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ReducedRead flag cached in GATKSAMRecord. 20% performance improvement

This commit is contained in:
Mark DePristo 2011-09-06 15:09:37 -04:00
parent f3ab7d7c0d
commit 284f83469b
2 changed files with 16 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -82,7 +82,7 @@ public class PileupElement {
// -------------------------------------------------------------------------- // --------------------------------------------------------------------------
private Integer getReducedReadQualityTagValue() { private Integer getReducedReadQualityTagValue() {
return (Integer)getRead().getAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG); return getRead().getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
} }
public boolean isReducedRead() { public boolean isReducedRead() {

16
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -41,6 +41,10 @@ public class GATKSAMRecord extends SAMRecord {
// because some values can be null, we don't want to duplicate effort // because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false; private boolean retrievedReadGroup = false;
/** A private cache for the reduced read quality. Null indicates the value hasn't be fetched yet or isn't available */
private boolean lookedUpReducedReadQuality = false;
private Integer reducedReadQuality;
// These temporary attributes were added here to make life easier for // These temporary attributes were added here to make life easier for
// certain algorithms by providing a way to label or attach arbitrary data to // certain algorithms by providing a way to label or attach arbitrary data to
// individual GATKSAMRecords. // individual GATKSAMRecords.
@ -338,7 +342,17 @@ public class GATKSAMRecord extends SAMRecord {
public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); } public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); } public Integer getIntegerAttribute(final String tag) {
if ( tag == ReadUtils.REDUCED_READ_QUALITY_TAG ) {
if ( ! lookedUpReducedReadQuality ) {
lookedUpReducedReadQuality = true;
reducedReadQuality = mRecord.getIntegerAttribute(tag);
}
return reducedReadQuality;
} else {
return mRecord.getIntegerAttribute(tag);
}
}
public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); } public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }