107 lines
3.0 KiB
Java
Executable File
107 lines
3.0 KiB
Java
Executable File
package org.broadinstitute.sting.secondarybase;
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import org.broadinstitute.sting.utils.BaseUtils;
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/**
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* BasecallingStats is a utility class to aggregate and emit basecalling
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* stats (total bases seen and consistency between basecalling methods).
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*
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* @author Kiran Garimella
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*/
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public class BasecallingStats {
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private int basesConsistent = 0;
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private int basesTotal = 0;
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private int readsTotal = 0;
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/**
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* Constructor that does nothing.
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*/
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public BasecallingStats() {}
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/**
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* Return the number of bases called identically by two different methods.
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*
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* @return the number of consistent bases.
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*/
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public int getBasesConsistent() {
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return basesConsistent;
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}
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/**
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* Return the total number of bases seen.
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*
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* @return the total number of bases seen.
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*/
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public int getBasesTotal() {
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return basesTotal;
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}
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/**
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* Return the total number of reads seen.
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*
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* @return the total number of reads seen.
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*/
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public int getReadsTotal() {
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return readsTotal;
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}
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/**
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* Return the percent of bases called consistently by two different methods.
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*
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* @return the percent of bases called consistently
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*/
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public double getPercentConsistent() {
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return 100.0*((double) getBasesConsistent())/((double) getBasesTotal());
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}
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/**
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* Updates the number of bases seen, the number of reads seen, and the number of consistent bases.
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*
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* @param rr the raw Illumina read
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* @param fpr the FourProb read
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*/
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public void update(RawRead rr, FourProbRead fpr) {
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for (int cycle = 0; cycle < fpr.size(); cycle++) {
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int rawBaseIndex = BaseUtils.simpleBaseToBaseIndex((char) rr.getSequence()[cycle]);
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int fpBaseIndex = fpr.get(cycle).indexAtRank(0);
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if (rawBaseIndex >= 0 && fpBaseIndex >= 0) {
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basesTotal++;
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if (rawBaseIndex == fpBaseIndex) {
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basesConsistent++;
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}
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}
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}
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readsTotal++;
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}
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/**
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* Returns basecalling stats info in a nicely formatted string.
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*
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* @return nicely formatted string containing basecalling stats
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*/
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public String toString() {
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return String.format(" Reads seen: %d; %% bases consistent: %d/%d (%2.2f%%)", getReadsTotal(), getBasesConsistent(), getBasesTotal(), getPercentConsistent());
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}
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/**
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* Periodically print a line containing basecalling stats after having seen a certain number of reads.
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*
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* @param interval the periodicity (in number of reads) of the messages given in number of bases observed
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*/
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public void notifyOnInterval(int interval) {
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if (getReadsTotal() > 0 && getReadsTotal() % interval == 0) {
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System.out.printf("%s\n", toString());
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}
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}
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/**
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* Immediately print a line containing basecalling stats.
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*/
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public void notifyNow() {
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System.out.printf("%s\n", toString());
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}
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}
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