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Renamed to BasecallingTrainer. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@752 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-20 00:03:46 +00:00
parent 01a3cb27c7
commit 08c9f4d86b
1 changed files with 9 additions and 18 deletions
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27
java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java → java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainer.java
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@ -19,11 +19,9 @@ import java.util.regex.Pattern;
* *
* @author Kiran Garimella * @author Kiran Garimella
*/ */
public class BasecallingTrainingSet { public class BasecallingTrainer {
private File bustardDir; private File bustardDir;
private int lane; private int lane;
private int cycleBegin;
private int cycleEnd;
private int trainingLimit; private int trainingLimit;
private ArrayList<RawRead> trainingData; private ArrayList<RawRead> trainingData;
@ -33,15 +31,11 @@ public class BasecallingTrainingSet {
* *
* @param bustardDir the Bustard directory for the sample * @param bustardDir the Bustard directory for the sample
* @param lane the lane for the sample * @param lane the lane for the sample
* @param cycleBegin the start cycle for the beginning of the read (0-based, inclusive)
* @param cycleEnd the stop cycle for the end of the read (0-based, inclusive)
* @param trainingLimit the number of training reads to accept * @param trainingLimit the number of training reads to accept
*/ */
public BasecallingTrainingSet(File bustardDir, int lane, int cycleBegin, int cycleEnd, int trainingLimit) { public BasecallingTrainer(File bustardDir, int lane, int trainingLimit) {
this.bustardDir = bustardDir; this.bustardDir = bustardDir;
this.lane = lane; this.lane = lane;
this.cycleBegin = cycleBegin;
this.cycleEnd = cycleEnd;
this.trainingLimit = trainingLimit; this.trainingLimit = trainingLimit;
} }
@ -69,12 +63,14 @@ public class BasecallingTrainingSet {
public void loadFirstNUnambiguousReadsTrainingSet() { public void loadFirstNUnambiguousReadsTrainingSet() {
this.trainingData = new ArrayList<RawRead>(trainingLimit); this.trainingData = new ArrayList<RawRead>(trainingLimit);
IlluminaParser iparser = new IlluminaParser(bustardDir, lane, cycleBegin, cycleEnd); IlluminaParser iparser = new IlluminaParser(bustardDir, lane);
RawRead rawread; RawRead rawread;
int numreads = 0; int numreads = 0;
while (numreads < trainingLimit && (rawread = iparser.next()) != null) { while (numreads < trainingLimit && iparser.next()) {
rawread = iparser.getRawRead();
int numAmbiguous = 0; int numAmbiguous = 0;
byte[] sequence = rawread.getSequence(); byte[] sequence = rawread.getSequence();
@ -171,16 +167,10 @@ public class BasecallingTrainingSet {
return trainingReads; return trainingReads;
} }
/**
* Correlate the perfect reads with their raw intensities. Sloooooooow.
*
* @param trainingReads the perfect reads, grouped by tile
* @return a training set of raw sequence, intensities, and quality scores (all set to 40 for these perfect bases)
*/
private ArrayList<RawRead> correlateReadsAndIntensities(Vector<HashMap<String, SAMRecord>> trainingReads) { private ArrayList<RawRead> correlateReadsAndIntensities(Vector<HashMap<String, SAMRecord>> trainingReads) {
ArrayList<RawRead> newTrainingData = new ArrayList<RawRead>(trainingLimit); ArrayList<RawRead> newTrainingData = new ArrayList<RawRead>(trainingLimit);
IlluminaParser iparser = new IlluminaParser(bustardDir, lane, cycleBegin, cycleEnd); IlluminaParser iparser = new IlluminaParser(bustardDir, lane);
int totalReadCount = 0; int totalReadCount = 0;
@ -190,7 +180,8 @@ public class BasecallingTrainingSet {
int tileReadCount = 0; int tileReadCount = 0;
RawRead iread; RawRead iread;
while (trainingReads.get(tile) != null && tileReadCount < trainingReads.get(tile).size() && (iread = iparser.next()) != null) { while (trainingReads.get(tile) != null && tileReadCount < trainingReads.get(tile).size() && iparser.next()) {
iread = iparser.getRawRead();
String readKey = iread.getReadKey(); String readKey = iread.getReadKey();
if (trainingReads.get(tile).containsKey(readKey)) { if (trainingReads.get(tile).containsKey(readKey)) {