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Nicer output when training off of perfect reads. Not that that works yet... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-15 20:07:08 +00:00
parent d1f3000afa
commit bfc40f54f0
1 changed files with 10 additions and 0 deletions
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10
java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java
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@ -182,6 +182,8 @@ public class BasecallingTrainingSet {
IlluminaParser iparser = new IlluminaParser(bustardDir, lane, cycleBegin, cycleEnd); IlluminaParser iparser = new IlluminaParser(bustardDir, lane, cycleBegin, cycleEnd);
int totalReadCount = 0;
for (int tile = 1; tile < trainingReads.size(); tile++) { for (int tile = 1; tile < trainingReads.size(); tile++) {
iparser.seekToTile(tile); iparser.seekToTile(tile);
@ -192,6 +194,13 @@ public class BasecallingTrainingSet {
String readKey = iread.getReadKey(); String readKey = iread.getReadKey();
if (trainingReads.get(tile).containsKey(readKey)) { if (trainingReads.get(tile).containsKey(readKey)) {
System.out.printf("\tTile %d: found %d of %d (%4.4f in tile, %4.4f total) \r",
tile,
tileReadCount,
trainingReads.get(tile).size(),
((double) tileReadCount)/((double) trainingReads.get(tile).size()),
((double) totalReadCount)/((double) trainingLimit));
byte[] quals = new byte[iread.getReadLength()]; byte[] quals = new byte[iread.getReadLength()];
for (int qualIndex = 0; qualIndex < quals.length; qualIndex++) { for (int qualIndex = 0; qualIndex < quals.length; qualIndex++) {
quals[qualIndex] = 40; quals[qualIndex] = 40;
@ -201,6 +210,7 @@ public class BasecallingTrainingSet {
newTrainingData.add(iread); newTrainingData.add(iread);
tileReadCount++; tileReadCount++;
totalReadCount++;
} }
} }
} }