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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
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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
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125 if (!compressed)
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126 {
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127 _r_fp1 = fileOpen( fileName1, "r");
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128
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129 if (_r_fp1 == NULL)
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130 {
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131 return 0;
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132 }
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133
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134 ch = fgetc(_r_fp1);
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135
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136 if ( pairedEnd && fileName2 != NULL )
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137 {
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138 _r_fp2 = fileOpen ( fileName2, "r" );
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139 if (_r_fp2 == NULL)
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140 {
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141 return 0;
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142 }
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143 }
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144 else
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145 {
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146 _r_fp2 = _r_fp1;
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147 }
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148
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149 readFirstSeq = &readFirstSeqTXT;
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150 readSecondSeq = &readSecondSeqTXT;
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151 }
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152 else
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153 {
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154
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155 _r_gzfp1 = fileOpenGZ (fileName1, "r");
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156
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157 if (_r_gzfp1 == NULL)
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158 {
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159 return 0;
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160 }
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161
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162 ch = gzgetc(_r_gzfp1);
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163
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164 if ( pairedEnd && fileName2 != NULL )
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165 {
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166 _r_gzfp2 = fileOpenGZ ( fileName2, "r" );
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167 if (_r_gzfp2 == NULL)
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168 {
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169 return 0;
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170 }
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171 }
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172 else
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173 {
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174 _r_gzfp2 = _r_gzfp1;
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175 }
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176
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177 readFirstSeq = &readFirstSeqGZ;
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178 readSecondSeq = &readSecondSeqGZ;
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179 }
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180
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181 if (ch == '>')
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182 *fastq = 0;
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183 else
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184 *fastq = 1;
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185
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186 // Counting the number of lines in the file
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187 while (readFirstSeq(dummy)) maxCnt++;
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188
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189 if (!compressed)
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190 {
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191 rewind(_r_fp1);
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192 }
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193 else
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194 {
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195 gzrewind(_r_gzfp1);
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196 }
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197
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198 // Calculating the Maximum # of sequences
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199 if (*fastq)
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200 {
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201 maxCnt /= 4;
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202 }
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203 else
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204 {
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205 maxCnt /= 2;
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206 }
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207
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208 if (pairedEnd && fileName2 != NULL )
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209 maxCnt *= 2;
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210
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211 list = getMem(sizeof(Read)*maxCnt);
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212
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213 while( readFirstSeq(name1) )
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214 {
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215 err1 = 0;
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216 err2 = 0;
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217 readFirstSeq(seq1);
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218 name1[strlen(name1)-1] = '\0';
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219
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220 if ( *fastq )
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221 {
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222 readFirstSeq(dummy);
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223 readFirstSeq(qual1);
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224 qual1[strlen(qual1)-1] = '\0';
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225 }
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226 else
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227 {
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228 sprintf(qual1, "*");
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229 }
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230
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231 // Cropping
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232 if (cropSize > 0)
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233 {
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234 seq1[cropSize] = '\0';
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235 if ( *fastq )
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236 qual1[cropSize] = '\0';
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237 }
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238
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239
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240 nCnt = 0;
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241 for (i=0; i<strlen(seq1); i++)
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242 {
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243 seq1[i] = toupper (seq1[i]);
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244 if (seq1[i] == 'N')
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245 {
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246 nCnt++;
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247 }
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248 else if (isspace(seq1[i]))
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249 {
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250
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251 seq1[i] = '\0';
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252 break;
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253 }
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254 }
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255
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256 if (nCnt > errThreshold)
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257 {
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258 err1 = 1;
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259 }
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260
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261 // Reading the second seq of pair-ends
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262 if (pairedEnd)
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263 {
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264 readSecondSeq(name2);
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265 readSecondSeq(seq2);
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266 name2[strlen(name2)-1] = '\0';
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267
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268
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269 if ( *fastq )
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270 {
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271 readSecondSeq(dummy);
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272 readSecondSeq(qual2);
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273
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274 qual2[strlen(qual2)-1] = '\0';
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275 }
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276 else
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277 {
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278 sprintf(qual2, "*");
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279 }
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280
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281
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282 // Cropping
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283 if (cropSize > 0)
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284 {
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285 seq2[cropSize] = '\0';
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286 if ( *fastq )
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287 qual2[cropSize] = '\0';
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288 }
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289
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290
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291 nCnt = 0;
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292 for (i=0; i<strlen(seq2); i++)
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293 {
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294 seq2[i] = toupper (seq2[i]);
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295 if (seq2[i] == 'N')
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296 {
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297 nCnt++;
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298
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299 }
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300 else if (isspace(seq2[i]))
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301 {
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302 seq2[i] = '\0';
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303 }
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304 }
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305 if (nCnt > errThreshold)
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306 {
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307 err2 = 1;
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308 }
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309
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310
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311 if (strlen(seq1) < strlen(seq2)) {
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312 seq2[strlen(seq1)] = '\0';
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313 if ( *fastq )
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314 qual2[strlen(seq1)] = '\0';
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315 if (!clipped) clipped = 2;
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316 }
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317 else if (strlen(seq1) > strlen(seq2)){
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318 seq1[strlen(seq2)] = '\0';
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319 if ( *fastq )
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320 qual1[strlen(seq2)] = '\0';
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321 if (!clipped) clipped = 1;
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322 }
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323
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324 if (clipped == 1 || clipped == 2){
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325 fprintf(stdout, "[PE mode Warning] Sequence lengths are different, read #%d is clipped to match.\n", clipped);
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326 clipped = 3;
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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
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333 if (!pairedEnd && !err1)
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334 {
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335 int _mtmp = strlen(seq1);
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336 list[seqCnt].hits = getMem (1+3*_mtmp+3+strlen(name1)+1);
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337 list[seqCnt].seq = list[seqCnt].hits + 1;
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338 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
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339 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
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340 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
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341
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342 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
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343 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
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344
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345 list[seqCnt].readNumber = seqCnt;
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346
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347 reverseComplete(seq1, rseq1, _mtmp);
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348 rseq1[_mtmp] = '\0';
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349 int i;
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350
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351 list[seqCnt].hits[0] = 0;
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352
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353 for (i=0; i<=_mtmp; i++)
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354 {
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355 list[seqCnt].seq[i] = seq1[i];
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356 list[seqCnt].rseq[i] = rseq1[i] ;
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357 list[seqCnt].qual[i] = qual1[i];
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358 }
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359
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360
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361 //MAKE HASH VALUE
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362 short code = 0;
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363
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364 for(i=0; i < 4; i++)
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365 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
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366 list[seqCnt].hashValue[0] = code;
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367
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368
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369 for(i = 1; i < _mtmp-3; i++)
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370 {
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371 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
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372 }
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373
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374
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375 code = 0;
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376 for(i=0; i < 4; i++)
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377 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
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378 list[seqCnt].rhashValue[0] = code;
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379
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380
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381 for(i = 1; i < _mtmp-3; i++)
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382 {
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383 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
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384 }
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385
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386 int j = 0;
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387 int tmpSize = _mtmp / (errThreshold+1);
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388
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389 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
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390 for(i=0; i < errThreshold+1; i++)
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391 {
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392 code = 0;
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393 for(j = 0; j < tmpSize; j++)
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394 {
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395 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
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396 }
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397 list[seqCnt].hashValSampleSize[i] = code;
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398 }
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399
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400 sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
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401
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402 seqCnt++;
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403
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404 }
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405 else if (pairedEnd && !err1 && !err2)
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406 {
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407
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408 // Naming Conventions X/1, X/2 OR X
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409 int tmplen = strlen(name1);
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410 if (strcmp(name1, name2) != 0)
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411 {
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412 tmplen = strlen(name1)-2;
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413 }
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414
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415 //first seq
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416 int _mtmp = strlen(seq1);
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417 list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
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418 list[seqCnt].seq = list[seqCnt].hits + 1;
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419 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
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420 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
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421 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
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422
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423 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
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424 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
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425 list[seqCnt].readNumber = seqCnt;
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426
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427 reverseComplete(seq1, rseq1, _mtmp);
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428 rseq1[_mtmp] = '\0';
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429 int i;
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430
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431 list[seqCnt].hits[0] = 0;
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432
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433 for (i=0; i<=_mtmp; i++)
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434 {
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435 list[seqCnt].seq[i] = seq1[i];
|
|
|
436 list[seqCnt].rseq[i] = rseq1[i] ;
|
|
|
437 list[seqCnt].qual[i] = qual1[i];
|
|
|
438 }
|
|
|
439
|
|
|
440
|
|
|
441 name1[tmplen]='\0';
|
|
|
442
|
|
|
443 //MAKE HASH VALUE
|
|
|
444 short code = 0;
|
|
|
445
|
|
|
446 for(i=0; i < 4; i++)
|
|
|
447 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
|
|
|
448 list[seqCnt].hashValue[0] = code;
|
|
|
449
|
|
|
450
|
|
|
451 for(i = 1; i < _mtmp-3; i++)
|
|
|
452 {
|
|
|
453 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
|
|
|
454 }
|
|
|
455
|
|
|
456
|
|
|
457 code = 0;
|
|
|
458 for(i=0; i < 4; i++)
|
|
|
459 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
|
|
|
460 list[seqCnt].rhashValue[0] = code;
|
|
|
461
|
|
|
462
|
|
|
463 for(i = 1; i < _mtmp-3; i++)
|
|
|
464 {
|
|
|
465 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
|
|
|
466 }
|
|
|
467
|
|
|
468 int j = 0;
|
|
|
469 int tmpSize = _mtmp / (errThreshold+1);
|
|
|
470
|
|
|
471 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
|
|
|
472 for(i=0; i < errThreshold+1; i++)
|
|
|
473 {
|
|
|
474 code = 0;
|
|
|
475 for(j = 0; j < tmpSize; j++)
|
|
|
476 {
|
|
|
477 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
|
|
|
478 }
|
|
|
479 list[seqCnt].hashValSampleSize[i] = code;
|
|
|
480 }
|
|
|
481
|
|
|
482 sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
|
|
|
483
|
|
|
484
|
|
|
485 seqCnt++;
|
|
|
486
|
|
|
487 //second seq
|
|
|
488 list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
|
|
|
489 list[seqCnt].seq = list[seqCnt].hits + 1;
|
|
|
490 list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
|
|
|
491 list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
|
|
|
492 list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
|
|
|
493
|
|
|
494 list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
|
|
|
495 list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
|
|
|
496 list[seqCnt].readNumber = seqCnt;
|
|
|
497
|
|
|
498 reverseComplete(seq2, rseq2, _mtmp);
|
|
|
499 rseq2[_mtmp] = '\0';
|
|
|
500
|
|
|
501 list[seqCnt].hits[0] = 0;
|
|
|
502
|
|
|
503 for (i=0; i<=_mtmp; i++)
|
|
|
504 {
|
|
|
505 list[seqCnt].seq[i] = seq2[i];
|
|
|
506 list[seqCnt].rseq[i] = rseq2[i] ;
|
|
|
507 list[seqCnt].qual[i] = qual2[i];
|
|
|
508 }
|
|
|
509
|
|
|
510
|
|
|
511 name2[tmplen]='\0';
|
|
|
512
|
|
|
513 //MAKE HASH VALUE
|
|
|
514 code = 0;
|
|
|
515
|
|
|
516 for(i=0; i < 4; i++)
|
|
|
517 code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
|
|
|
518 list[seqCnt].hashValue[0] = code;
|
|
|
519
|
|
|
520
|
|
|
521 for(i = 1; i < _mtmp-3; i++)
|
|
|
522 {
|
|
|
523 list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
|
|
|
524 }
|
|
|
525
|
|
|
526
|
|
|
527 code = 0;
|
|
|
528 for(i=0; i < 4; i++)
|
|
|
529 code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
|
|
|
530 list[seqCnt].rhashValue[0] = code;
|
|
|
531
|
|
|
532
|
|
|
533 for(i = 1; i < _mtmp-3; i++)
|
|
|
534 {
|
|
|
535 list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
|
|
|
536 }
|
|
|
537
|
|
|
538 j = 0;
|
|
|
539 tmpSize = _mtmp / (errThreshold+1);
|
|
|
540
|
|
|
541 list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
|
|
|
542 for(i=0; i < errThreshold+1; i++)
|
|
|
543 {
|
|
|
544 code = 0;
|
|
|
545 for(j = 0; j < tmpSize; j++)
|
|
|
546 {
|
|
|
547 code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
|
|
|
548 }
|
|
|
549 list[seqCnt].hashValSampleSize[i] = code;
|
|
|
550 }
|
|
|
551
|
|
|
552 sprintf(list[seqCnt].name,"%s%c", ((char*)name2)+1,'\0');
|
|
|
553
|
|
|
554 seqCnt++;
|
|
|
555
|
|
|
556 }
|
|
|
557 else
|
|
|
558 {
|
|
|
559 discarded++;
|
|
|
560 }
|
|
|
561 }
|
|
|
562
|
|
|
563 if (seqCnt > 0)
|
|
|
564 {
|
|
|
565 SEQ_LENGTH = strlen(list[0].seq);
|
|
|
566 }
|
|
|
567 else
|
|
|
568 {
|
|
|
569 fprintf(stdout, "ERROR: No reads can be found for mapping\n");
|
|
|
570 return 0;
|
|
|
571 }
|
|
|
572
|
|
|
573
|
|
|
574 // Closing Files
|
|
|
575 if (!compressed)
|
|
|
576 {
|
|
|
577 fclose(_r_fp1);
|
|
|
578 if ( pairedEnd && fileName2 != NULL )
|
|
|
579 {
|
|
|
580 fclose(_r_fp2);
|
|
|
581 }
|
|
|
582 }
|
|
|
583 else
|
|
|
584 {
|
|
|
585 gzclose(_r_gzfp1);
|
|
|
586 if ( pairedEnd && fileName2 != NULL)
|
|
|
587 {
|
|
|
588 gzclose(_r_fp2);
|
|
|
589 }
|
|
|
590 }
|
|
|
591
|
|
|
592 //qsort(list, seqCnt, sizeof(Read), toCompareRead);
|
|
|
593
|
|
|
594 adjustQual(list, seqCnt);
|
|
|
595
|
|
|
596 *seqList = list;
|
|
|
597 *seqListSize = seqCnt;
|
|
|
598
|
|
|
599
|
|
|
600 _r_seq = list;
|
|
|
601 _r_seqCnt = seqCnt;
|
|
|
602
|
|
|
603 if ( pairedEnd ) discarded *= 2;
|
|
|
604
|
|
|
605 if (seqCnt>1)
|
|
|
606 fprintf(stdout, "%d sequences are read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
|
|
|
607 else
|
|
|
608 fprintf(stdout, "%d sequence is read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
|
|
|
609
|
|
|
610
|
|
|
611
|
|
|
612 return 1;
|
|
|
613 }
|
|
|
614 /**********************************************/
|
|
|
615 void loadSamplingLocations(int **samplingLocs, int * samplingLocsSize)
|
|
|
616 {
|
|
|
617 int i;
|
|
|
618 int samLocsSize = errThreshold + 1;
|
|
|
619 int *samLocs = getMem(sizeof(int)*samLocsSize);
|
|
|
620
|
|
|
621 for (i=0; i<samLocsSize; i++)
|
|
|
622 {
|
|
|
623 samLocs[i] = (SEQ_LENGTH / samLocsSize) *i;
|
|
|
624 if ( samLocs[i] + WINDOW_SIZE > SEQ_LENGTH)
|
|
|
625 samLocs[i] = SEQ_LENGTH - WINDOW_SIZE;
|
|
|
626 }
|
|
|
627
|
|
|
628 // Outputing the sampling locations
|
|
|
629
|
|
|
630 /*
|
|
|
631
|
|
|
632 int j;
|
|
|
633 for (i=0; i<SEQ_LENGTH; i++)
|
|
|
634 {
|
|
|
635 fprintf(stdout, "-");
|
|
|
636 }
|
|
|
637 fprintf(stdout, "\n");
|
|
|
638
|
|
|
639 for ( i=0; i<samLocsSize; i++ )
|
|
|
640 {
|
|
|
641 for ( j=0; j<samLocs[i]; j++ )
|
|
|
642 {
|
|
|
643 fprintf(stdout," ");
|
|
|
644 }
|
|
|
645 for (j=0; j<WINDOW_SIZE; j++)
|
|
|
646 {
|
|
|
647 fprintf(stdout,"+");
|
|
|
648 }
|
|
|
649 fprintf(stdout, "\n");
|
|
|
650 fflush(stdout);
|
|
|
651 }
|
|
|
652
|
|
|
653
|
|
|
654 for ( i=0; i<SEQ_LENGTH; i++ )
|
|
|
655 {
|
|
|
656 fprintf(stdout, "-");
|
|
|
657 }
|
|
|
658 fprintf(stdout, "\n");
|
|
|
659
|
|
|
660 */
|
|
|
661
|
|
|
662 *samplingLocs = samLocs;
|
|
|
663 *samplingLocsSize = samLocsSize;
|
|
|
664 _r_samplingLocs = samLocs;
|
|
|
665 }
|
|
|
666
|
|
|
667 void finalizeReads(char *fileName)
|
|
|
668 {
|
|
|
669 FILE *fp1=NULL;
|
|
|
670
|
|
|
671 if (fileName != NULL)
|
|
|
672 {
|
|
|
673 fp1 = fileOpen(fileName, "w");
|
|
|
674 }
|
|
|
675 if (pairedEndMode)
|
|
|
676 _r_seqCnt /=2;
|
|
|
677
|
|
|
678 int i=0;
|
|
|
679 for (i = 0; i < _r_seqCnt; i++)
|
|
|
680 {
|
|
|
681 if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual,"*")!=0)
|
|
|
682 {
|
|
|
683 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);
|
|
|
684 }
|
|
|
685 else if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0)
|
|
|
686 {
|
|
|
687 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]);
|
|
|
688 }
|
|
|
689 else if (!pairedEndMode && _r_seq[i].hits[0] == 0 && strcmp(_r_seq[i].qual, "*")!=0)
|
|
|
690 {
|
|
|
691 fprintf(fp1,"@%s\n%s\n+\n%s\n", _r_seq[i].name, _r_seq[i].seq, _r_seq[i].qual);
|
|
|
692 }
|
|
|
693 else if (!pairedEndMode && _r_seq[i].hits[0] == 0)
|
|
|
694 {
|
|
|
695 fprintf(fp1,">%s\n%s\n", _r_seq[i].name, _r_seq[i].seq);
|
|
|
696 }
|
|
|
697 }
|
|
|
698
|
|
|
699 fclose(fp1);
|
|
|
700 if (pairedEndMode)
|
|
|
701 _r_seqCnt *= 2;
|
|
|
702
|
|
|
703 for (i = 0; i < _r_seqCnt; i++)
|
|
|
704 {
|
|
|
705 freeMem(_r_seq[i].hits,0);
|
|
|
706 }
|
|
|
707
|
|
|
708
|
|
|
709 freeMem(_r_seq,0);
|
|
|
710 freeMem(_r_samplingLocs,0);
|
|
|
711 }
|
|
|
712
|
|
|
713 void adjustQual(Read *list, int seqCnt){
|
|
|
714 /* This function will automatically determine the phred_offset and readjust quality values if needed */
|
|
|
715 int i,j,q, offset=64;
|
|
|
716 int len = strlen(list[0].qual);
|
|
|
717
|
|
|
718 for (i=0; i<10000 && i<seqCnt; i++){
|
|
|
719 for (j=0;j<len;j++){
|
|
|
720 q = (int) list[i].qual[j] - offset;
|
|
|
721 if (q < 0){
|
|
|
722 offset = 33;
|
|
|
723 break;
|
|
|
724 }
|
|
|
725 }
|
|
|
726 if (offset == 33)
|
|
|
727 break;
|
|
|
728 }
|
|
|
729
|
|
|
730 if (offset == 64){
|
|
|
731 fprintf(stdout, "[Quality Warning] Phred offset is 64. Readjusting to 33.\n");
|
|
|
732 fflush(stdout);
|
|
|
733 for (i=0;i<seqCnt;i++){
|
|
|
734 for (j=0;j<len;j++){
|
|
|
735 list[i].qual[j] -= 31;
|
|
|
736 }
|
|
|
737 }
|
|
|
738 }
|
|
|
739 }
|
|
|
740
|
|
|
741
|
|
|
742
|
|
|
743 /*void finalizeOEAReads(char *fileName)
|
|
|
744 {
|
|
|
745 FILE *fp1=NULL;
|
|
|
746 FILE *fp2=NULL;
|
|
|
747
|
|
|
748 //printf("OEA%s\n", fileName);
|
|
|
749 char fileNameOEA1[200];
|
|
|
750 char fileNameOEA2[200];
|
|
|
751 sprintf(fileNameOEA1, "%s_OEA1", fileName);
|
|
|
752 sprintf(fileNameOEA2, "%s_OEA2", fileName);
|
|
|
753
|
|
|
754
|
|
|
755 if (fileName != NULL)
|
|
|
756 {
|
|
|
757 fp1 = fileOpen(fileNameOEA1, "w");
|
|
|
758 fp2 = fileOpen(fileNameOEA2, "w");
|
|
|
759 }
|
|
|
760 if (pairedEndMode)
|
|
|
761 _r_seqCnt /=2;
|
|
|
762
|
|
|
763 int i=0;
|
|
|
764 printf("%d\n", _r_seqCnt);
|
|
|
765 for (i = 0; i < _r_seqCnt; i++)
|
|
|
766 {
|
|
|
767 if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] != 0 && strcmp(_r_seq[2*i].qual, "*")==0)
|
|
|
768 {
|
|
|
769 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);
|
|
|
770 }
|
|
|
771 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)
|
|
|
772 {
|
|
|
773 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);
|
|
|
774 }
|
|
|
775 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)
|
|
|
776 {
|
|
|
777 fprintf(fp1,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name,
|
|
|
778 _r_seq[2*i].seq,
|
|
|
779 _r_seq[2*i].qual,
|
|
|
780 _r_seq[2*i+1].name,
|
|
|
781 _r_seq[2*i+1].seq,
|
|
|
782 _r_seq[2*i+1].qual);
|
|
|
783 }
|
|
|
784 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 )
|
|
|
785 {
|
|
|
786 fprintf(fp2,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name,
|
|
|
787 _r_seq[2*i].seq,
|
|
|
788 _r_seq[2*i].qual,
|
|
|
789 _r_seq[2*i+1].name,
|
|
|
790 _r_seq[2*i+1].seq,
|
|
|
791 _r_seq[2*i+1].qual);
|
|
|
792 }
|
|
|
793 }
|
|
|
794
|
|
|
795 fclose(fp1);
|
|
|
796 fclose(fp2);
|
|
|
797
|
|
|
798 }*/
|
