Open bachev opened 7 years ago
And of course I forgot to attach the demo files. Here they are. rs_midline_error.tar.gz
Thank you for using RAPSearch2! I’ll look into it!
On Sep 27, 2016, at 11:51 AM, Bastien Chevreux notifications@github.com wrote:
And of course I forgot to attach the demo files. Here they are. rs_midline_error.tar.gz https://github.com/zhaoyanswill/RAPSearch2/files/496156/rs_midline_error.tar.gz — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/30#issuecomment-249925819, or mute the thread https://github.com/notifications/unsubscribe-auth/AETkp1fOEP2Cb0xZ7Td6-zRmihYn4tS_ks5quUmBgaJpZM4KH3gn.
The midline in alignments has a different length from the query and Sbjct line, leading to parsing errors later on when writing/using parsers. I have attached an example which demonstrates this.
When run, one will get an alignment like this:
gi|255767013:c2429585-2428389 vs RIBBA_PORGI ...
Query: 733 EEPVLVRVHSECLTGDVFGSHRCDCG...
........... EP+LVR+HS C TGD+FGS RCDCG...
Sbjct: 250 NEPILVRMHSSCATGDIFGSMRCDCG...
Notice how the midline has a blank as "first" alignment character. In XML output, the blank is even completely swallowed:
<Hsp_qseq>EEPVLVRVHSECLT...
<Hsp_hseq>NEPILVRMHSSCAT...
<Hsp_midline>EP+LVR+HS C...
I think the error is triggered by the fast mode.
Bastien