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Changed the intensities array order from cycle,channel to channel,cycle. This, I'm told, is a far more efficient allocation strategy. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1084 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-24 15:41:06 +00:00
parent 3112302ec9
commit 7b5d8d7604
2 changed files with 19 additions and 9 deletions
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9
java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
View File

@ -98,7 +98,8 @@ public class BasecallingReadModel {
double[] fourIntensity = new double[4];
for (int channel = 0; channel < 4; channel++) {
fourIntensity[channel] = (double) ints[cycle][channel];
//fourIntensity[channel] = (double) ints[cycle][channel];
fourIntensity[channel] = (double) ints[channel][cycle];
}
basemodels[cycle].addMeanPoint(probMatrix, fourIntensity);
@ -135,7 +136,8 @@ public class BasecallingReadModel {
double[] fourIntensity = new double[4];
for (int channel = 0; channel < 4; channel++) {
fourIntensity[channel] = (double) ints[cycle][channel];
//fourIntensity[channel] = (double) ints[cycle][channel];
fourIntensity[channel] = (double) ints[channel][cycle];
}
basemodels[cycle].addCovariancePoint(probMatrix, fourIntensity);
@ -207,7 +209,8 @@ public class BasecallingReadModel {
double[] fourIntensity = new double[4];
for (int channel = 0; channel < 4; channel++) {
fourIntensity[channel] = (double) read.getIntensities()[cycle][channel];
//fourIntensity[channel] = (double) read.getIntensities()[cycle][channel];
fourIntensity[channel] = (double) read.getIntensities()[channel][cycle];
}
fpr.add(cycle, computeProbabilities(cycle, basePrev, qualPrev, fourIntensity));

19
java/src/org/broadinstitute/sting/secondarybase/RawRead.java
View File

@ -58,7 +58,8 @@ public class RawRead implements Comparable<RawRead> {
sequence = pastedReadString[1][4].substring(cycleBegin, cycleEnd + 1).getBytes();
quals = new byte[sequence.length];
intensities = new short[sequence.length][4];
//intensities = new short[sequence.length][4];
intensities = new short[4][sequence.length];
for (int cycle = cycleBegin, offset = 0; cycle <= cycleEnd; cycle++, offset++) {
byte maxQual = -50;
@ -75,7 +76,8 @@ public class RawRead implements Comparable<RawRead> {
double doubleChannelIntensity = Double.valueOf(pastedReadString[0][fullReadIndex]);
short shortChannelIntensity = (short) doubleChannelIntensity;
intensities[offset][channel] = shortChannelIntensity;
//intensities[offset][channel] = shortChannelIntensity;
intensities[channel][offset] = shortChannelIntensity;
}
}
}
@ -181,14 +183,14 @@ public class RawRead implements Comparable<RawRead> {
/**
* Get the raw read intensities.
*
* @return the (readLength)x(numChannels) array of raw intensities
* @return the (numChannels)x(readLength) array of raw intensities
*/
public short[][] getIntensities() { return intensities; }
/**
* Set the raw intensities.
*
* @param intensities the (readLength)x(numChannels) array of raw intensities
* @param intensities the (numChannels)x(readLength) array of raw intensities
*/
public void setIntensities(short[][] intensities) { this.intensities = intensities; }
@ -239,12 +241,17 @@ public class RawRead implements Comparable<RawRead> {
byte[] newSequence = new byte[cycleStop - cycleStart + 1];
byte[] newQuals = new byte[cycleStop - cycleStart + 1];
short[][] newIntensities = new short[cycleStop - cycleStart + 1][4];
//short[][] newIntensities = new short[cycleStop - cycleStart + 1][4];
short[][] newIntensities = new short[4][cycleStop - cycleStart + 1];
for (int cycle = cycleStart, offset = 0; cycle <= cycleStop; cycle++, offset++) {
newSequence[offset] = sequence[cycle];
newQuals[offset] = quals[cycle];
newIntensities[offset] = intensities[cycle];
//newIntensities[offset] = intensities[cycle];
for (int channel = 0; channel < 4; channel++) {
newIntensities[channel][offset] = intensities[channel][cycle];
}
}
subRead.setSequence(newSequence);