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Make AbstractFastaSequenceFile serializable by Kryo for Spark. #1408

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Aug 13, 2019
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Make AbstractFastaSequenceFile serializable by Kryo for Spark. #1408

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8 changes: 6 additions & 2 deletions src/main/java/htsjdk/samtools/reference/AbstractFastaSequenceFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,8 +35,10 @@

import java.io.File;
import java.io.InputStream;
import java.io.Serializable;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.function.Supplier;

/**
* Provide core sequence dictionary functionality required by all fasta file readers.
Expand All @@ -62,7 +64,8 @@ abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
AbstractFastaSequenceFile(final Path path) {
this.path = path;
this.source = path == null ? "unknown" : path.toAbsolutePath().toString();
this.dictionary = new Lazy<>(() -> findAndLoadSequenceDictionary(path));
// ensure lambda is serializable (by Kryo, when used with Spark)
this.dictionary = new Lazy<>((Supplier<SAMSequenceDictionary> & Serializable) (() -> findAndLoadSequenceDictionary(path)));
}

/**
Expand All @@ -74,7 +77,8 @@ abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
AbstractFastaSequenceFile(final Path path, final String source, final SAMSequenceDictionary sequenceDictionary) {
this.path = path;
this.source = source;
this.dictionary = new Lazy<>(() -> sequenceDictionary);
// ensure lambda is serializable (by Kryo, when used with Spark)
this.dictionary = new Lazy<>((Supplier<SAMSequenceDictionary> & Serializable) (() -> sequenceDictionary));
}

/** Attempts to find and load the sequence dictionary if present. */
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