Small change to debug printing code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1521 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia
parent
c3aaca1262
commit
ada4c5a13c
|
|
@ -27,8 +27,8 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
public boolean suppressPrinting = false;
|
||||
|
||||
//String HLAdatabaseFile = "/Users/shermanjia/Work/HLA.sam";
|
||||
//String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.sam";
|
||||
String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.sam";
|
||||
String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.sam";
|
||||
//String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.sam";
|
||||
|
||||
|
||||
|
||||
|
|
@ -39,17 +39,20 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
int[] HLAstartpos;
|
||||
int[] HLAstoppos;
|
||||
int numHLAlleles = 0;
|
||||
int numInterval = 1;
|
||||
double[][] Prob; String[][] Alleles;
|
||||
int j1, k1, j2, k2;
|
||||
int iAstart = -1, iAstop = -1, iBstart = -1, iBstop = -1, iCstart = -1, iCstop = -1;
|
||||
|
||||
Hashtable Scores = new Hashtable();
|
||||
|
||||
boolean DatabaseLoaded = false;
|
||||
boolean PrintedOutput = false;
|
||||
boolean DEBUG = false;
|
||||
boolean DEBUG = true;
|
||||
|
||||
public Pair<Long, Long> reduceInit() {
|
||||
//Load sequences corresponding to HLA alleles from sam file
|
||||
|
||||
if (!DatabaseLoaded){
|
||||
try{
|
||||
out.printf("Reading HLA database ...");
|
||||
|
|
@ -58,6 +61,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
BufferedReader br = new BufferedReader(new InputStreamReader(in));
|
||||
String strLine; String [] s = null;
|
||||
//Read File Line By Line
|
||||
int i = 0;
|
||||
while ((strLine = br.readLine()) != null) {
|
||||
s = strLine.split("\\t");
|
||||
if (s.length>=10){
|
||||
|
|
@ -66,6 +70,16 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
HLAcigars.add(s[5]);
|
||||
HLAnames.add(s[0]);
|
||||
HLApositions.add(s[3]);
|
||||
if (s[0].indexOf("HLA_A") > -1){
|
||||
if (iAstart < 0){iAstart=i;}
|
||||
iAstop = i; i++;
|
||||
}else if (s[0].indexOf("HLA_B") > -1){
|
||||
if (iBstart < 0){iBstart=i;}
|
||||
iBstop = i; i++;
|
||||
}else if (s[0].indexOf("HLA_C") > -1){
|
||||
if (iCstart < 0){iCstart=i;}
|
||||
iCstop = i; i++;
|
||||
}
|
||||
}
|
||||
}
|
||||
in.close();
|
||||
|
|
@ -73,7 +87,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
HLAstartpos = new int[n]; HLAstoppos = new int[n];
|
||||
Prob = new double[n][n];
|
||||
|
||||
for (int i = 0; i < n; i++){
|
||||
for (i = 0; i < n; i++){
|
||||
//Find start and stop positions for each allele
|
||||
HLAstartpos[i]=Integer.parseInt(HLApositions.get(i));
|
||||
HLAstoppos[i]=HLAstartpos[i]+HLAreads.get(i).length()-1;
|
||||
|
|
@ -86,9 +100,9 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
j1 = i;
|
||||
if (HLAnames.get(i).equals("HLA_A*01010101"))
|
||||
k1 = i;
|
||||
if (HLAnames.get(i).equals("HLA_A*110201"))
|
||||
if (HLAnames.get(i).equals("HLA_A*110101"))
|
||||
j2 = i;
|
||||
if (HLAnames.get(i).equals("HLA_A*0109"))
|
||||
if (HLAnames.get(i).equals("HLA_A*0114"))
|
||||
k2 = i;
|
||||
}
|
||||
out.printf("DONE!\n");
|
||||
|
|
@ -97,11 +111,20 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
}
|
||||
|
||||
DatabaseLoaded = true;
|
||||
out.printf("Comparing reads to database ...\n");
|
||||
out.printf("Comparing to database ...\n");
|
||||
|
||||
|
||||
//For debugging: prints which HLA alleles were indexed before
|
||||
if (DEBUG){out.printf("%s,%s\t%s,%s\n",HLAnames.get(j1),HLAnames.get(k1),HLAnames.get(j2),HLAnames.get(k2));}
|
||||
if (j1 > k1){int tmp = k1; k1 = j1; j1 = tmp;}
|
||||
if (j2 > k2){int tmp = k2; k2 = j2; j2 = tmp;}
|
||||
|
||||
if (DEBUG){
|
||||
out.printf("Astart[%s]\tAstop[%s]\tBstart[%s]\tBstop[%s]\tCstart[%s]\tCstop[%s]\tnumAlleles[%s]\n",iAstart,iAstop,iBstart,iBstop,iCstart,iCstop,numHLAlleles);
|
||||
out.printf("%s,%s\t%s,%s\n",HLAnames.get(j1),HLAnames.get(k1),HLAnames.get(j2),HLAnames.get(k2));
|
||||
}
|
||||
}
|
||||
out.printf("Computing for interval %s...\n",numInterval);
|
||||
numInterval++;
|
||||
return new Pair<Long,Long>(0l,0l);
|
||||
}
|
||||
|
||||
|
|
@ -177,6 +200,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
int numCs = 0;
|
||||
int numGs = 0;
|
||||
int numTs = 0;
|
||||
int depth = 0;
|
||||
String c1 = ""; String c2 = "";
|
||||
long pos_k = 0; long pos_j = 0;
|
||||
|
||||
|
|
@ -202,81 +226,109 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
char base = read.getReadString().charAt(offset);
|
||||
byte qual = read.getBaseQualities()[offset];
|
||||
int mapquality = read.getMappingQuality();
|
||||
if (mapquality >= 5 && BaseUtils.simpleBaseToBaseIndex(base) != -1) {
|
||||
if (base == 'A'){numAs++;}
|
||||
if (base == 'C'){numCs++;}
|
||||
if (base == 'T'){numTs++;}
|
||||
if (base == 'g'){numGs++;}
|
||||
if (mapquality >= 10 && BaseUtils.simpleBaseToBaseIndex(base) != -1) {
|
||||
if (base == 'A'){numAs++; depth++;}
|
||||
if (base == 'C'){numCs++; depth++;}
|
||||
if (base == 'T'){numTs++; depth++;}
|
||||
if (base == 'G'){numGs++; depth++;}
|
||||
//consider base in likelihood calculations if it looks good and has high mapping score
|
||||
gl.add(base, qual, read, offset);
|
||||
}
|
||||
}
|
||||
|
||||
//Debugging purposes
|
||||
if (DEBUG) {out.printf("A[%s]\tC[%s]\tT[%s]\tg[%s]\t",numAs,numCs,numTs,numGs);}
|
||||
if (DEBUG) {
|
||||
|
||||
|
||||
//Store confidence scores - this is a local hash that we use to get likelihood given a particular genotype
|
||||
Scores = new Hashtable();
|
||||
for ( DiploidGenotype g : DiploidGenotype.values() ) {
|
||||
Scores.put(g.toString(), gl.getLikelihood(g));
|
||||
out.printf("A[%s]\tC[%s]\tT[%s]\tG[%s]\t",numAs,numCs,numTs,numGs);
|
||||
//out.printf("COV[%s]\t",G.getCoverage());
|
||||
}
|
||||
|
||||
//Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.
|
||||
String homref = String.valueOf(ref.getBase())+String.valueOf(ref.getBase());
|
||||
Double homreflikelihood = Double.parseDouble((String) Scores.get(homref).toString());
|
||||
if (depth > 0){
|
||||
//Store confidence scores - this is a local hash that we use to get likelihood given a particular genotype
|
||||
Scores = new Hashtable();
|
||||
for ( DiploidGenotype g : DiploidGenotype.values() ) {
|
||||
Scores.put(g.toString(), G.getLikelihood(g));
|
||||
//also hash other combination not stored by DiploidGenotype
|
||||
if (g.toString().equals("AC")) Scores.put("CA", G.getLikelihood(g));
|
||||
if (g.toString().equals("AG")) Scores.put("GA", G.getLikelihood(g));
|
||||
if (g.toString().equals("AT")) Scores.put("TA", G.getLikelihood(g));
|
||||
if (g.toString().equals("CG")) Scores.put("GC", G.getLikelihood(g));
|
||||
if (g.toString().equals("CT")) Scores.put("TC", G.getLikelihood(g));
|
||||
if (g.toString().equals("GT")) Scores.put("TG", G.getLikelihood(g));
|
||||
}
|
||||
|
||||
//Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.
|
||||
String homref = String.valueOf(ref.getBase())+String.valueOf(ref.getBase());
|
||||
Double homreflikelihood = Double.parseDouble((String) Scores.get(homref).toString());
|
||||
|
||||
|
||||
//Update likelihood for each combinations of alleles
|
||||
Double likelihood = 0.0;
|
||||
String r1 = "", r2 = "", s1 = "", s2 = "";
|
||||
for (int j = 0; j < numHLAlleles; j++){
|
||||
//Update likelihood for each combinations of alleles
|
||||
Double likelihood = 0.0;
|
||||
String r1 = "", r2 = "", s1 = "", s2 = "";
|
||||
for (int j = 0; j < numHLAlleles; j++){
|
||||
|
||||
//check if allele 1 overlaps current position
|
||||
if (loc >= HLAstartpos[j] && loc <= HLAstoppos[j]){
|
||||
pos_j = loc - HLAstartpos[j];
|
||||
c1 = Character.toString(Character.toUpperCase(HLAreads.get(j).charAt((int) pos_j)));
|
||||
//check if allele 1 overlaps current position
|
||||
if (loc >= HLAstartpos[j] && loc <= HLAstoppos[j]){
|
||||
pos_j = loc - HLAstartpos[j];
|
||||
c1 = Character.toString(Character.toUpperCase(HLAreads.get(j).charAt((int) pos_j)));
|
||||
|
||||
//Extract bases for HLA alleles indicated in reduceInit (for debugging)
|
||||
if (j == j1) r1 = c1;
|
||||
if (j == k1) r2 = c1;
|
||||
if (j == j2) s1 = c1;
|
||||
if (j == k2) s2 = c1;
|
||||
//Extract bases for HLA alleles indicated in reduceInit (for debugging)
|
||||
if (j == j1) r1 = c1;
|
||||
if (j == k1) r2 = c1;
|
||||
if (j == j2) s1 = c1;
|
||||
if (j == k2) s2 = c1;
|
||||
|
||||
//Updade likelihoods
|
||||
for (int k = 0; k < numHLAlleles; k++){
|
||||
//Only check A-A, B-C, C-C combinations
|
||||
int kStart = 0, kStop = 0;
|
||||
if (j >= iAstart && j <= iAstop){
|
||||
kStart = iAstart; kStop = iAstop;
|
||||
} else if (j >= iBstart && j <= iBstop){
|
||||
kStart = iBstart; kStop = iBstop;
|
||||
} else if (j >= iCstart && j <= iCstop){
|
||||
kStart = iCstart; kStop = iCstop;
|
||||
}
|
||||
|
||||
//check if allele 2 overlaps current position
|
||||
if (loc >= HLAstartpos[k] && loc <= HLAstoppos[k]){
|
||||
pos_k = loc - HLAstartpos[k];
|
||||
c2 = Character.toString(Character.toUpperCase(HLAreads.get(k).charAt((int) pos_k)));
|
||||
//Fill half-matrix only to speed up process
|
||||
if (j > kStart){kStart = j;}
|
||||
|
||||
//updates likelihoods for both permutations of the alleles, normalized to the likelihood for homozygous reference
|
||||
|
||||
if (Scores.containsKey(c1 + c2)){
|
||||
if (DEBUG){
|
||||
//out.printf("j[%s],k[%s,%s]\t",j,kStart,kStop);
|
||||
}
|
||||
|
||||
likelihood = Double.parseDouble((String) Scores.get(c1 + c2).toString());
|
||||
Prob[j][k]= Prob[j][k]+ likelihood - homreflikelihood;
|
||||
//Update likelihoods
|
||||
for (int k = kStart; k <= kStop; k++){
|
||||
|
||||
}else if(Scores.containsKey(c2 + c1)){
|
||||
|
||||
likelihood = Double.parseDouble((String) Scores.get(c2 + c1).toString());
|
||||
Prob[j][k]= Prob[j][k]+ likelihood - homreflikelihood;
|
||||
//check if allele 2 overlaps current position
|
||||
if (loc >= HLAstartpos[k] && loc <= HLAstoppos[k]){
|
||||
pos_k = loc - HLAstartpos[k];
|
||||
c2 = Character.toString(Character.toUpperCase(HLAreads.get(k).charAt((int) pos_k)));
|
||||
|
||||
//updates likelihoods for both permutations of the alleles, normalized to the likelihood for homozygous reference
|
||||
if (!homref.equals(c1+c2)){
|
||||
if (Scores.containsKey(c1 + c2)){
|
||||
//out.printf("j[%s],k[%s],g[%s],s[%.0f]\t",j,k,c1+c2,Scores.get(c1 + c2));
|
||||
likelihood = Double.parseDouble((String) Scores.get(c1 + c2).toString());
|
||||
Prob[j][k]= Prob[j][k]+ likelihood - homreflikelihood;
|
||||
} else{
|
||||
if (DEBUG){
|
||||
//out.printf("\nCharacters [%s] not found,j[%s],k[%s],%s,%s\n",c1+c2,j,k,HLAnames.get(j),HLAnames.get(k));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if ( DEBUG ){
|
||||
//Debugging: print updated likelihoods for 2 sets of HLA alleles, as well as normalized likelihoods for all 10 genotypes
|
||||
out.printf("%s%s:%5.0f\t%s%s:%5.0f\t",r1,r2,Prob[j1][k1],s1,s2,Prob[j2][k2]);
|
||||
for ( DiploidGenotype g : DiploidGenotype.values() ) {
|
||||
out.printf("%s %5.0f\t",g.toString(),likelihood - homreflikelihood);
|
||||
if ( DEBUG ){
|
||||
//Debugging: print updated likelihoods for 2 sets of HLA alleles, as well as normalized likelihoods for all 10 genotypes
|
||||
out.printf("%s%s:%5.0f\t%s%s:%5.0f\t",r1,r2,Prob[j1][k1],s1,s2,Prob[j2][k2]);
|
||||
for ( DiploidGenotype g : DiploidGenotype.values() ) {
|
||||
out.printf("%s %5.0f\t",g.toString(),G.getLikelihood(g)-homreflikelihood);
|
||||
}
|
||||
out.printf("\n");
|
||||
}
|
||||
out.printf("\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return context.getReads().size();
|
||||
|
|
@ -309,26 +361,26 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
|
||||
//Find max scores for each HLA gene.
|
||||
for (int i = 0; i < numHLAlleles; i++){
|
||||
for (int j = 0; j < numHLAlleles; j++){
|
||||
if (i >= j){
|
||||
//Print likelihoods for all alleles
|
||||
for (int j = i; j < numHLAlleles; j++){
|
||||
//Print likelihoods for all alleles
|
||||
if (!DEBUG){
|
||||
out.printf("%s\t%s\t%5.0f\n",HLAnames.get(i),HLAnames.get(j),Prob[i][j]);
|
||||
}
|
||||
|
||||
if (HLAnames.get(i).indexOf("HLA_A") > -1 && HLAnames.get(j).indexOf("HLA_A") > -1){
|
||||
if (Prob[i][j] > maxA){
|
||||
maxA2 = maxA; i_maxA_2 = i_maxA; j_maxA_2 = j_maxA;
|
||||
maxA = Prob[i][j]; i_maxA = i; j_maxA = j;
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_B") > -1 && HLAnames.get(j).indexOf("HLA_B") > -1){
|
||||
if (Prob[i][j] > maxB){
|
||||
maxB2 = maxB; i_maxB_2 = i_maxB; j_maxB_2 = j_maxB;
|
||||
maxB = Prob[i][j]; i_maxB = i; j_maxB = j;
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_C") > -1 && HLAnames.get(j).indexOf("HLA_C") > -1){
|
||||
if (Prob[i][j] > maxC){
|
||||
maxC2 = maxC; i_maxC_2 = i_maxC; j_maxC_2 = j_maxC;
|
||||
maxC = Prob[i][j]; i_maxC = i; j_maxC = j;
|
||||
}
|
||||
if (HLAnames.get(i).indexOf("HLA_A") > -1 && HLAnames.get(j).indexOf("HLA_A") > -1){
|
||||
if (Prob[i][j] > maxA){
|
||||
maxA2 = maxA; i_maxA_2 = i_maxA; j_maxA_2 = j_maxA;
|
||||
maxA = Prob[i][j]; i_maxA = i; j_maxA = j;
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_B") > -1 && HLAnames.get(j).indexOf("HLA_B") > -1){
|
||||
if (Prob[i][j] > maxB){
|
||||
maxB2 = maxB; i_maxB_2 = i_maxB; j_maxB_2 = j_maxB;
|
||||
maxB = Prob[i][j]; i_maxB = i; j_maxB = j;
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_C") > -1 && HLAnames.get(j).indexOf("HLA_C") > -1){
|
||||
if (Prob[i][j] > maxC){
|
||||
maxC2 = maxC; i_maxC_2 = i_maxC; j_maxC_2 = j_maxC;
|
||||
maxC = Prob[i][j]; i_maxC = i; j_maxC = j;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -336,33 +388,30 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
|
|||
|
||||
//Print alleles with the highest likelihoods
|
||||
for (int i = 0; i < numHLAlleles; i++){
|
||||
for (int j = 0; j < numHLAlleles; j++){
|
||||
if (i >= j){
|
||||
if (HLAnames.get(i).indexOf("HLA_A") > -1 && HLAnames.get(j).indexOf("HLA_A") > -1){
|
||||
if (Prob[i][j] == maxA && maxA > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxA,maxA-maxA2);
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_B") > -1 && HLAnames.get(j).indexOf("HLA_B") > -1){
|
||||
if (Prob[i][j] == maxB && maxB > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxB,maxB-maxB2);
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_C") > -1 && HLAnames.get(j).indexOf("HLA_C") > -1){
|
||||
if (Prob[i][j] == maxC && maxC > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxC,maxC-maxC2);
|
||||
}
|
||||
for (int j = i; j < numHLAlleles; j++){
|
||||
if (HLAnames.get(i).indexOf("HLA_A") > -1 && HLAnames.get(j).indexOf("HLA_A") > -1){
|
||||
if (Prob[i][j] == maxA && maxA > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxA,maxA-maxA2);
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_B") > -1 && HLAnames.get(j).indexOf("HLA_B") > -1){
|
||||
if (Prob[i][j] == maxB && maxB > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxB,maxB-maxB2);
|
||||
}
|
||||
} else if (HLAnames.get(i).indexOf("HLA_C") > -1 && HLAnames.get(j).indexOf("HLA_C") > -1){
|
||||
if (Prob[i][j] == maxC && maxC > 0){
|
||||
out.printf("%s\t%s\t%5.0f\t%5.0f\tBEST\n",HLAnames.get(i),HLAnames.get(j),maxC,maxC-maxC2);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
//2nd Highest likelihoods
|
||||
for (int i = 0; i < numHLAlleles; i++){
|
||||
for (int j = 0; j < numHLAlleles; j++){
|
||||
if (i >= j){
|
||||
if (Prob[i][j] == maxA2){
|
||||
//out.printf("2nd Highest likelihood: %5.0f in %s and %s; i=%s, j=%s\n",maxA2,HLAnames.get(i),HLAnames.get(j),i,j);
|
||||
}
|
||||
for (int j = i; j < numHLAlleles; j++){
|
||||
if (Prob[i][j] == maxA2){
|
||||
//out.printf("2nd Highest likelihood: %5.0f in %s and %s; i=%s, j=%s\n",maxA2,HLAnames.get(i),HLAnames.get(j),i,j);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue