Dan MacLean comments

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                                            Dan MacLean

Parsing Alignment Object

Hi @jpearl01 Looks like we never implemented this. It is kind of complicated, but I can see why you'd want to do it. I found this discussion on how it...

index fails using samtools v1.0+ when providing .bai filename

Does SAMtools generate the .bai by default? Then use that unless a filename is given - so yes, implement an mv if providing a filename doesn't work.

index fails using samtools v1.0+ when providing .bai filename

Then I think your proposed fix is sensible - mv to the provided name if it is there, but dont pass the provided name to SAMtools. MonkeyPatch

Writing alignments to file

Hi, can you clarify what you require. I guess you want to process an alignment, removing some of the sequence, create a new Bio::DB::Alignment object and write that to a...

Writing alignments to file

The official samtools C API function for writing to BAM isn't implemented yet, as it is a bit complicated and we considered most users would want to use BAM as...

Who uses Cytoscape.js?

PINet - http://pinet.tsl.ac.uk Tool for The Sainsbury Laboratory network analyses

Set font to one installed by default

Thanks for response, I missed the notice in the README. I think it was likely off screen when I cut and paste the example to test the package. I imagine...

Proposed workflow

I think there's a delay here that could be bad for getting the notice that junior authors deserve. By only notifying the badging system after the paper is published there...