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Removed 'backed' last cache hit hard references; it seems that that i… #1645

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Removed 'backed' last cache hit hard references; it seems that that i… #1645

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28 changes: 5 additions & 23 deletions src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.lang.ref.WeakReference;
import java.lang.ref.SoftReference;
import java.net.URL;
import java.nio.file.Path;
import java.util.ArrayList;
Expand All @@ -58,13 +58,7 @@ public class ReferenceSource implements CRAMReferenceSource {
private final ReferenceSequenceFile rsFile;
private int downloadTriesBeforeFailing = 2;

private final Map<String, WeakReference<byte[]>> cacheW = new HashMap<>();

// Optimize for locality of reference by maintaining the backing reference bases for the most recent request.
// Failure to do this will result in the bases being aggressively GC'd when the only other reference to them
// is the weak reference hash map above, resulting in much thrashing.
private byte[] backingReferenceBases;
private int backingContigIndex;
private final Map<String, SoftReference<byte[]>> cache = new HashMap<>();

public ReferenceSource(final File file) {
this(IOUtil.toPath(file));
Expand Down Expand Up @@ -116,7 +110,7 @@ else if (Defaults.USE_CRAM_REF_DOWNLOAD) {
}

private byte[] findInCache(final String name) {
final WeakReference<byte[]> weakReference = cacheW.get(name);
final SoftReference<byte[]> weakReference = cache.get(name);
if (weakReference != null) {
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Can you explicitly check for an empty array here as well, and throw an informative error if you encounter one?

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Under what circumstances the bases array would be an empty array as supposed to a null (claimed by the GC)?

final byte[] bytes = weakReference.get();
if (bytes != null)
Expand All @@ -133,7 +127,7 @@ private byte[] addToCache(final String sequenceName, final byte[] bases) {
for (int i = 0; i < bases.length; i++) {
bases[i] = StringUtil.toUpperCase(bases[i]);
}
cacheW.put(sequenceName, new WeakReference<>(bases));
cache.put(sequenceName, new SoftReference<>(bases));
return bases;
}

Expand Down Expand Up @@ -196,13 +190,9 @@ public byte[] getReferenceBasesByRegion(

// this implementation maintains the entire reference sequence, and hands out whatever region
// of it is requested
final byte[] bases = getBackingBases(sequenceRecord);
final byte[] bases = getReferenceBases(sequenceRecord, false);

if (bases != null) {
// cache the backing bases to prevent thrashing due to aggressive GC
backingReferenceBases = bases;
backingContigIndex = sequenceRecord.getSequenceIndex();

if (zeroBasedStart >= bases.length) {
throw new IllegalArgumentException(String.format("Requested start %d is beyond the sequence length %s",
zeroBasedStart,
Expand All @@ -213,14 +203,6 @@ public byte[] getReferenceBasesByRegion(
return bases;
}

private byte[] getBackingBases(final SAMSequenceRecord sequenceRecord) {
if (backingReferenceBases != null && backingContigIndex == sequenceRecord.getSequenceIndex()) {
return backingReferenceBases;
} else {
return getReferenceBases(sequenceRecord, false);
}
}

private byte[] findBasesByName(final String name, final boolean tryVariants) {
if (rsFile == null || !rsFile.isIndexed())
return null;
Expand Down