samtools/htsjdk — pull request #79 by eitanbanks (2014-08-13 17:49:16+00:00)
Title: Removed closing of internal output stream directly in the BCF2Writer.

BCF2Writer.close() was calling outputStream.close() and then super.close();
but in IndexingVariantContextWriter's (the super class of BCF2Writer) close() method
it also calls outputStream.close(). So we were double-closing the output stream.

This manifests itself as a problem when we try to write e.g. a compressed bcf file
because the close method tries to do a final write (which fails on the 2nd close).