Re: [Samtools-devel] Multiple PP entries and merging files

[James B. <jk...@sa...>]

On Wed, Mar 13, 2013 at 10:07:56AM +0000, Peter Cock wrote:
> On Tue, Apr 3, 2012 at 7:14 PM, Nils Homer <nil...@gm...> wrote:
> >>> Moving into the future, I would like
> >>> to submit more patches to samtools to provide easier access to the
> >>> underlying data types. For example, an improved SAM Header data structure on
> >>> which merging and manipulating SAM headers is easier (see:
> >>> https://github.com/nh13/samtools/tree/smt_header).
> 
> Maybe you and Nils have some overlapping interest here?

Ah yes, I hadn't noticed this before - I even looked in HTSlib
too. I seemed to have been looking over another samtools network on
github and didn't see this set of forks. Ugh!

It looks like Nils implementation is pretty complete and a shame I
didn't spot it before hand. My own implementation, as it currently
stands (incomplete) can be seen at:

staden.svn.sourceforge.net/viewvc/staden/io_lib/trunk/io_lib/sam_header.c?revision=3198&view=markup

(and similarly sam_header.h)

However this isn't compatible with samtools as it's part of the wider
Io_lib package (aka libstaden-read). 

It seems we have some non-overlapping features though, so maybe can
amalgamate ideas.

Thanks,

James

-- 
James Bonfield (jk...@sa...) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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