combined reads and score/depth calculation

[irleader]

When will two peptides be combined into one read? When they have exactly the same sequence (but different modifications are OK)?

When calculating match score/ unique match score, will the read's score be calculated twice if it's a combined read from two peptides?

Also for depth calculation, will positional score from a combined read be taken into account multiple times as well?

[douweschulte]

1. When the sequence is the same, while reading in stitch strips all modifications so peptides with the same sequence but a different modification pattern are still combined.
2. The match score is the same, the original reason of combining was to remove duplicate alignments for the same sequence which lowers the runtime of the program. The area is the sum of all peptides, the local confidence and peptide level confidence scores are also combined.
3. As the area is the sum of all peptides and the area is taken into account in the depth of coverage (log10 of the area) the combined peptides is accounted for.