Re: [Samtools-devel] Indexing a BAM Index (BAI)

[John M. <jm...@sa...>]

On 1 Dec 2014, at 15:11, Jim Robinson <jro...@br...> wrote:
> I use the java gzip library to un-gzip it, and it has a bug if there are 
> more than one blocks.   So for IGV it has to be gzipped.

This is the bug mentioned in a footnote in §4.1 of the SAM spec.  I haven't tested it and it would be wise to carry on saying must-be-plain-gzipped for use with older installations or if it gets broken again, but it seems this may have been fixed in more recent JDKs:

	http://bugs.java.com/view_bug.do?bug_id=4763158

    John

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