WARNING: This repo is currently missing a key functionality, specifically a script to add the XM tag to each read. I intend to refactor these 6 scripts to simplify and speed-up the conversion process, although this is not a high priority for me at this time.

Python scripts to convert Lister-style alignment files from Lister et al. Nature (2009 and 2011) to BAM format (Binary Sequence Alignment/Map format, see http://samtools.sourceforge.net/SAM1.pdf).

The Lister-style files can be downloaded from http://neomorph.salk.edu/human_methylome/data.html (2009 data) and http://neomorph.salk.edu/ips_methylomes/ (2011 data).

WARNING: While I have attempted to make the output files compatible with Bismark's SAM format so that, for example, they play nice with bismark_methylation_extractor, there are a couple of problems. Please see the issue at https://github.com/PeteHaitch/Lister2BAM/issues/1 for a patch to bismark_methylation_extractor which fixes two problems.