Researcher reports a discrepancy in code comments (two occasions) vs. what is actually implemented in the code. The concern is that pairHMM actually performs global alignment (Durbin Figure 4.2) but the code comments indicate local alignment and Durbin Figure 4.3.
Hello, thank you for your reply.
The algorithm is clear to me, from what I read of the code it is effectively the right of figure 4.1 (or 4.2 without the start and end states for simplicity) that is used and not 4.3
Therefore my concern, the comments in the source code clearly state that 4.3 is used and that it is local alignment, while the code in fact does global alignment.
It makes more sense to do global alignment (sequence to sequence, like Needleman-Wunsch) and this is what the codes seems to do (does).
Researcher reports a discrepancy in code comments (two occasions) vs. what is actually implemented in the code. The concern is that pairHMM actually performs global alignment (Durbin Figure 4.2) but the code comments indicate local alignment and Durbin Figure 4.3.
Hello, thank you for your reply. The algorithm is clear to me, from what I read of the code it is effectively the right of figure 4.1 (or 4.2 without the start and end states for simplicity) that is used and not 4.3
Therefore my concern, the comments in the source code clearly state that 4.3 is used and that it is local alignment, while the code in fact does global alignment.
It makes more sense to do global alignment (sequence to sequence, like Needleman-Wunsch) and this is what the codes seems to do (does).
Thank you for your answer.
This Issue was generated from your forums