Searching with zero errors #17
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eaasna
commented
Dec 7, 2023
| TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); | ||
| TScore mismatchIndel = -(TScore)1000; | ||
| if (eps > 0.001) // avoid division by 0 | ||
| mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); |
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To avoid division by zero Stellar did not allow 0% error rates, although they appear in the benchmark in the paper. The workaround to this was using a very small 0.0001 error rate, but this led to a very large mismatch score which led to the issues described above.
SGSSGene
approved these changes
Dec 15, 2023
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The mismatch indel score in the scoring scheme is usually an inverse of the error rate i.e. the smaller the error rate the bigger the negative value of the mismatch score. Need to set a lower bound for the mismatch score.
Otherwise, for a very small error rate the seed extension does not stop in time. Not sure of the mechanism for the extension not stopping (likely has to do with this line that only forces an update of the scoring scheme for extremely low error rates).
Downstream the consequences of a longer seed extension are: