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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Very old version of htsjdk.jar #42

Closed tseemann closed 7 years ago

tseemann commented 7 years ago

I just noticed pilon uses a quite old version of htsjdk.jar (1.x).

Would it be worth upgrading to the latest 2.x series? I worry that many bugs have been fixed in the last two years?

http://samtools.github.io/htsjdk/

w1bw commented 7 years ago

Pilon doesn't do very sophisticated things with htsjdk; mostly scanning reads in a bam and querying reads mapping to a given contig, so I haven't worried about keeping very up-to-date. However, since I'm working on some experimental additions to pilon, I'll keep that in mind!