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Updates after seeing a certain number of reads, not a certain number of bases. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@947 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-09 01:01:36 +00:00
parent 65d0675a4e
commit 6506504a60
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/secondarybase/BasecallingStats.java
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@ -83,17 +83,17 @@ public class BasecallingStats {
* @return nicely formatted string containing basecalling stats
*/
public String toString() {
return String.format("%% bases consistent: %d/%d (%2.2f%%)", getBasesConsistent(), getBasesTotal(), getPercentConsistent());
return String.format(" Reads seen: %d; %% bases consistent: %d/%d (%2.2f%%)", getReadsTotal(), getBasesConsistent(), getBasesTotal(), getPercentConsistent());
}
/**
* Periodically print a line containing basecalling stats.
* Periodically print a line containing basecalling stats after having seen a certain number of reads.
*
* @param interval the periodicity of the messages given in number of bases observed
* @param interval the periodicity (in number of reads) of the messages given in number of bases observed
*/
public void notifyOnInterval(int interval) {
if (getBasesTotal() > 0 && getBasesTotal() % interval == 0) {
System.out.printf("%s\r", toString());
if (getReadsTotal() > 0 && getReadsTotal() % interval == 0) {
System.out.printf("%s\n", toString());
}
}