Output matched linkers into a CSV file

[mmokrejs]

It turns out that to verify what nxtrim has found during SW matching ( issue #37 ) we need a simple output, ideally per output type (when --separate was used) so we end up with 4 individual files (mp, pe, se, unknown).

The TAB-delimited format would be:

${readname}/$direction $linker_name $linker_start $linker_end $similarity $matched_sequence

If only one output file will be used, then I propose:

${readname}/$direction $linker_name $linker_start $linker_end $out_type $similarity $matched_sequence

$direction is used to delineate forward vs. reverse reads (R1 vs R2). E.g. NB501598:62:HFYJ5AFXX:1:21310:6408:6560/1 and NB501598:62:HFYJ5AFXX:1:21310:6408:6560/2