ImputeAllelesWalker fills missing portions of HLA dictionary based on best allele matches
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1729 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* FindClosestAlleleWalker finds the most similar HLA allele per read
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*/
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package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.playground.gatk.walkers.HLAcaller.ReadCigarFormatter;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.walkers.*;
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import java.io.FileInputStream;
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import java.io.BufferedReader;
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import java.io.DataInputStream;
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import java.io.InputStreamReader;
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import java.util.ArrayList;
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import java.util.Hashtable;
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import java.util.List;
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import java.lang.Math;
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/**
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*
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* @author shermanjia
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*/
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@Requires({DataSource.READS, DataSource.REFERENCE})
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public class ImputeAllelesWalker extends ReadWalker<Integer, Integer> {
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String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.sam";
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String ClosestAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.closest";
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boolean DatabaseLoaded = false;
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boolean DEBUG = false;
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ArrayList<String> HLAreads = new ArrayList<String>();
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ArrayList<String> HLAcigars = new ArrayList<String>();
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ArrayList<String> HLAnames = new ArrayList<String>();
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ArrayList<String> HLApositions = new ArrayList<String>();
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double[] SingleAlleleFrequencies;
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int numHLAlleles = 0;
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int[] HLAstartpos;
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int[] HLAstoppos;
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int minstartpos = 0;
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int maxstoppos = 0;
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int HLA_A_start = 30018310;
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int HLA_A_end = 30021211;
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int HLA_B_start = 31430239;
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int HLA_B_end = 31432914;
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int HLA_C_start = 31344925;
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int HLA_C_end = 31347827;
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ArrayList<String> PolymorphicSites = new ArrayList<String>();
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Hashtable ClosestAllele = new Hashtable();
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int iAstart = -1, iAstop = -1, iBstart = -1, iBstop = -1, iCstart = -1, iCstop = -1;
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ReadCigarFormatter formatter = new ReadCigarFormatter();
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public Integer reduceInit() {
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if (!DatabaseLoaded){
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try{
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out.printf("Reading HLA database ...\n");
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FileInputStream fstream = new FileInputStream(HLAdatabaseFile);
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DataInputStream in = new DataInputStream(fstream);
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BufferedReader br = new BufferedReader(new InputStreamReader(in));
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String strLine; String [] s = null;
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//Read File Line By Line
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int i = 0;
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while ((strLine = br.readLine()) != null) {
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s = strLine.split("\\t");
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if (s.length>=10){
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//Parse the reads with cigar parser
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HLAreads.add(formatter.FormatRead(s[5],s[9]));
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HLAcigars.add(s[5]);
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HLAnames.add(s[0]);
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HLApositions.add(s[3]);
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if (s[0].indexOf("HLA_A") > -1){
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if (iAstart < 0){iAstart=i;}
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iAstop = i; i++;
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}else if (s[0].indexOf("HLA_B") > -1){
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if (iBstart < 0){iBstart=i;}
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iBstop = i; i++;
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}else if (s[0].indexOf("HLA_C") > -1){
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if (iCstart < 0){iCstart=i;}
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iCstop = i; i++;
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}
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}
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}
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in.close();
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int n = HLApositions.size(); numHLAlleles = n;
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HLAstartpos = new int[n]; HLAstoppos = new int[n];
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SingleAlleleFrequencies = new double[n];
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for (i = 0; i < n; i++){
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//Find start and stop positions for each allele
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HLAstartpos[i]=Integer.parseInt(HLApositions.get(i));
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HLAstoppos[i]=HLAstartpos[i]+HLAreads.get(i).length()-1;
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if (minstartpos == 0){minstartpos = HLAstartpos[i];}
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minstartpos = Math.min(minstartpos, HLAstartpos[i]);
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maxstoppos = Math.max(maxstoppos, HLAstoppos[i]);
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SingleAlleleFrequencies[i]=0.0;
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//Initialize matrix of probabilities / likelihoods
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}
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out.printf("DONE! Read %s alleles\n",HLAreads.size());
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}catch (Exception e){//Catch exception if any
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System.err.println("Error: " + e.getMessage());
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}
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try{
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out.printf("Reading closest allele file ...");
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FileInputStream fstream = new FileInputStream(ClosestAllelesFile);
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DataInputStream in = new DataInputStream(fstream);
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BufferedReader br = new BufferedReader(new InputStreamReader(in));
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String strLine; String [] s = null;
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//Read File Line By Line
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int count = 0;
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while ((strLine = br.readLine()) != null) {
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s = strLine.split("\\t");
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ClosestAllele.put(s[0], s[2]);
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// out.printf("loading: %s\t%s\n",s[0],s[2]);
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count++;
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}
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in.close();
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out.printf("Done! Read %s alleles\n",count);
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}catch (Exception e){//Catch exception if any
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System.err.println("Error: " + e.getMessage());
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}
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char c;
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DatabaseLoaded = true;
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out.printf("Imputing alleles ...\n");
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if (DEBUG){
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//out.printf("Astart[%s]\tAstop[%s]\tBstart[%s]\tBstop[%s]\tCstart[%s]\tCstop[%s]\tnumAlleles[%s]\n",iAstart,iAstop,iBstart,iBstop,iCstart,iCstop,numHLAlleles);
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}
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}
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return 0;
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}
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public Integer map(char[] ref, SAMRecord read) {
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int readstart = read.getAlignmentStart();
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int readstop = read.getAlignmentEnd();
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int startimputation = 0, stopimputation = 0;
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String s1 = formatter.FormatRead(read.getCigarString(), read.getReadString());
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char c;
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String readstring = "", name = "", cigar = "", qualitystring = "";
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int numM = 0, numI = 0, numD = 0;
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name = read.getReadName();
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String matchedAllele = (String) ClosestAllele.get(name);
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//out.printf("%s\t%s\n",name,matchedAllele);
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int index = HLAnames.indexOf(matchedAllele);
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String matchedRead = HLAreads.get(index);
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if (name.indexOf("HLA_A") > -1){
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startimputation = HLA_A_start;
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stopimputation = HLA_A_end;
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} else if (name.indexOf("HLA_B") > -1){
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startimputation = HLA_B_start;
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stopimputation = HLA_B_end;
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} else if (name.indexOf("HLA_C") > -1){
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startimputation = HLA_C_start;
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stopimputation = HLA_C_end;
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}
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for (int i = startimputation; i <= stopimputation; i++){
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//if position is within read
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if (i >= readstart && i <= readstop){
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c = s1.charAt(i-readstart);
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//if position is not missing
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if (c != 'D'){
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readstring = readstring + c;
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qualitystring = qualitystring + 'I';
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numM++;
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if (numD > 0){
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cigar = cigar + String.valueOf(numD) + "D";
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numD = 0;
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} else if (numI > 0){
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cigar = cigar + String.valueOf(numI) + "I";
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numI = 0;
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}
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//if position is missing, get base from matched allele
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}else{
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c = matchedRead.charAt(i-HLAstartpos[index]);
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//if matched allele is also missing / deleted at position
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if (c == 'D'){
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numD++;
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if (numM > 0){
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cigar = cigar + String.valueOf(numM) + "M";
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numM = 0;
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}
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//if matched allele is not missing / deleted at position
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}else{
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readstring = readstring + c;
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qualitystring = qualitystring + 'I';
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numM++;
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if (numD > 0){
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cigar = cigar + String.valueOf(numD) + "D";
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numD = 0;
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} else if (numI > 0){
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cigar = cigar + String.valueOf(numI) + "I";
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numI = 0;
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}
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}
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}
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//if position is outside of range of read, look at matched allele
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}else{
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//if within range of matched allele
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if (i >= HLAstartpos[index] && i <= HLAstoppos[index]){
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c = matchedRead.charAt(i-HLAstartpos[index]);
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//if matched allele is also missing / deleted at position
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if (c == 'D'){
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numD++;
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if (numM > 0){
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cigar = cigar + String.valueOf(numM) + "M";
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numM = 0;
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}
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//if matched allele is not missing / deleted at position
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}else{
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readstring = readstring + c;
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qualitystring = qualitystring + 'I';
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numM++;
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if (numD > 0){
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cigar = cigar + String.valueOf(numD) + "D";
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numD = 0;
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} else if (numI > 0){
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cigar = cigar + String.valueOf(numI) + "I";
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numI = 0;
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}
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}
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}else{
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numD++;
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if (numM > 0){
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cigar = cigar + String.valueOf(numM) + "M";
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numM = 0;
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}
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}
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}
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}
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if (numM > 0){
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cigar = cigar + String.valueOf(numM) + "M";
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}else if(numD > 0){
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cigar = cigar + String.valueOf(numD) + "D";
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}else if(numI > 0){
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cigar = cigar + String.valueOf(numI) + "I";
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}
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out.printf("%s\t0\t6\t%s\t99\t%s\t*\t0\t0\t%s\t%s\n",name,startimputation,cigar,readstring,qualitystring);
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return 1;
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}
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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}
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