Program: 25955
Project: 25955
Buggy source:
public MNISTReader(String labelFilename,String imageFilename,int depth){
  try {
    if (depth != 1 && depth != 3) {
      throw new AIFHError("String_Node_Str");
    }
    DataInputStream labels;
    DataInputStream images;
    if (labelFilename.toLowerCase().endsWith("String_Node_Str")) {
      labels=new DataInputStream(new GZIPInputStream(new FileInputStream(labelFilename)));
    }
 else {
      labels=new DataInputStream(new FileInputStream(labelFilename));
    }
    if (imageFilename.toLowerCase().endsWith("String_Node_Str")) {
      images=new DataInputStream(new GZIPInputStream(new FileInputStream(imageFilename)));
    }
 else {
      images=new DataInputStream(new FileInputStream(imageFilename));
    }
    int magicNumber=labels.readInt();
    if (magicNumber != 2049) {
      throw new AIFHError("String_Node_Str" + magicNumber + "String_Node_Str");
    }
    magicNumber=images.readInt();
    if (magicNumber != 2051) {
      throw new AIFHError("String_Node_Str" + magicNumber + "String_Node_Str");
    }
    this.numLabels=labels.readInt();
    this.numImages=images.readInt();
    this.numRows=images.readInt();
    this.numCols=images.readInt();
    if (this.numLabels != this.numImages) {
      StringBuilder str=new StringBuilder();
      str.append("String_Node_Str");
      str.append("String_Node_Str" + this.numLabels + "String_Node_Str");
      str.append("String_Node_Str" + this.numImages + "String_Node_Str");
      throw new AIFHError(str.toString());
    }
    byte[] labelsData=new byte[this.numLabels];
    labels.read(labelsData);
    int imageVectorSize=this.numCols * this.numRows;
    byte[] imagesData=new byte[this.numLabels * imageVectorSize];
    images.read(imagesData);
    this.data=new ArrayList<>();
    int imageIndex=0;
    for (int i=0; i < this.numLabels; i++) {
      int label=labelsData[i];
      double[] inputData=new double[imageVectorSize * depth];
      int outputIndex=0;
      int t=imageIndex;
      for (int k=0; k < depth; k++) {
        imageIndex=t;
        for (int j=0; j < imageVectorSize; j++) {
          inputData[outputIndex++]=((double)(imagesData[imageIndex++] & 0xff)) / 255.0;
        }
      }
      double[] idealData=new double[10];
      idealData[label]=1.0;
      this.data.add(new BasicData(inputData,idealData,null));
    }
    images.close();
    labels.close();
  }
 catch (  IOException ex) {
    throw new AIFHError(ex);
  }
}

Fixed version (ground truth):
public MNISTReader(String labelFilename,String imageFilename,int depth){
  try {
    if (depth != 1 && depth != 3) {
      throw new AIFHError("String_Node_Str");
    }
    DataInputStream labels;
    DataInputStream images;
    if (labelFilename.toLowerCase().endsWith("String_Node_Str")) {
      labels=new DataInputStream(new GZIPInputStream(new FileInputStream(labelFilename)));
    }
 else {
      labels=new DataInputStream(new FileInputStream(labelFilename));
    }
    if (imageFilename.toLowerCase().endsWith("String_Node_Str")) {
      images=new DataInputStream(new GZIPInputStream(new FileInputStream(imageFilename)));
    }
 else {
      images=new DataInputStream(new FileInputStream(imageFilename));
    }
    int magicNumber=labels.readInt();
    if (magicNumber != 2049) {
      throw new AIFHError("String_Node_Str" + magicNumber + "String_Node_Str");
    }
    magicNumber=images.readInt();
    if (magicNumber != 2051) {
      throw new AIFHError("String_Node_Str" + magicNumber + "String_Node_Str");
    }
    this.numLabels=labels.readInt();
    this.numImages=images.readInt();
    this.numRows=images.readInt();
    this.numCols=images.readInt();
    if (this.numLabels != this.numImages) {
      StringBuilder str=new StringBuilder();
      str.append("String_Node_Str");
      str.append("String_Node_Str" + this.numLabels + "String_Node_Str");
      str.append("String_Node_Str" + this.numImages + "String_Node_Str");
      throw new AIFHError(str.toString());
    }
    byte[] labelsData=new byte[this.numLabels];
    labels.readFully(labelsData);
    int imageVectorSize=this.numCols * this.numRows;
    byte[] imagesData=new byte[this.numLabels * imageVectorSize];
    images.readFully(imagesData);
    this.data=new ArrayList<>();
    int imageIndex=0;
    for (int i=0; i < this.numLabels; i++) {
      int label=labelsData[i];
      double[] inputData=new double[imageVectorSize * depth];
      int outputIndex=0;
      int t=imageIndex;
      for (int k=0; k < depth; k++) {
        imageIndex=t;
        for (int j=0; j < imageVectorSize; j++) {
          inputData[outputIndex++]=((double)(imagesData[imageIndex++] & 0xff)) / 255.0;
        }
      }
      double[] idealData=new double[10];
      idealData[label]=1.0;
      this.data.add(new BasicData(inputData,idealData,null));
    }
    images.close();
    labels.close();
  }
 catch (  IOException ex) {
    throw new AIFHError(ex);
  }
}