Pilon version 1.4

This is a release of minor usability enhancements and bug fixes. Results obtained with v1.3 should not change with v1.4.

Bug fixes:

1. Fixed crash when input genome had small (<100b) FASTA elements.
2. Get rid of spurious "unknown cigar op=H" message when input BAMs have alignments with hard-clipped bases.
3. It will now only try to improve local base accuracy if --fix bases is active (see below); it was erroneously fixing local bases if any fixes at all were being done.

Enhancements:

1. If a --fix argument begins with "+" or "-", it now adds or removes the fix mode from the list of fixes. If it does not begin with +/-, it sets the fix list to the argument, as before. For example --fix gaps will fix only gaps; --fix -gaps will fix the default things, but not gaps. The list of fix types being applied is now printed in the standard output log.
2. Added --defaultqual qual option to set the default base quality used when input BAMs don't contain quals; default is 15, which was the previously hardcoded value.
3. The number and percentage of bases in the input genome which were confirmed as correct are now printed to the standard output log.

--bruce, 5 Sep 2013

Pilon version 1.3

This release does not change actual results, but it does fix a bug in VCF file generation.

Occasionally, in reporting results of local reassembly via structural variant (SV) records, Pilon would report incorrect bases in the REF column. If there were also small events (single base changes or small indels) within the reassembled region, those changes were being reflected in the REF column, when it should be reporting original bases from the input genome. This is now fixed.

--bruce, 14 Aug 2013

Pilon version 1.2

Changes since v1.1:

1. Fixed a bug which could cause Pilon's internal assembler to get
   into a recursion loop, eventually exhausting memory;
2. Added an optional argument --K to set the Kmer size used in the
   internal assembler. The default remains 47.

This version is not likely to change any results, though there are
improbable cases in which the new version could possibly yield a
slightly different local reassembly result (e.g., a shorter partial
gap fill or partial large insertion event). No such differences were
found in my usual test cases.

--bruce, 24 Jul 2013

Pilon version 1.1

This is a bug fix release which will not change results from v1.0. The changes are:

1. Fix ability to use --unpaired bams (caused a crash under v1.0);
2. Document --nostrays optional argument in help string;
3. Simplify the version string printed at beginning of output.

--bruce, 7 Jul 2013

Pilon version 1.0

This is the inital public release of Pilon.

There are three differences between v0.9 and v1.0:

1. I refactored a block of duplicate code to be shared between "gap filling" and "break fixing", and in the process, I fixed an unintentional difference between them which caused local jump reads to be excluded in the local reassemblies for small gaps. This only affects gap filling, so is not relevant to variant calling. It slightly improves the test cases, eliminating one of the incorrectly closed gaps in Strep and making it a partial fill, and it does a better partial fill on one gap in each of F11 and Haarlem.
2. Fixed a bug in the computation of mean base and mapping quality fields (BQ and MQ) in the VCF where there were reads with deletion calls. I had noticed nonsensical BQ and MQ values for a deletion call when Sakina pulled up an example in a presentation. This does not affect any actual variant calls; it just reports more accurate values for the mean base and mapping quality in some cases.
3. I have eliminated a few of the more esoteric tracks, and renamed the "confirmed" track to "unconfirmed", since it's really showing places where the input genome is not confirmed. The documentation at broadinstitute.org/software/pilon has been updated accordingly

--bruce, 27 May 2013

Pilon version 0.9

This was the initial public beta release of Pilon. For more details see:

http://broadinstitute.org/software/pilon

--bruce, 22 May 2013