v2.06

• Now using more conservative assembly triggers
• Added trigger for more sensitive assembly (enables modest improvement for some longer inserts)
• Accomodate reads spanning multiple indels for observed indel contig generation
• Correction to affine gap penalty calculations in contig alignment
• Contigs now left aligned during semi-global alignment instead of post-hoc
• Ported semi-global aligner to C (for speed improvement)
• Parameterized final BAM compression level (consider using 1 for intermediate files that are to be deleted)
• Parameterize anchor length / mismatches (consider using this along with --cons for amplicon data)
• Parameterize max reads per region