min_threshold counts

[kdcurry]

• Widen LOG_LIKELIHOOD_DIFF_TOLERANCE to 1e-5 (from 1e-9)
• Fix bug to keep_counts when min-abundance threshold is applied
• In the case where min-abundance threshold is applied, “unclassified mapped” reads were counted after the min-abundance threshold was applied, even for the output without the min-abundance threshold applied. This has been corrected, resulting in two separate unclassified mapped counts (and two output sequence files if --output-unclassified if enforced)