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.