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Added option --se/--single_end <list>. This sets single-end mapping mode explicitly giving a
list of file names as <list>. The filenames may be provided as a comma , or colon :-separated
list.
Added option --genome_folder <path/to/genome> as alternative to supplying the genome as the
first argument.
Added an option --rg_tag to print an @RG header line as well as and RG:Z: tag to each read.
The ID and SAMPLE fields default to 'SAMPLE', but can be specified manually with --rg_id or --rg_sample.
Added new option --ambig_bam for Bowtie2-mode only, which writes out a single alignment for
sequences with multiple alignments to a special file ending in .ambiguous.bam. The alignments
are in Bowtie2 format and do not any contain Bismark specific entries such as the methylation
call etc. These ambiguous BAM files are intended to be used as coverage estimators for variant
callers. Works for single-end and paired-end alignments in single or multi-core mode.
Added the new options --cram and --cram_ref to Bismark for both paired- and single-end alignments
in single or multi-core mode. This option requires Samtools version 1.2 or higher. A genome
FastA reference may be supplied as a single file with the option --cram_ref; if this is not
specified the file is derived from the reference FastA file(s) used for the Bismark run, and written
to the file Bismark_genome_CRAM_reference.mfa into the output directory.
deduplicate_bismark
Added better handling of cases when the input file was empty (died for percentage calculation
instead of calling it N/A)
Added a note mentioning that Read1 and Read2 of paired-end files are expected to follow each
other in two consecutive lines and possibly require name-sorting prior to deduplication. Also
added a check that reads the first 100000 lines to see if the file appears to have been sorted
and bail out if this is true.
methylation extractor
Added support for CRAM files (this option requires Samtools version 1.2 or higher)
bismark2bedGraph
Changed the way gzip compressed input files are handled when using the UNIX sort command (i.e. with --scaffolds/--gazillion or without --ample_memory
coverage2cytosine
Added option --gzip to compress output files. This currently only works for the default CpG_report
and CX_report output files (and thus not with the option --gc or --split_files. The option --gzip
is now also passed on from the bismark_methylation_extractor.
Added a check to bail if no information was found in the coverage file, e.g. if a wrong file path for a .cov.gz file had been specified
