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PerSampleDownsamplingReadsIterator: fix for incorrect use of DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL 

Notify all downsamplers in our pool of the current global genomic position every
DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL position changes, not every single
positional change after that threshold is first reached.
This commit is contained in:
David Roazen 2012-09-21 22:22:59 -04:00
parent 133085469f
commit 34eed20aa6
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
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@ -158,10 +158,10 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator {
numPositionalChanges++;
}
// If the number of times we've changed position exceeds a certain threshold, inform all
// downsamplers of the current position in the read stream. This is to prevent downsamplers
// for samples with sparser reads than others from getting stuck too long in a pending state.
if ( numPositionalChanges > DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL ) {
// Periodically inform all downsamplers of the current position in the read stream. This is
// to prevent downsamplers for samples with sparser reads than others from getting stuck too
// long in a pending state.
if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
perSampleDownsampler.signalNoMoreReadsBefore(read);
updateEarliestPendingRead(perSampleDownsampler);