panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9

[dwbellott]

I was able to run jtk successfully with the example reads, but I ran into an issue using my own nanopore reads.

Here is the tail of the output, running with verbose = 2

[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3774	2	1.000	1.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3775	1	0.000	0.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3776	2	1.000	1.000
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3788	2	1.000	1.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3790	2	1.000	1.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3794	2	1.000	1.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3797	2	1.000	1.000
[2024-10-11T12:04:33Z DEBUG haplotyper::phmm_likelihood_correction] ARI	3811	1	0.000	0.000

jtk panicked at this same point 20 times before it failed (although I am running with threads = 1) . If I just grep for 'panic' in the output I can see:

thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 5 but the index is 5
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 7 but the index is 7
thread '<unnamed>' panicked at haplotyper/src/phmm_likelihood_correction.rs:353:9:
index out of bounds: the len is 6 but the index is 6

Following issue #8, I checked to see if I had any duplicate read names, but I do not.

Any idea what is causing this?

Thanks!