Allow merging of mapped datasets for deduplication?

[FelixKrueger]

Can we explore the possibility to supply several BAM files to deduplicate_bismark so that they are treated as one big file? This might be a useful feature when the same sample gets sequenced several times to increase read depth, and be an alternative to going back and merging at the FastQ stage.

[FelixKrueger]

I have now added an option --multiple to the deduplicator to treat several input SAM/BAM files as the same sample. 285f46e.

It seems to work well for SAM/BAM files with BAM or SAM output. CRAM not tested yet.

[xiuru]

Hi Felix,
Can you add a new flag like 'prefix' to deduplicate_bismark? When i treat multi bam files together, i prefer to use 'prefix' to name the output files.

Thank you~~

[FelixKrueger]

Can't you just do something like:
mv multiple.bam prefix
once the deduplication is complete?

[xiuru]

Yes, i did it in this way. Sorry for my stupid question :)