[Seqan-dev] 1/2/4/8 A/C/G/T representation

[Bayo Lau <bayo.lau@gmail.com>]

Hello,

I've trying out the new seqan (f1ec3e8f9e91b8c6bb7c02cdaef1fe7577f94a19).

One thing I noticed when using BAM I/O (with seqan::BamFileIn and seqan::BamAlignmentRecord )is that the seqan::BamAlignmentRecord::seq type seems to be seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, and when I static_cast the base calls, the values are 1/2/4/8 for ACGT. I wonder if there's a formal way to map them back to 0/1/2/3 (I just hacked up my own mapping function now)? or am i doing anything wrong.

Thanks for the help.

Bayo