I am using htsjdk.variant.vcf.VCFFileReader class to parse .vcf document, so I've got a constructor
VCFFileReader vcfReader = new VCFFileReader(inputFile, false);
and some code like
for (VariantContext variantContext : vcfReader) {
//..
}
vcfReader.close()
Unfortunately, my file isn't released after I close VCFReader (even if it is an empty cycle), but in construction like
VCFFileReader vcfReader = new VCFFileReader(inputFile, false);
vcfReader.close();
Everything is ok. Does anybody know how to solve it?
Thanks
•
written
by
timofeevbog •
To be sure that your Reader is closed, use a try/finally statement
VCFFileReader in=null;
try {
in=new VCFFileReader(inputFile, false);
for(VariantContext ctx: in)
{
/* something */
}
}
finally
{
htsjdk.samtools.util.CloserUtil.close(in);
}
Thanks for your reply, but I still can't delete file even after this construction.
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Are you sure the code gets to vcfReader.close()?
Yes, it gets
how do you know that the file isn't realeased ? an exception ? what's in the loop ?
I can't delete my file after vcfReader.close()
Are you sure nothing else is accessing it? What does
lsofsay?