Allowing the + sign as valid symbol when considering UMIs in --bclconvert mode (more details)
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Changelog
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Allowing the + sign as valid symbol when considering UMIs in --bclconvert mode (more details)
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)
Just a few fixes, also added two flavours of scripts for merging coverage files (e.g. for when R1 and R2 had been run in single-end mode)
exit 0 that would terminate runs after processing a single (set of) input file(s).##...
Added entirely new documentation website, built using Material for Mkdocs. Thanks to @ewels for a fantastic (late-night) effort to break up and restructure what had become a fairly unwieldy monolithic beast of markdown document...
Added docs for cytosine context summary, useful for GpC methylation...
--strandID which reports the alignment strand identity for paired-end, non-directional libraries, e.g. YS:Z:CTOT. This information may be difficult to obtain if third party tools interfered with the read ordering (admittedly there is a fine balance of read reporting position, FLAG, Read 1 and Genome conversion state to make it work in the first place. More inf...