VCFProgramPreProcessPipe.java

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package edu.mayo.bior.pipeline.VCFProgramPipes;

import java.util.NoSuchElementException;

import com.tinkerpop.pipes.AbstractPipe;

import edu.mayo.pipes.exceptions.InvalidPipeInputException;
import edu.mayo.pipes.history.History;

/**
 *
 * @author m102417
 */
public class VCFProgramPreProcessPipe extends AbstractPipe<History, String> {
    
    private int mNumColsToSave = 7;
    private int mLineNumber = 0;
    
    public VCFProgramPreProcessPipe(){
        
    }
    
    public VCFProgramPreProcessPipe(int colsToSave){
    	mNumColsToSave = colsToSave;
    }

    @Override
    protected String processNextStart() throws NoSuchElementException {
    	History history = this.starts.next();
    	validateColumns(history);
        return getFirstXColumnsPlusDot(history);
    }
    

	private void validateColumns(History history) {
		mLineNumber++;
		
		// Skip line if it has 0 cols - may be end line
		if(history.size() == 0 || (history.size() == 1 && history.get(0).trim().length() == 0) )
			throw new NoSuchElementException("Line " + mLineNumber + " (without headers): Blank line encountered - assuming end of input stream");
		// Throw exception 
		else if(history.size() < mNumColsToSave)
			throw new InvalidPipeInputException("Line " + mLineNumber 
					+ " (without headers): Number of columns in input file was less than " 
					+ mNumColsToSave + ".\nActual # of columns: " + history.size() + "\n"
					+ "Line: [" + history.getMergedData("\t") + "]", this);
	}

	private String getFirstXColumnsPlusDot(History history) {
		StringBuilder sb = new StringBuilder();
		for(int i=0; i<mNumColsToSave;i++){
			sb.append(history.get(i));
			sb.append("\t");
	    }
		sb.append(".");
		return sb.toString();
	}
}