Is it possible to output query positions

[moorembioinfo]

Hi,

In matches.tsv (python StrobeMap) is it possible to output both reference and query match positions.

Thanks and best regards,

Matt

[moorembioinfo]

Or actually is it fine to assume that the end position on the reference will be from the refpos in the outpt +length of match and never -length of match

[ksahlin]

Yes, it is always refpos + match_length, never refpos - match_length. Reverse complement matches of the query sequences will be under a separate query header named > query_name Reverse.

However, your question made me realize that I should probably implement an option to output the query match length as a fifth column. The query match length may be slightly different from the reference length since NAMs are approximate.

Best, K

[moorembioinfo]

Brilliant, thanks!