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Added some debugging stuff (writes model parameters to one file per cycle). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@304 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-06 22:00:58 +00:00
parent 0fc8a90553
commit 5a5c6d1276
3 changed files with 79 additions and 5 deletions
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57
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingBaseModel.java
View File

@ -8,6 +8,8 @@ import cern.colt.matrix.linalg.Algebra;
import org.broadinstitute.sting.utils.QualityUtils;
import java.io.*;
/**
* BasecallingBaseModel is a class that represents the statistical
* model for all bases at a given cycle. It allows for easy, one
@ -59,15 +61,34 @@ public class BasecallingBaseModel {
/**
* Add a single training point to the model.
*
* @param basePrev the previous cycle's base call (A, C, G, T, or * for the first cycle)
* @param baseCur the current cycle's base call (A, C, G, T)
* @param qualCur the quality score for the current cycle's base call
* @param fourintensity the four intensities for the current cycle's base call
*/
public void addTrainingPoint(char basePrev, char baseCur, byte qualCur, double[] fourintensity) {
int basePrevIndex = baseToBaseIndex(basePrev);
int baseCurIndex = baseToBaseIndex(baseCur);
int actualBasePrevIndex = baseToBaseIndex(basePrev);
int actualBaseCurIndex = baseToBaseIndex(baseCur);
double actualWeight = QualityUtils.qualToProb(qualCur);
double otherTheories = (basePrev == '*') ? 3.0 : 15.0;
cern.jet.math.Functions F = cern.jet.math.Functions.functions;
for (int basePrevIndex = 0; basePrevIndex < 4; basePrevIndex++) {
for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
// We want to upweight the correct theory as much as we can and spread the remainder out evenly between all other hypotheses.
double weight = (basePrevIndex == actualBasePrevIndex && baseCurIndex == actualBaseCurIndex) ? actualWeight : ((1.0 - actualWeight)/otherTheories);
DoubleMatrix1D weightedChannelIntensities = (DoubleFactory1D.dense).make(fourintensity);
weightedChannelIntensities.assign(F.mult(weight));
runningChannelSums[basePrevIndex][baseCurIndex].assign(weightedChannelIntensities, F.plus);
counts[basePrevIndex][baseCurIndex] += weight;
}
}
/*
if (basePrevIndex >= 0 && baseCurIndex >= 0) {
for (int channel = 0; channel < 4; channel++) {
double weight = QualityUtils.qualToProb(qualCur);
@ -83,6 +104,7 @@ public class BasecallingBaseModel {
counts[basePrevIndex][baseCurIndex]++;
}
*/
readyToCall = false;
}
@ -148,6 +170,27 @@ public class BasecallingBaseModel {
return probdist;
}
public void write(File outparam) {
try {
PrintWriter writer = new PrintWriter(outparam);
for (int basePrevIndex = 0; basePrevIndex < 4; basePrevIndex++) {
for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
writer.print("mean_" + baseIndexToBase(basePrevIndex) + "" + baseIndexToBase(baseCurIndex) + " : [ ");
for (int channel = 0; channel < 4; channel++) {
writer.print(runningChannelSums[basePrevIndex][baseCurIndex].getQuick(channel)/counts[basePrevIndex][baseCurIndex]);
writer.print(" ");
}
writer.print("]\n");
}
}
writer.close();
} catch (IOException e) {
}
}
/**
* Utility method for converting a base ([Aa*], [Cc], [Gg], [Tt]) to an index (0, 1, 2, 3);
* @param base
@ -171,4 +214,14 @@ public class BasecallingBaseModel {
return -1;
}
private char baseIndexToBase(int baseIndex) {
switch (baseIndex) {
case 0: return 'A';
case 1: return 'C';
case 2: return 'G';
case 3: return 'T';
default: return '.';
}
}
}

15
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingReadModel.java
View File

@ -1,5 +1,7 @@
package org.broadinstitute.sting.playground.fourbasecaller;
import java.io.File;
/**
* BasecallingReadModel represents the statistical models for
* all bases in all cycles. It allows for easy, one-pass
@ -28,6 +30,7 @@ public class BasecallingReadModel {
/**
* Add a single training point to the model.
*
* @param cycle the cycle for which this point should be added
* @param basePrev the previous base
* @param baseCur the current base
@ -82,4 +85,16 @@ public class BasecallingReadModel {
return new FourProb(baseindices, probs);
}
/**
* Writes model parameters to a file per cycle.
*
* @param dir the directory where the parameters should be written
*/
public void write(File dir) {
for (int cycle = 0; cycle < basemodels.length; cycle++) {
File outparam = new File(dir.getPath() + "/param." + cycle);
basemodels[cycle].write(outparam);
}
}
}

12
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
View File

@ -45,7 +45,7 @@ public class FourBaseRecaller extends CommandLineProgram {
bread = bfp.next();
int cycle_offset = (END <= 1) ? 0 : bread.getIntensities().length/2;
BasecallingReadModel p = new BasecallingReadModel(bread.getFirstReadSequence().length());
BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length());
int queryid;
// learn initial parameters
@ -61,12 +61,16 @@ public class FourBaseRecaller extends CommandLineProgram {
byte qualCur = quals[cycle];
double[] fourintensity = intensities[cycle + cycle_offset];
p.addTrainingPoint(cycle, basePrev, baseCur, qualCur, fourintensity);
model.addTrainingPoint(cycle, basePrev, baseCur, qualCur, fourintensity);
}
queryid++;
} while (queryid < TRAINING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null);
File debugout = new File(OUT.getParentFile().getPath() + "/model/");
debugout.mkdir();
model.write(debugout);
// call bases
SAMFileHeader sfh = new SAMFileHeader();
SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, OUT);
@ -89,7 +93,7 @@ public class FourBaseRecaller extends CommandLineProgram {
byte qualPrev = (cycle == 0) ? 0 : bestqual[cycle - 1];
double[] fourintensity = intensities[cycle + cycle_offset];
FourProb fp = p.computeProbabilities(cycle, basePrev, qualPrev, fourintensity);
FourProb fp = model.computeProbabilities(cycle, basePrev, qualPrev, fourintensity);
asciiseq[cycle] = (byte) fp.baseAtRank(0);
bestqual[cycle] = fp.qualAtRank(0);
@ -102,6 +106,8 @@ public class FourBaseRecaller extends CommandLineProgram {
queryid++;
} while (queryid < CALLING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null);
sfw.close();
return 0;
}