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1 package filters;
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2
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3 import java.io.File;
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4 import java.io.FileNotFoundException;
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5 import java.io.FileWriter;
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6 import java.io.IOException;
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7 import java.util.Scanner;
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8 import datastructures.ReadLine;
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9
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10 public class ReadFilter extends Filter{
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11
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12 File input, output;
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13
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14 /**
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15 * Constructs a SamAdapter object. The output of an adaption is written to the
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16 * given file outputFileName.
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17 *
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18 * @param inputFileName the name of the read alignment input file.
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19 * @param outputFileName the name of the output file containing the reduced
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20 * format of the read alignment file. It must ends with ".red".
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21 */
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22 public ReadFilter(String inputFileName, String outputFileName) {
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23 super(inputFileName, outputFileName);
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24 input = new File(inputFileName);
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25 output = new File(outputFileName);
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26 }
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27
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28 /**
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29 * <P>
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30 * Uses ReadLine zu reduce each line of the read alignment file to following format:<BR>
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31 * <name> <chrom> <start> <end> (tab delimited).
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32 * </P>
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33 * In the following we list the 12 fields of the sam-alignment-file. We mark the fields we are
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34 * interessted in with (!!):
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35 * <PRE>
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36 * 1. <QNAME> : Query pair NAME if paired; or Query NAME if unpaired (Ex: 6:105:18438:14421) (!!)
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37 * 2. <FLAG> : bitwise FLAG a₀a₁a₂a₃a₄a₅a₆a₇a₈a₉a₁₀ (Ex: 0 forward, 16 reverse strand)
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38 * a₀ : the read is paired in sequencing, (no matter whether it is mapped in a pair)
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39 * a₁ : the read is mapped in a proper pair
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40 * a₂ : the query sequence itself is unmapped
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41 * a₃ : the mate is unmapped
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42 * a₄ : strand of the query (0 for forward; 1 for reverse strand)
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43 * a₅ : strand of the mate
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44 * a₆ : the read is the first read in a pair
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45 * a₇ : the read is the second read in a pair
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46 * a₈ : the alignment is not primary
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47 * a₉ : the read fails platform/vendor quality checks
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48 * a₁₀: the read is either a PCR duplicate or an optical duplicate
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49 * 3. <RNAME> : Reference sequence NAME (Ex: chr10) (!!)
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50 * 4. <POS> : 1-based leftmost POSition/coordinate of the clipped sequence (Ex: 60041) (!!)
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51 * 5. <MAPQ> : MAPping Quality (Ex: 0)
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52 * (phred-scaled posterior probability that the mapping position of this read is incorrect)
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53 * 6. <CIGAR> : extended CIGAR string (Ex: 150M)
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54 * 7. <MRNM> : Mate Reference sequence NaMe; “=” if the same as <RNAME> (Ex:*)
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55 * 8. <MPOS> : 1-based leftmost Mate POSition of the clipped sequence (Ex: 0)
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56 * 9. <ISIZE> : inferred Insert SIZE (Ex: 0)
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57 * 10. <SEQ> : query SEQuence; “=” for a match to the reference; n/N/. for ambiguity; cases are not maintained (!!)
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58 * (Ex: TGTTGTTGTTATTTCTGAATGACATTTACTTTGCTGCTCTTTATTTTGCG
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59 * TATTTAAAACTATTAGATCGTGTGATTATATTTGACAGGTCTTAATTGAC
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60 * GCGCTGTTCAGCCCTTTGAGTTCGGTTGAGTTTTGTGTTGGAGAATTTTC)
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61 * 11. <QUAL> : query QUALity; ASCII-33 gives the Phred base quality
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62 * (Ex: /.8349-7:95@=8999;1:=;===AABD:=@A;>AD:E:9@==69<;@B3CBC@B8B;B89=8=3;@@@.:->>B?
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63 * C4CBB8EDGDD8GDEEDEEE8EBA9B???=B;,8:+5;;A??>?#############################)
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64 * 12. [<TAG>:<VTYPE>:<VALUE> [...]]: TAG/Value TYPE/match <VTYPE> (space allowed)
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65 * (Ex: XT:A:R NM:i:2 X0:i:2 X1:i:0)
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66 * </PRE>
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67 */
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68 public void filter() {
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69 FileWriter fw = null;
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70 Scanner s = null;
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71
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72 try {
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73 s= new Scanner(input);
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74 } catch (FileNotFoundException e) {
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75 System.err.println("sam file not found");
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76 e.printStackTrace();
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77 }
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78
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79 try {
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80 if(output == null){
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81 output = new File(input.getName().
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82 substring(0,input.getName().lastIndexOf("."))+".rsam");
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83 }
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84
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85 fw = new FileWriter(output);
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86
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87 } catch (IOException e) {
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88 System.err.println("Error generating rsam file");
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89 e.printStackTrace();
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90 }
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91
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92 String rawline;
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93 ReadLine line = null;
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94
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95 do{
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96 rawline = s.nextLine();
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97 }while(rawline.startsWith("@"));
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98
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99 do{
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100 try {
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101 line = new ReadLine(rawline);
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102 fw.write(line+"\r\n");
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103 } catch (IOException e) {
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104 System.err.println("Error writing reduced form of:\n"+rawline);
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105 e.printStackTrace();
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106 }
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107 if(s.hasNextLine())
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108 rawline = s.nextLine();
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109 }while(s.hasNextLine());
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110
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111
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112 try {
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113 fw.write(line +"\r\n");
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114 } catch (IOException e) {
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115 System.err.println("Error writing reduced form of:\n"+line);
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116 e.printStackTrace();
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117 }
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118
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119 try {
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120 fw.close();
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121 } catch (IOException e) {
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122 System.err.println("Error closing file");
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123 e.printStackTrace();
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124 }
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125 s.close();
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126
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127 System.out.println("READS FILE:");
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128 System.out.println(input.getAbsolutePath()+" reduced to "+
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129 output.getAbsolutePath());
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130 sort();
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131 }
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132
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133
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134 public void sort() {
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135 Runtime rt = Runtime.getRuntime();
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136 try {
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137 String rawOutput = output.getAbsolutePath();
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138 String outputName = output.getName();
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139 String pathname = output.getParentFile().getAbsolutePath()+"/"+outputName+"Sorted";
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140
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141 output = new File(pathname);
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142 String tmpD=output.getParentFile().getAbsolutePath();
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143
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144 if(!output.exists())output.createNewFile();
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145 String command = "sort -k2,2 -k3n,3 -T "+tmpD+" "+rawOutput;
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146 Process p = rt.exec(command);
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147 Scanner ps = new Scanner(p.getInputStream());
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148
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149 FileWriter fw = new FileWriter(output);
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150 while(ps.hasNextLine()){
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151 String nextLine = ps.nextLine();
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152 fw.write(nextLine+"\n");
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153 }
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154 fw.close();
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155
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156 Scanner psStdErr=new Scanner(p.getErrorStream());
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157 while(psStdErr.hasNextLine()){
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158 String errLine=psStdErr.nextLine();
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159 System.out.println(errLine);
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160 }
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161
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162 new File(rawOutput).delete();
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163 new File(pathname).renameTo(new File(rawOutput));
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164 System.out.println("Reduced file "+new File(rawOutput).getAbsolutePath()+" sorted\n");
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165
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166 } catch (IOException e1) {
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167 e1.printStackTrace();
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168 }
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169 }
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170
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171
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172 public String toString(){
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173 return "ReadFilter";
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174 }
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175
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176
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177 }
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