search

BIO-DIKU / SeqScan

Pattern matching in biological sequences
GNU General Public License v2.0
4 stars 0 forks source link

Default start position should be 1 #35

Closed maasha closed 8 years ago

maasha commented 9 years ago

Currently it is 0, however, the README says it should be 1 and since match positions are 1-indexed.

RasmusFonseca commented 8 years ago

Not completely sure what this means. We start matching from the first character of the sequence. Are you saying reported matches are 0-indexed but should be 1-indexed or are you saying that we are missing support for indicating starting position?

maasha commented 8 years ago

I am saying that biologist can't count from zero so hits needs to be 1-based. To them zero only makes sense in a situation with no hits = zero hits. All the examples in the README are 1-based.

I can't remember if --start is implemented.

On Sun, Mar 20, 2016 at 9:38 PM, Rasmus Fonseca notifications@github.com wrote:

Not completely sure what this means. We start matching from the first character of the sequence. Are you saying reported matches are 0-indexed but should be 1-indexed or are you saying that we are missing support for indicating starting position?

— You are receiving this because you were assigned. Reply to this email directly or view it on GitHub https://github.com/BIO-DIKU/SeqScan/issues/35#issuecomment-199016271

RasmusFonseca commented 8 years ago

Fixed by adding 1 to the position in Match::Print