Access to the noiseless reads

Hi! Thanks for the very useful simulator. I just wanted to ask if during the simulation of FASTQ file, there is any way to access the noiseless read generated from the FASTA file (before performing InDel and substitution), and write them to a file. This would be useful for FASTQ denoising experiments, as we can compare with the noiseless reads.

I see that the Read class has seq, raw_read and ref_read. I believe seq is the final read to be output by the simulator. Was confused, which one of the raw & ref reads are the noiseless reads.

class Read {
public:
    vector<char>   seq;
    vector<char>   raw_read;
    vector<char>   ref_read;
    vector<char>   quality_vals;
    vector<Indel>  indels;
    vector<int>    error_pos;
    ReadPair      &pair;
    int            mask_end_len;

    Read(ReadPair &_pair)
        : pair(_pair), mask_end_len(0)
    { }

    inline int num_in_pair() const;
    inline char orientation() const;
};

It might also be useful to add a mode for this. (ART has a similar facility, inbuilt in the tool)

Thanks!

galaxy001 / pirs

Access to the noiseless reads #6