Strange bug in VCFEncoder.addGenotypeData when reading a list of Variant and then using the list in a multithreaded env. #1026
Description
Subject of the issue
Genotypes in variantcontext look mutable (??)
Minimal example
I've posted an example here: https://gist.github.com/lindenb/7ee76e30dfb662048fff3cf6125b980d
Description
This is a strange bug, may be it's not about htsjdk but I would be happy to know the cause of this.
I'm reading a list of variants from a VCFFileReader:
final CloseableIterator<VariantContext> iter2=vcfFileReader.iterator();
final List<VariantContext> inMemoryVariants = Collections.unmodifiableList(iter2.stream().
limit(3).
collect(Collectors.toList())
);
iter2.close();
vcfFileReader.close();
this read-only List is then used by some java Threads , I wait for the end of the thread and I write some variants of a new VCF file:
final VariantContextWriter w = (...)
final VCFHeader header2= (...)
w.writeHeader(header2);
w.add(bestResult.ctx1);
w.add(bestResult.ctx2);
w.close();
but here, I get an exception form VCFEncoder.writeAllele called from addGenotypeData :
java.lang.RuntimeException: Allele C* is not an allele in the variant context
at htsjdk.variant.vcf.VCFEncoder.writeAllele
at the beginning of VCFEncoder.addGenotypeData if I add the statement below, I see my message on stderr: boummm3 {C=1, .=., T*=0} [C*, C*] class java.util.HashMap
final List<Allele> saveAllele = Collections.unmodifiableList(g.getAlleles());
if(!alleleMap.containsKey(g.getAllele(0))) {
System.err.println(
" boummm3 "+alleleMap+" "+saveAllele+" "+alleleMap.getClass());
}
Adding the following statement (accessing the alleles) before using the list inMemoryVariants fixes the problem.
inMemoryVariants.forEach(C->{long i=C.getGenotypes().stream().flatMap(G->G.getAlleles().stream()).count();});`
I'm puzlled, do you have any idea ?
Your environment
- version of htsjdk 2.13.0
- version of java 1_8_152
- which OS linux 32