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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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Support for CSI indices #96

Open SergejN opened 5 years ago

SergejN commented 5 years ago

Dear Pilon team,

could you please add support for indices generated with the "samtools index -c " command? It is necessary to correct large genomic sequences, such as those of the axolotl. As of now, Pilon throws a runtime exception saying that the BAM file should be indexed.

thanks a lot!

SergejN commented 5 years ago

I might have found a workaround solution for that. It turns out that Pilon uses an older version of htsjdk (2.14.0). If you unpack the pilon jar file, replace the contents of the htsjdk with the recent release (2.19.0) and pack the jar file again, it works.