0.6.1

• Added the --ignoreNH option, which allows inclusion of multimappers normally excluded with the NH flag.

0.6.0

• Added the minConversionEfficiency option, which allows filtering out incompletely converted alignments on the fly. Note that doing this is generally NOT recommended. (issue #61)
• Fixed various segfaults and other issues related to mappability filtering (courtesy of @Valiec)

0.5.3

• Fixed an issue with the perRead subcommand, wherein the requireFlags option didn't fully work (a read would pass if it had at least one of the required flags set, rather than all of them). (issue #117)

0.5.2

Rewrote how read-pair overlap handling is performed. It now uses the constructor/destructor mechanism from htslib instead of using internal htslib structures and functions. This allows supporting newer htslib versions. Currently 1.11 is the only tested and working version, due to changes in the pileup constructor interface in it. (issue #99)

0.5.1

Fixed some memory errors that were causing crashes like in #93

0.5.0

• Fixed an issue with the --cytosine_report option where the reported chromosome name could be wrong IF the input BAM files were very sparse and multiple threads were used. (issue #88)
• libBigWig is now an external dependency as it's needed for handling the "binary bismap format"
• Added support for blacklisting reads according to a "binary bismap file". See here for details. Code for this was contributed by @Valiec and @bwlang at New England Biolabs.

0.4.0

• Switched to an external htslib. It is currently compatible with htslib versions 1.4 through 1.9 (the latest one at the time of release).
• Added the --perRead option, as used in https://www.biorxiv.org/content/10.1101/481283v1
• Removed the --maxDepth option, it's not longer required.
• Fixed issue #58, the --keepDupes flag now changes --ignoreFlags.
• Fixed issue #59, the confidence intervals should no longer extend outside of [0, 1].

0.3.0

• Added multithreading to the extract and mbias functions.
• Added the ability to avoid sites with likely variants
• Fixed handling of strand in BED files (it was always ignored previously) and added a --keepStrand option to explicitly request that strand be included.
• Fixed processing of CHH and CHG elements at the ends of contigs. These were sometimes skipped before.

0.2.1

• The --methylKit option output methylation values between 0-1 rather than 0-100. This has been corrected.

0.2.0

• Changed the package name from PileOMeth to MethylDackel. It is unfortunate that the temporary "PileOMeth" name stuck around for so long.
• Fixed the plotting where the sometimes the plotted lines escape the bounds of the graph. The cause for this was that read #2 was being ignored when the graph bounds were being computed.
• Added the --requireFlags/-r option, which is equivalent to the -f option in samtools. The default is 0, which requires nothing.