Re: [Samtools-help] New Picard Module

[Alec W. <al...@br...>]

Hi Harry,

We appreciate contributions to the Picard tools, while at the same time are reluctant to take on additional support burden.  Is there a reason why this needs to go into the Picard library itself, rather than being a separate tool that uses the Picard library?  If there are things that are not public that need to be made public in order to facilitate this, please let me know.

Thanks, Alec

On Jun 27, 2013, at 6:32 AM, Harry Noyes <ha...@li...> wrote:

> I have written a Picard Module for the picard.analysis package  that parses a Bam file using the acceptRead method and extracts contigs and builds Scaffolds of adjacent contigs based on user supplied criteria for gap length between contigs. Prints out a gff3 file for Scaffold co-ordinates. This is the same functionality as the samTools TargetCut programme except that it uses a different model for joining contigs into Scaffolds and users can supply the parameters of the model. It runs slower than targetcut and generates shorter scaffolds when using default parameters. However it does have a few bells and whistles that are not available with targetcut.
> 
> Users can supply a set of co-ordinates where they do not scaffolds reported, eg within repeats.
> A lot of metadata is also generated. mean and N50 lengths of contigs, scaffolds and gaps, % reference covered, mean coverage of contigs, distribution of contig lengths.
> 
> Is there any interest in incorporating it into the Picard tools project? If so are there systematic tests that need to be run on it? The jar and java files for the class are available from our website at: http://www.genomics.liv.ac.uk/tryps/HaploSeq.html
> 
> Cheers
> 
> Harry
> 
>  
> Harry Noyes
> Room 231 BioSciences Building
> University of Liverpool
> Crown Street
> Liverpool
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> 0151 795 4512
> www.genomics.liv.ac.uk/tryps
> ha...@li...
> 
> 
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