Bismark

• now using 4 cores for merging multiple BAM files (more details #707)

• fixed a corner case when reads were aligned in FastA mode with --parallel and in addition either --ambiguous and/or --unmapped (see #723)

deduplicate_bismark

• added check to see if the UMI appears to be in the middle of the readID, e.g. if added by bcl-convert (prompted in #699). Also added new option --bclconvert to use this internal UMI instead of the one at the end. Also allowing the + symbol now for dual-indexed runs

bismark2bedGraph

• fixed a bug in non-CpG methylation call for CHH context (more details #647)

coverage2cytosine

• Expanded option --ff into --ffs to extract four, five, and six nucleotide contexts to enable hexamer context analyses. More details here: #717

filter_non_conversion

• changed shebang line to use env

bismark2report