*.res and *.mapstat scores

[alvanuffelen]

Hi Philip

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Can it be that *.res reports a different score than *.mapstat?

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In *.res, the score is 256471 for a certain template.
In *.mapstat the score is 256485 for the same template.

Looking further into it, the score of *.res seems to be the sum of the alignment scores of the reads in *.frag.gz for that template.
The score of *.mapstat is the sum of the aliment scores of the reads in *.frag_raw.gz for that template.
So there is a small discrepancy between some reported scores in *.frag_raw.gz and *.frag.gz for the same read and same template.

Also, in the manual, it states for *.res:
Score: Is the ConClave score (accumulated alignment score), from all reads that were accepted to match this template.
And for *mapstat:
mapScoreSum: Accumulated mapping score, the same as the ConClave score.

Does that mean that *.frag.gz reports the mapping scores while *.frag_raw.gz reports the alignment scores?

[ptlcc]

Hi Al

It depends a bit on the parameters used, but there might be some differences between the two.
If the “-mem_mode” flag has been used, the score in the *.res file will be the summed mapping (instead of alignment) score towards the template, after ConClave.
The score in the mapstat file is the summed alignment score, where there is a reward for end alignment which will cause the small discrepancy you see.

I agree that the manual needs an update to specify these things more clearly.

Best,
Philip