Pilon version 1.9

This release contains several enhancements and heuristic changes designed to make PIlon more resilient when presented with problematic sequencing data:

1. Reads marked as failing vendor quality control checks will no longer be used by default. To include them, use the new option --nonpf (which replaces the --pf option, reflecting the change in default behavior).
2. Reads marked as duplicates in the BAM will no longer be used unless the new --duplicates option is specified.
3. The threshold for triggering local reassemblies based on percentage of bad pairs at a given location is now relative to the overall percentage of bad pairs, not an absolute percentage. This helps reduce the number of spurious local reassemblies when used with poorly constructed mate pair libraries.

This release is also more conservative about reporting partial large events in variant calling (opening gaps in assembly improvement) when used with --fix +breaks (implied by the --variant option):

1. If Pilon does a local reassembly which is not closed, it will not make a change if the partially assembled sequence matches the input genome.
2. If a loop in the assembly graph is detected, e.g., from a tandem repeat, it will not make a change.

This version includes an experimental (not extensively tested) multithreading capability. If the --threads <N> option is provided, then initial BAM scans and input FASTA element processing will be done in parallel. This is very coarse-grained multithreading, but it ought to provide some speedup for large genomes.

Finally, this release fixes a bug which occasionally prevented small deletions from being applied to the output .fasta and .changes files; the VCF output was correct.

--bruce, 29 Oct 2014