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0
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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
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44 #include <stdio.h>
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45 #include <stdlib.h>
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46 #include <string.h>
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47 #include <ctype.h>
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48 #include <zlib.h>
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49 #include "Common.h"
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50 #include "Reads.h"
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51
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52 #define CHARCODE(a) (a=='A' ? 0 : (a=='C' ? 1 : (a=='G' ? 2 : (a=='T' ? 3 : 4))))
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53
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54 FILE *_r_fp1;
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55 FILE *_r_fp2;
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56 gzFile _r_gzfp1;
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57 gzFile _r_gzfp2;
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58 Read *_r_seq;
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59 int _r_seqCnt;
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60 int *_r_samplingLocs;
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61
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62 /**********************************************/
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63 char *(*readFirstSeq)(char *);
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64 char *(*readSecondSeq)(char *);
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65 /**********************************************/
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66 char *readFirstSeqTXT( char *seq )
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67 {
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68 return fgets(seq, SEQ_MAX_LENGTH, _r_fp1);
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69 }
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70
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71 /**********************************************/
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72 char *readSecondSeqTXT( char *seq )
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73 {
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74 return fgets(seq, SEQ_MAX_LENGTH, _r_fp2);
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75 }
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76 /**********************************************/
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77 char *readFirstSeqGZ( char *seq )
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78 {
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79 return gzgets(_r_gzfp1, seq, SEQ_MAX_LENGTH);
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80 }
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81
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82 /**********************************************/
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83 char *readSecondSeqGZ( char *seq )
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84 {
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85 return gzgets(_r_gzfp2, seq, SEQ_MAX_LENGTH);
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86 }
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87 /**********************************************/
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88 int toCompareRead(const void * elem1, const void * elem2)
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89 {
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90 return strcmp(((Read *)elem1)->seq, ((Read *)elem2)->seq);
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91 }
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92 /**********************************************/
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93 int readAllReads(char *fileName1,
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94 char *fileName2,
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95 int compressed,
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96 unsigned char *fastq,
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97 unsigned char pairedEnd,
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98 Read **seqList,
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99 unsigned int *seqListSize)
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100 {
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101 double startTime=getTime();
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102
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103 char seq1[SEQ_MAX_LENGTH];
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104 char rseq1[SEQ_MAX_LENGTH];
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105 char name1[SEQ_MAX_LENGTH];
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106 char qual1[SEQ_MAX_LENGTH];
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107 char seq2[SEQ_MAX_LENGTH];
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108 char rseq2[SEQ_MAX_LENGTH];
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109 char name2[SEQ_MAX_LENGTH];
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110 char qual2[SEQ_MAX_LENGTH];
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111
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112 char dummy[SEQ_MAX_LENGTH];
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113 char ch;
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114 int err1, err2;
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115 int nCnt;
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116 int discarded = 0;
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117 int seqCnt = 0;
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118 int maxCnt = 0;
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119 int i;
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120 Read *list = NULL;
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121
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122 int clipped = 0;
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123
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124 if (!compressed)
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125 {
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126 _r_fp1 = fileOpen( fileName1, "r");
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127
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128 if (_r_fp1 == NULL)
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129 {
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130 return 0;
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131 }
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132
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133 ch = fgetc(_r_fp1);
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134
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135 if ( pairedEnd && fileName2 != NULL )
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136 {
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137 _r_fp2 = fileOpen ( fileName2, "r" );
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138 if (_r_fp2 == NULL)
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139 {
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140 return 0;
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141 }
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142 }
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143 else
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144 {
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145 _r_fp2 = _r_fp1;
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146 }
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147
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148 readFirstSeq = &readFirstSeqTXT;
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149 readSecondSeq = &readSecondSeqTXT;
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150 }
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151 else
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152 {
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153
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154 _r_gzfp1 = fileOpenGZ (fileName1, "r");
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155
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156 if (_r_gzfp1 == NULL)
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157 {
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158 return 0;
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159 }
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160
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161 ch = gzgetc(_r_gzfp1);
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162
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163 if ( pairedEnd && fileName2 != NULL )
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164 {
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165 _r_gzfp2 = fileOpenGZ ( fileName2, "r" );
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166 if (_r_gzfp2 == NULL)
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167 {
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168 return 0;
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169 }
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170 }
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171 else
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172 {
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173 _r_gzfp2 = _r_gzfp1;
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174 }
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175
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176 readFirstSeq = &readFirstSeqGZ;
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177 readSecondSeq = &readSecondSeqGZ;
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178 }
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179
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180 if (ch == '>')
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181 *fastq = 0;
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182 else
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183 *fastq = 1;
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184
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185 // Counting the number of lines in the file
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186 while (readFirstSeq(dummy)) maxCnt++;
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187
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188 if (!compressed)
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189 {
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190 rewind(_r_fp1);
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191 }
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192 else
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193 {
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194 gzrewind(_r_gzfp1);
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195 }
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196
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197 // Calculating the Maximum # of sequences
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198 if (*fastq)
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199 {
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200 maxCnt /= 4;
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201 }
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202 else
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203 {
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204 maxCnt /= 2;
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205 }
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206
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207 if (pairedEnd && fileName2 != NULL )
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208 maxCnt *= 2;
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209
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210 list = getMem(sizeof(Read)*maxCnt);
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211
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212 while( readFirstSeq(name1) )
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213 {
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214 err1 = 0;
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215 err2 = 0;
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216 readFirstSeq(seq1);
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217 name1[strlen(name1)-1] = '\0';
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218
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219 if ( *fastq )
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220 {
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221 readFirstSeq(dummy);
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222 readFirstSeq(qual1);
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223 qual1[strlen(qual1)-1] = '\0';
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224 }
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225 else
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226 {
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227 sprintf(qual1, "*");
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228 }
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229
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230 // Cropping
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231 if (cropSize > 0)
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232 {
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233 seq1[cropSize] = '\0';
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234 if ( *fastq )
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235 qual1[cropSize] = '\0';
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236 }
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237
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238
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239 nCnt = 0;
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240 for (i=0; i<strlen(seq1); i++)
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241 {
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242 seq1[i] = toupper (seq1[i]);
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243 if (seq1[i] == 'N')
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244 {
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245 nCnt++;
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246 }
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247 else if (isspace(seq1[i]))
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248 {
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249
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250 seq1[i] = '\0';
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251 break;
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252 }
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253 }
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254
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255 if (nCnt > errThreshold)
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256 {
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257 err1 = 1;
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258 }
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259
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260 // Reading the second seq of pair-ends
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261 if (pairedEnd)
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262 {
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263 readSecondSeq(name2);
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264 readSecondSeq(seq2);
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265 name2[strlen(name2)-1] = '\0';
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266
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267
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268 if ( *fastq )
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269 {
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270 readSecondSeq(dummy);
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271 readSecondSeq(qual2);
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272
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273 qual2[strlen(qual2)-1] = '\0';
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274 }
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275 else
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276 {
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277 sprintf(qual2, "*");
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278 }
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279
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280
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281 // Cropping
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282 if (cropSize > 0)
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283 {
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284 seq2[cropSize] = '\0';
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285 if ( *fastq )
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286 qual2[cropSize] = '\0';
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287 }
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288
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289
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290 nCnt = 0;
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291 for (i=0; i<strlen(seq2); i++)
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292 {
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293 seq2[i] = toupper (seq2[i]);
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294 if (seq2[i] == 'N')
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295 {
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296 nCnt++;
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297
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298 }
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299 else if (isspace(seq2[i]))
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300 {
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301 seq2[i] = '\0';
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302 }
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303 }
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304 if (nCnt > errThreshold)
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305 {
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306 err2 = 1;
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307 }
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308
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309
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310 if (strlen(seq1) < strlen(seq2)) {
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311 seq2[strlen(seq1)] = '\0';
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312 if ( *fastq )
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313 qual2[strlen(seq1)] = '\0';
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314 if (!clipped) clipped = 2;
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315 }
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316 else if (strlen(seq1) > strlen(seq2)){
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317 seq1[strlen(seq2)] = '\0';
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318 if ( *fastq )
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319 qual1[strlen(seq2)] = '\0';
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320 if (!clipped) clipped = 1;
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321 }
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322
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323 if (clipped == 1 || clipped == 2){
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324 fprintf(stdout, "[PE mode warning] Sequence lengths are different, read #%d is clipped to match.\n", clipped);
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325 clipped = 3;
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326 }
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327
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328
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329
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330 }
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331
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332 if (!pairedEnd && !err1)
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333 {
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334 int _mtmp = strlen(seq1);
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335 list[seqCnt].hits = getMem (1+3*_mtmp+3+strlen(name1)+1);
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336 list[seqCnt].seq = list[seqCnt].hits + 1;
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337 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
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338 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
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339 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
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340
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341 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
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342 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
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343
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344 list[seqCnt].readNumber = seqCnt;
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345
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346 reverseComplete(seq1, rseq1, _mtmp);
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347 rseq1[_mtmp] = '\0';
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348 int i;
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349
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350 list[seqCnt].hits[0] = 0;
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351
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352 for (i=0; i<=_mtmp; i++)
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353 {
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354 list[seqCnt].seq[i] = seq1[i];
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355 list[seqCnt].rseq[i] = rseq1[i] ;
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356 list[seqCnt].qual[i] = qual1[i];
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357 }
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358
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359
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360 //MAKE HASH VALUE
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361 short code = 0;
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362
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363 for(i=0; i < 4; i++)
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364 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
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365 list[seqCnt].hashValue[0] = code;
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366
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367
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368 for(i = 1; i < _mtmp-3; i++)
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369 {
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370 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
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371 }
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372
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373
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374 code = 0;
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375 for(i=0; i < 4; i++)
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376 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
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377 list[seqCnt].rhashValue[0] = code;
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378
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379
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380 for(i = 1; i < _mtmp-3; i++)
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381 {
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382 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
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383 }
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384
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385 int j = 0;
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386 int tmpSize = _mtmp / (errThreshold+1);
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387
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388 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
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389 for(i=0; i < errThreshold+1; i++)
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390 {
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391 code = 0;
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392 for(j = 0; j < tmpSize; j++)
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393 {
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394 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
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395 }
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396 list[seqCnt].hashValSampleSize[i] = code;
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397 }
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398
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399 sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
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400
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401 seqCnt++;
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402
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403 }
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404 else if (pairedEnd && !err1 && !err2)
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405 {
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406
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407 // Naming Conventions X/1, X/2 OR X
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408 int tmplen = strlen(name1);
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409 if (strcmp(name1, name2) != 0)
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410 {
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411 tmplen = strlen(name1)-2;
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412 }
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413
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414 //first seq
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415 int _mtmp = strlen(seq1);
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416 list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
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417 list[seqCnt].seq = list[seqCnt].hits + 1;
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418 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
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419 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
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420 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
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421
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422 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
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423 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
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424 list[seqCnt].readNumber = seqCnt;
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425
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426 reverseComplete(seq1, rseq1, _mtmp);
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427 rseq1[_mtmp] = '\0';
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428 int i;
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429
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430 list[seqCnt].hits[0] = 0;
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431
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432 for (i=0; i<=_mtmp; i++)
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433 {
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434 list[seqCnt].seq[i] = seq1[i];
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435 list[seqCnt].rseq[i] = rseq1[i] ;
|
|
|
436 list[seqCnt].qual[i] = qual1[i];
|
|
|
437 }
|
|
|
438
|
|
|
439
|
|
|
440 name1[tmplen]='\0';
|
|
|
441
|
|
|
442 //MAKE HASH VALUE
|
|
|
443 short code = 0;
|
|
|
444
|
|
|
445 for(i=0; i < 4; i++)
|
|
|
446 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
|
|
|
447 list[seqCnt].hashValue[0] = code;
|
|
|
448
|
|
|
449
|
|
|
450 for(i = 1; i < _mtmp-3; i++)
|
|
|
451 {
|
|
|
452 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
|
|
|
453 }
|
|
|
454
|
|
|
455
|
|
|
456 code = 0;
|
|
|
457 for(i=0; i < 4; i++)
|
|
|
458 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
|
|
|
459 list[seqCnt].rhashValue[0] = code;
|
|
|
460
|
|
|
461
|
|
|
462 for(i = 1; i < _mtmp-3; i++)
|
|
|
463 {
|
|
|
464 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
|
|
|
465 }
|
|
|
466
|
|
|
467 int j = 0;
|
|
|
468 int tmpSize = _mtmp / (errThreshold+1);
|
|
|
469
|
|
|
470 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
|
|
|
471 for(i=0; i < errThreshold+1; i++)
|
|
|
472 {
|
|
|
473 code = 0;
|
|
|
474 for(j = 0; j < tmpSize; j++)
|
|
|
475 {
|
|
|
476 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
|
|
|
477 }
|
|
|
478 list[seqCnt].hashValSampleSize[i] = code;
|
|
|
479 }
|
|
|
480
|
|
|
481 sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
|
|
|
482
|
|
|
483
|
|
|
484 seqCnt++;
|
|
|
485
|
|
|
486 //second seq
|
|
|
487 list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
|
|
|
488 list[seqCnt].seq = list[seqCnt].hits + 1;
|
|
|
489 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
|
|
|
490 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
|
|
|
491 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
|
|
|
492
|
|
|
493 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
|
|
|
494 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
|
|
|
495 list[seqCnt].readNumber = seqCnt;
|
|
|
496
|
|
|
497 reverseComplete(seq2, rseq2, _mtmp);
|
|
|
498 rseq2[_mtmp] = '\0';
|
|
|
499
|
|
|
500 list[seqCnt].hits[0] = 0;
|
|
|
501
|
|
|
502 for (i=0; i<=_mtmp; i++)
|
|
|
503 {
|
|
|
504 list[seqCnt].seq[i] = seq2[i];
|
|
|
505 list[seqCnt].rseq[i] = rseq2[i] ;
|
|
|
506 list[seqCnt].qual[i] = qual2[i];
|
|
|
507 }
|
|
|
508
|
|
|
509
|
|
|
510 name2[tmplen]='\0';
|
|
|
511
|
|
|
512 //MAKE HASH VALUE
|
|
|
513 code = 0;
|
|
|
514
|
|
|
515 for(i=0; i < 4; i++)
|
|
|
516 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
|
|
|
517 list[seqCnt].hashValue[0] = code;
|
|
|
518
|
|
|
519
|
|
|
520 for(i = 1; i < _mtmp-3; i++)
|
|
|
521 {
|
|
|
522 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
|
|
|
523 }
|
|
|
524
|
|
|
525
|
|
|
526 code = 0;
|
|
|
527 for(i=0; i < 4; i++)
|
|
|
528 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
|
|
|
529 list[seqCnt].rhashValue[0] = code;
|
|
|
530
|
|
|
531
|
|
|
532 for(i = 1; i < _mtmp-3; i++)
|
|
|
533 {
|
|
|
534 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
|
|
|
535 }
|
|
|
536
|
|
|
537 j = 0;
|
|
|
538 tmpSize = _mtmp / (errThreshold+1);
|
|
|
539
|
|
|
540 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
|
|
|
541 for(i=0; i < errThreshold+1; i++)
|
|
|
542 {
|
|
|
543 code = 0;
|
|
|
544 for(j = 0; j < tmpSize; j++)
|
|
|
545 {
|
|
|
546 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
|
|
|
547 }
|
|
|
548 list[seqCnt].hashValSampleSize[i] = code;
|
|
|
549 }
|
|
|
550
|
|
|
551 sprintf(list[seqCnt].name,"%s%c", ((char*)name2)+1,'\0');
|
|
|
552
|
|
|
553 seqCnt++;
|
|
|
554
|
|
|
555 }
|
|
|
556 else
|
|
|
557 {
|
|
|
558 discarded++;
|
|
|
559 }
|
|
|
560 }
|
|
|
561
|
|
|
562 if (seqCnt > 0)
|
|
|
563 {
|
|
|
564 SEQ_LENGTH = strlen(list[0].seq);
|
|
|
565 }
|
|
|
566 else
|
|
|
567 {
|
|
|
568 fprintf(stdout, "ERROR: No reads can be found for mapping\n");
|
|
|
569 return 0;
|
|
|
570 }
|
|
|
571
|
|
|
572
|
|
|
573 // Closing Files
|
|
|
574 if (!compressed)
|
|
|
575 {
|
|
|
576 fclose(_r_fp1);
|
|
|
577 if ( pairedEnd && fileName2 != NULL )
|
|
|
578 {
|
|
|
579 fclose(_r_fp2);
|
|
|
580 }
|
|
|
581 }
|
|
|
582 else
|
|
|
583 {
|
|
|
584 gzclose(_r_gzfp1);
|
|
|
585 if ( pairedEnd && fileName2 != NULL)
|
|
|
586 {
|
|
|
587 gzclose(_r_fp2);
|
|
|
588 }
|
|
|
589 }
|
|
|
590
|
|
|
591 //qsort(list, seqCnt, sizeof(Read), toCompareRead);
|
|
|
592
|
|
|
593 adjustQual(list, seqCnt);
|
|
|
594
|
|
|
595 *seqList = list;
|
|
|
596 *seqListSize = seqCnt;
|
|
|
597
|
|
|
598
|
|
|
599 _r_seq = list;
|
|
|
600 _r_seqCnt = seqCnt;
|
|
|
601
|
|
|
602 if ( pairedEnd ) discarded *= 2;
|
|
|
603
|
|
|
604 if (seqCnt>1)
|
|
|
605 fprintf(stdout, "%d sequences are read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
|
|
|
606 else
|
|
|
607 fprintf(stdout, "%d sequence is read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
|
|
|
608
|
|
|
609
|
|
|
610
|
|
|
611 return 1;
|
|
|
612 }
|
|
|
613 /**********************************************/
|
|
|
614 void loadSamplingLocations(int **samplingLocs, int * samplingLocsSize)
|
|
|
615 {
|
|
|
616 int i;
|
|
|
617 int samLocsSize = errThreshold + 1;
|
|
|
618 int *samLocs = getMem(sizeof(int)*samLocsSize);
|
|
|
619
|
|
|
620 for (i=0; i<samLocsSize; i++)
|
|
|
621 {
|
|
|
622 samLocs[i] = (SEQ_LENGTH / samLocsSize) *i;
|
|
|
623 if ( samLocs[i] + WINDOW_SIZE > SEQ_LENGTH)
|
|
|
624 samLocs[i] = SEQ_LENGTH - WINDOW_SIZE;
|
|
|
625 }
|
|
|
626
|
|
|
627 // Outputing the sampling locations
|
|
|
628
|
|
|
629 /*
|
|
|
630
|
|
|
631 int j;
|
|
|
632 for (i=0; i<SEQ_LENGTH; i++)
|
|
|
633 {
|
|
|
634 fprintf(stdout, "-");
|
|
|
635 }
|
|
|
636 fprintf(stdout, "\n");
|
|
|
637
|
|
|
638 for ( i=0; i<samLocsSize; i++ )
|
|
|
639 {
|
|
|
640 for ( j=0; j<samLocs[i]; j++ )
|
|
|
641 {
|
|
|
642 fprintf(stdout," ");
|
|
|
643 }
|
|
|
644 for (j=0; j<WINDOW_SIZE; j++)
|
|
|
645 {
|
|
|
646 fprintf(stdout,"+");
|
|
|
647 }
|
|
|
648 fprintf(stdout, "\n");
|
|
|
649 fflush(stdout);
|
|
|
650 }
|
|
|
651
|
|
|
652
|
|
|
653 for ( i=0; i<SEQ_LENGTH; i++ )
|
|
|
654 {
|
|
|
655 fprintf(stdout, "-");
|
|
|
656 }
|
|
|
657 fprintf(stdout, "\n");
|
|
|
658
|
|
|
659 */
|
|
|
660
|
|
|
661 *samplingLocs = samLocs;
|
|
|
662 *samplingLocsSize = samLocsSize;
|
|
|
663 _r_samplingLocs = samLocs;
|
|
|
664 }
|
|
|
665
|
|
|
666 void finalizeReads(char *fileName)
|
|
|
667 {
|
|
|
668 FILE *fp1=NULL;
|
|
|
669
|
|
|
670 if (fileName != NULL)
|
|
|
671 {
|
|
|
672 fp1 = fileOpen(fileName, "w");
|
|
|
673 }
|
|
|
674 if (pairedEndMode)
|
|
|
675 _r_seqCnt /=2;
|
|
|
676
|
|
|
677 int i=0;
|
|
|
678 for (i = 0; i < _r_seqCnt; i++)
|
|
|
679 {
|
|
|
680 if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual,"*")!=0)
|
|
|
681 {
|
|
|
682 fprintf(fp1,"@%s/1\n%s\n+\n%s\n@%s/2\n%s\n+\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].qual, _r_seq[i*2].name, _r_seq[i*2+1].seq, _r_seq[i*2+1].qual);
|
|
|
683 }
|
|
|
684 else if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0)
|
|
|
685 {
|
|
|
686 fprintf(fp1, ">%s/1\n%s\n>%s/2\n%shits=%d\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq, _r_seq[2*i+1].hits[0]);
|
|
|
687 }
|
|
|
688 else if (!pairedEndMode && _r_seq[i].hits[0] == 0 && strcmp(_r_seq[i].qual, "*")!=0)
|
|
|
689 {
|
|
|
690 fprintf(fp1,"@%s\n%s\n+\n%s\n", _r_seq[i].name, _r_seq[i].seq, _r_seq[i].qual);
|
|
|
691 }
|
|
|
692 else if (!pairedEndMode && _r_seq[i].hits[0] == 0)
|
|
|
693 {
|
|
|
694 fprintf(fp1,">%s\n%s\n", _r_seq[i].name, _r_seq[i].seq);
|
|
|
695 }
|
|
|
696 }
|
|
|
697
|
|
|
698 fclose(fp1);
|
|
|
699 if (pairedEndMode)
|
|
|
700 _r_seqCnt *= 2;
|
|
|
701
|
|
|
702 for (i = 0; i < _r_seqCnt; i++)
|
|
|
703 {
|
|
|
704 freeMem(_r_seq[i].hits,0);
|
|
|
705 }
|
|
|
706
|
|
|
707
|
|
|
708 freeMem(_r_seq,0);
|
|
|
709 freeMem(_r_samplingLocs,0);
|
|
|
710 }
|
|
|
711
|
|
|
712 void adjustQual(Read *list, int seqCnt){
|
|
|
713 /* This function will automatically determine the phred_offset and readjust quality values if needed */
|
|
|
714 }
|
|
|
715
|
|
|
716
|
|
|
717
|
|
|
718 /*void finalizeOEAReads(char *fileName)
|
|
|
719 {
|
|
|
720 FILE *fp1=NULL;
|
|
|
721 FILE *fp2=NULL;
|
|
|
722
|
|
|
723 //printf("OEA%s\n", fileName);
|
|
|
724 char fileNameOEA1[200];
|
|
|
725 char fileNameOEA2[200];
|
|
|
726 sprintf(fileNameOEA1, "%s_OEA1", fileName);
|
|
|
727 sprintf(fileNameOEA2, "%s_OEA2", fileName);
|
|
|
728
|
|
|
729
|
|
|
730 if (fileName != NULL)
|
|
|
731 {
|
|
|
732 fp1 = fileOpen(fileNameOEA1, "w");
|
|
|
733 fp2 = fileOpen(fileNameOEA2, "w");
|
|
|
734 }
|
|
|
735 if (pairedEndMode)
|
|
|
736 _r_seqCnt /=2;
|
|
|
737
|
|
|
738 int i=0;
|
|
|
739 printf("%d\n", _r_seqCnt);
|
|
|
740 for (i = 0; i < _r_seqCnt; i++)
|
|
|
741 {
|
|
|
742 if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] != 0 && strcmp(_r_seq[2*i].qual, "*")==0)
|
|
|
743 {
|
|
|
744 fprintf(fp1,">%s/1\n%s\n>%s/2\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq);
|
|
|
745 }
|
|
|
746 else if (pairedEndMode && _r_seq[2*i].hits[0] != 0 && _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual, "*")==0)
|
|
|
747 {
|
|
|
748 fprintf(fp2, ">%s/1\n%s\n>%s/2\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq);
|
|
|
749 }
|
|
|
750 else if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] != 0 && strcmp(_r_seq[2*i].qual, "*")!=0)
|
|
|
751 {
|
|
|
752 fprintf(fp1,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name,
|
|
|
753 _r_seq[2*i].seq,
|
|
|
754 _r_seq[2*i].qual,
|
|
|
755 _r_seq[2*i+1].name,
|
|
|
756 _r_seq[2*i+1].seq,
|
|
|
757 _r_seq[2*i+1].qual);
|
|
|
758 }
|
|
|
759 else if ( pairedEndMode && _r_seq[2*i].hits[0] != 0 && _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual, "*")!=0 )
|
|
|
760 {
|
|
|
761 fprintf(fp2,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name,
|
|
|
762 _r_seq[2*i].seq,
|
|
|
763 _r_seq[2*i].qual,
|
|
|
764 _r_seq[2*i+1].name,
|
|
|
765 _r_seq[2*i+1].seq,
|
|
|
766 _r_seq[2*i+1].qual);
|
|
|
767 }
|
|
|
768 }
|
|
|
769
|
|
|
770 fclose(fp1);
|
|
|
771 fclose(fp2);
|
|
|
772
|
|
|
773 }*/
|
