Vesion 0.3.0:

   * Added `--nOT`, `--nOB`, `--nCTOT` and `--nCTOB`, which are related to `--OT` and similar. The difference is that the specified number of bases will be ignored, regardless of read length. So `--nOT 5,5,5,5` will result in the 5 bases on either end of both reads being ignored.

Version 0.2.1:

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

Version 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.

Version 0.1.13:

   * Added the `--ignoreFlags`/`-F` option, which is equivalent to the -F option in samtools. The default is 0xF00, which ignores duplicates, QC fail, secondary, and supplemental alignments.

Version 0.1.12:

   * Fixed handling of hard-clipped bases, which caused a segfault before.

Version 0.1.11:

   * The --minDepth/-d option is actually recognized now. Sorry about that!

Version 0.1.10:

   * Added the --version/-v option.
   * Fixed the -h/--help option, which actually wasn't recognized before!
   * Added the --minDepth option.
   * Fixed handling of the `XG` auxiliary tag, since some aligners other than bismark are using it (and for different purposes). This is the single biggest annoyance of custom auxiliary tags.

Version 0.1.9:

   * Added the --methylKit option
   * Added automated testing with `make test`

Version 0.1.8:

   * Fix compilation issues with clang

Version 0.1.7:

   * BED files are now sorted properly before extraction, so nothing is skipped now.
   * The entire BED file isn't iterated over when there's no overlap. This significantly speed things up.
   * The first alignment overlapping a given BED interval is no longer ignored.

Version 0.1.6 :

   * Fixed a bug in the --mergeContext option that sometimes resulted in incorrect mergin and duplicate lines.

Version 0.1.5 :

    * htslib is no longer a submodule, but instead version 1.2.1 is directly included. This enables easier integration into Galaxy.

Version 0.1.4 :

    * Fixed a bug in getStrand() that handled SE alignments incorrectly.

Version 0.1.3 :

    * Added the --mergeContext option to `PileOMeth extract`.
    * Added the `PileOMeth mergeContext` command. This can only be used for the default output.
    * Added this file.
    * The header line of each output file is now modified according to the presence of --logit, --fraction, and --counts.

Version 0.1.2 :

    * Fixed a mistake in the Makefile, where "prefix" was used rather than "path".
    * Added the --logit, --counts, and --fraction option, thanks to Tim Triche

Version 0.1.1 :

    * Document the output format in README.md.
    * Convert the 4th column in the output file(s) to contain the methylation level from 0-100, rather than 0-1000.

Version 0.1.0 :

    * First actual release. The code seems to be stable enough now to be usable.