[EMBOSS] SAM as a sequence input and output format?

[Charles Plessy]

Dear EMBOSS developers,

I often look for a sequence format that would put all the information on a
single line easy to parse with a Perl or sed filter, and was wondering if – in
the absence of a better alternative – it would be possible for EMBOSS to
include the SAM format as a sequence format.

  http://samtools.sourceforge.net/samtools.shtml

It may look heretic at a first sight, but I see that other projects are also
using SAM as format to store sequences with qualities:

http://picard.sourceforge.net/command-line-overview.shtml#FastqToSam

Have a nice day,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan