Bismark Release v0.23.0

the command deduplicate_bismark --barcode *bam now works again. Previously the output file names were accidentally all derived from the first supplied file in --barcode (= UMI) mode (it had been fixed for normal files in 0.22.2).
Changed the way the library auto-detection works to only look at the @PG ID:Bismark line of the SAM header (to only look for the Bismark command)

Added a new option --ucsc to bismark2bedGraph and bismark_methylation_extractor that will produce a UCSC-ready bedGraph file if the genome version used came from Ensembl. This option (i) prefixes chromosome names with 'chr', and (ii) changes the mitochondrial chromosome from 'MT' to 'chrM'. In addition, it will also write out a new file ending in .chromosome_sizes.txt for easier use of bedGraphToBigWig. More here.
Changed the way the library auto-detection works to only look at the @PG ID:Bismark line of the SAM header.

Added a new output file for all cytosine context methylation totals. More information here: #321.
Added new option --drach/--m6A. Most m6A sites are found in the conserved sequence motif DRACH (where D=G/A/U, R=G/A, H=A/U/C), and if bound by anti-m6A antibody, it causes the reverse transcriptase to introduce C to T transitions at the cytosine which follows A in the DRACH motif. This option also sets a coverage threshold of at 1 unless specified explicitly. This is a very specialised option and should only be used by experimentalists looking at m6A methylation (where the C to T transition acts as a proxy of m6A).

Samples with absolutely 0 methylation calls in some context are now excluded from the graphical HTML output (as they break rendering the entire summary graph section). These samples and their statistics do still appear in the file bismark_summary_report.txt. More information here: #315.

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