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60 void gzOutputQ(SAM map)
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61 {
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62 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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63 map.QNAME,
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64 map.FLAG,
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65 map.RNAME,
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66 map.POS,
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67 map.MAPQ,
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68 map.CIGAR,
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69 map.MRNAME,
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70 map.MPOS,
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71 map.ISIZE,
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72 map.SEQ,
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73 map.QUAL);
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74
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75 int i;
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76
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77 for ( i = 0; i < map.optSize; i++)
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78 {
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79 switch (map.optFields[i].type)
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80 {
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81 case 'A':
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82 gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
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83 break;
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84 case 'i':
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85 gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
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86 break;
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87 case 'f':
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88 gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
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89 break;
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90 case 'Z':
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91 case 'H':
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92 gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
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93 break;
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94 }
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95 }
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96 gzprintf(_out_gzfp, "\n");
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97 }
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98
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99 void outputQ(SAM map)
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100 {
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101
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102 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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103 map.QNAME,
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104 map.FLAG,
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105 map.RNAME,
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106 map.POS,
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107 map.MAPQ,
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108 map.CIGAR,
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109 map.MRNAME,
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110 map.MPOS,
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111 map.ISIZE,
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112 map.SEQ,
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113 map.QUAL);
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114
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115
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116 int i;
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117
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118 for ( i = 0; i < map.optSize; i++)
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119 {
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120 switch (map.optFields[i].type)
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121 {
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122 case 'A':
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123 fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
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124 break;
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125 case 'i':
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126 fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
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127 break;
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128 case 'f':
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129 fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
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130 break;
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131 case 'Z':
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132 case 'H':
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133 fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
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134 break;
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135 }
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136 }
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137
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138 fprintf(_out_fp, "\n");
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139 }
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140
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141 int initOutput ( char *fileName, int compressed)
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142 {
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143 if (compressed)
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144 {
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145 char newFileName[strlen(mappingOutputPath)+strlen(fileName)+4];
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146 sprintf(newFileName, "%s%s.gz", mappingOutputPath, fileName);
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147 _out_gzfp = fileOpenGZ(newFileName, "w1f");
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148 if (_out_gzfp == Z_NULL)
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149 {
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150 return 0;
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151 }
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152
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153 finalizeOutput = &finalizeGZOutput;
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154
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155 output = &gzOutputQ;
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156 }
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157 else
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158 {
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159
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160 char newFileName[strlen(mappingOutputPath)+strlen(fileName)];
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161 sprintf(newFileName, "%s%s", mappingOutputPath, fileName);
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162
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163 _out_fp = fileOpen(newFileName, "w");
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164 if (_out_fp == NULL)
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165 {
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166 return 0;
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167 }
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168
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169 finalizeOutput = &finalizeTXOutput;
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170 output = &outputQ;
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171 }
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172 return 1;
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173 }
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174
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175
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