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Don't put null entries into the key array

This commit is contained in:
Eric Banks 2012-06-13 11:43:44 -04:00
parent bdf5945dcc
commit 81993b08e2
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java
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@ -110,7 +110,7 @@ public class BQSRKeyManager {
* @return one key in long representation per covariate * @return one key in long representation per covariate
*/ */
public Long[] longsFromAllKeys(final Long[] allKeys, final EventType eventType) { public Long[] longsFromAllKeys(final Long[] allKeys, final EventType eventType) {
final Long[] allFinalKeys = new Long[optionalCovariatesInfo.length > 0 ? optionalCovariatesInfo.length : 1]; // Generate one key per optional covariate final ArrayList<Long> allFinalKeys = new ArrayList<Long>(); // Generate one key per optional covariate
int covariateIndex = 0; int covariateIndex = 0;
long masterKey = 0L; // This will be a master key holding all the required keys, to replicate later on long masterKey = 0L; // This will be a master key holding all the required keys, to replicate later on
@ -128,13 +128,13 @@ public class BQSRKeyManager {
long newKey = masterKey | (covariateKey << optionalCovariateOffset); long newKey = masterKey | (covariateKey << optionalCovariateOffset);
newKey |= (optionalCovariatesInfo[i].covariateID << optionalCovariateIDOffset); newKey |= (optionalCovariatesInfo[i].covariateID << optionalCovariateIDOffset);
allFinalKeys[i] = newKey; // add this key to the list of keys allFinalKeys.add(newKey); // add this key to the list of keys
} }
if (optionalCovariatesInfo.length == 0) // special case when we have no optional covariates if (optionalCovariatesInfo.length == 0) // special case when we have no optional covariates
allFinalKeys[0] = masterKey; allFinalKeys.add(masterKey);
return allFinalKeys; return allFinalKeys.toArray(new Long[allFinalKeys.size()]);
} }
/** /**