0.22.2

• Added FAQ document for questions that keep coming up. Will be populated over time.

Bismark

• the option --non_bs_mm is now only allowed in end-to-end mode

• Fixed the calculation of non bisulfite mismatches for paired-end data which happened correctly only when R2 had an InDel (see here)

• When the option -u was used in conjunction with --parallel, only -u sequences will be written to the temporary subset files for each spawn of Bismark (previously, the entire file was split for --parallel, but then only a small subset of those files was used for -u, which resulted in very long runs even for a small number of analysed sequences)

deduplicate_bismark

• the command deduplicate_bismark *bam now works again. Previously the output file names were accidentally all derived from the first supplied file.

coverage2cytosine

• Added new option --coverage_threshold INT. Positions have to be covered by at least INT calls (irrespective of their methylation state) before they get reported. For NOMe-seq, the minimum threshold is automatically set to 1 unless specified explicitly. Setting a coverage threshold does not work in conjunction with --merge_CpGs (as all genomix CpGs are required for this). Default: 0 (i.e. all genomic positions get reported)

bismark2report

• added seconds to the timestamp report statement (which caused a warning on certain, but not all, platforms)

bismark2summary

• Now reads splitting reports even for non-deduplicated files (such as RRBS).