Version 1.21 introduces two new --fix options for assembly improvement: snps and indels. Prior to this release, the bases fix option was used to control alignment-based (as opposed to assembly-based) fixes of both SNPs and small indels. Now, fixing of SNPs and small indels can be controlled independently. The --fix bases option is retained for back-compatibility, and is equivalent to specifying both snps and indels.

For example, to use Illumina data to try to get rid of potential suprious indels in a pacbio assembly without changing anything else, one could use --fix indels.

This version also fixes an integer overflow bug caused genome sizes > 2Gb to be printed as negative size.

--bruce, 9 Dec 2016