convertCoordinates.java

import java.util.ArrayList;
import java.util.Arrays;

public class convertCoordinates {

	private static String convertLine(String line) {
		
		//split line
		String[] fields = line.split("\t");
		//split chromosome field into starts and ends of exon chunks used in pseudojunction
		String[] chrom = fields[2].split("[-]");

		
		if(line.charAt(0) == '@'){//return header
			return line;
		}
		else if ( fields[5].equals("*") && ( fields[2].length() != 1 || Integer.parseInt(fields[3]) != 0 ) ){//remove genomic position of read if it has no mapping quality assigned 
			//System.out.println("malformed read");
			fields[2] = "*";
			fields[3] = "0";
			String newline = Arrays.toString(fields).replace(", ", "\t").replaceAll("[\\[\\]]", "");
			return newline;
				
		}
		else if (chrom.length == 1) { //return read if it maps directly to the genome and not to a splice junction 
			return line;
		}
		else{ //adjust cigar string based on exon start/ends in the the pseudochromosome 
			String newline = parseMultiexon(fields,chrom);
			return newline;
		}
	}

	
	
	private static String parseMultiexon(String[] fields, String[] chrom) {
		ArrayList<Integer> exonStarts = new ArrayList<Integer>();
		ArrayList<Integer> exonEnds = new ArrayList<Integer>();
		ArrayList<Integer> cmLength = new ArrayList<Integer>();
		
		int readStartRel = Integer.parseInt(fields[3]);
		String newcigar = "";
		
		/*
		 * get numbers and characters from cigar string
		 */
		String cigar = fields[5];
		String[] cigarnumsTmp = cigar.split("[MIDNSHP]");
		int[] cigarnums = new int[cigarnumsTmp.length];
		int cigarsum = 0;
		for(int i = 0; i < cigarnumsTmp.length; i++){
			cigarnums[i] = Integer.parseInt(cigarnumsTmp[i]);
			cigarsum += cigarnums[i]; 
		}
		String cigarlettersTmp[] = cigar.split("[0-9]+");//.toString().toCharArray();
		String cigarletters[] = Arrays.copyOfRange(cigarlettersTmp, 1, cigarlettersTmp.length);
		
		/*
		 * get exon starts and ends as well as individual and cumulative exon lengths
		 */
		int len = 0;
		for(int i = 1; i < chrom.length; i++){
			
			if( i % 2 == 0){
				exonEnds.add(Integer.parseInt(chrom[i]));
				len += exonEnds.get(exonEnds.size()-1) - exonStarts.get(exonStarts.size()-1) +1;
				cmLength.add(new Integer(len));
			}
			else{
				exonStarts.add(Integer.parseInt(chrom[i]));
			}
		}

		/*
		 * find the exon that contains the read start
		 */
		int readStartIdx = -1;
		int readStartAbs = -1;
		if(readStartRel <= cmLength.get(0)){
			readStartIdx = 0;
			readStartAbs = exonStarts.get(0) + readStartRel - 1;
		}
		for(int i = 1; i < cmLength.size(); i++){
			if(readStartRel <= cmLength.get(i) && readStartRel > cmLength.get(i-1)){
				readStartIdx = i;
				readStartAbs = exonStarts.get(i) + (readStartRel-cmLength.get(i-1))-1;
			}
		}

        
		if(cigar.equals("*")){
			newcigar = "*";
		}
		else{
			int currCigarPos = 0;
			int currReadPos = exonEnds.get(readStartIdx) - readStartAbs + 1;
			int readRemain = cigarsum;
			boolean found = false;

			for(int i = 0; i < cigarnums.length; i++){
        		
				if(!cigarletters[i].equals("I") && !cigarletters[i].equals("S") && !cigarletters[i].equals("H")){        			
					currCigarPos += cigarnums[i];
				}
        		
				while(currCigarPos > currReadPos && !found && readStartIdx < exonEnds.size()-1){
					int len1 = cigarnums[i] - (currCigarPos - currReadPos);
					cigarnums[i] -= len1;
					int Nlength = exonStarts.get(readStartIdx+1) - exonEnds.get(readStartIdx) - 1 ;
        			
					if(len1>0){//only include current cigarchar and length if it is larger than zero
						newcigar = newcigar + String.valueOf(len1) + cigarletters[i] + String.valueOf(Nlength) + "N";
					}
					else{
						newcigar = newcigar + String.valueOf(Nlength) + "N";
					}
					readRemain -= len1;

					readStartIdx++;
        			
					if(exonEnds.get(readStartIdx) - exonStarts.get(readStartIdx) + 1 < readRemain){
						currReadPos += (exonEnds.get(readStartIdx) - exonStarts.get(readStartIdx) + 1);
					}
					else{
						currReadPos += readRemain;
					}
				}
				if(cigarnums[i]>0){
					newcigar = newcigar + String.valueOf(cigarnums[i]) + cigarletters[i];
				}
			}
		}

		String sep = "\t";
		String newLine = fields[0] + sep + fields[1] + sep + chrom[0] + sep + readStartAbs + sep + fields[4] + sep + newcigar + sep;
		for(int i = 6; i < fields.length-1; i++){
			newLine += fields[i]+sep;
		}
		newLine += fields[fields.length-1];
		return newLine;
	}


	public static void main(String[] args) {
		try {
			java.io.BufferedReader stdin = new java.io.BufferedReader(new java.io.InputStreamReader(System.in));
			String line;
	       
			//iterate through each line of the sam file
			while((line = stdin.readLine()) !=null){
				String convertedLine = convertLine(line);
				System.out.println(convertedLine);
			}
		}	  
		catch (java.io.IOException e) { System.out.println(e); }
		catch (NumberFormatException e) { System.out.println(e); }
	}
}