Comments (3)
Thank you for such a quick update! Have confirmed that it behave as expected.
from pyhmmer.
Hi @chtsai0105, thank you for the bug report. I'm also getting a segfault using the test snippet you provided, I'll try to understand what's going on.
from pyhmmer.
The DigitalSequenceBlock.translate
method was occasionally writing to the wrong buffer, namely the sequence of the last protein of the block. Depending to how you'd slice, you could end up writing out of the buffer bounds, and get a segfault later! That's why you were seeing different behaviour based on the sequence coordinates.
I have patched the bug, updated tests to pick up any regression, and will make a new release with the patch.
from pyhmmer.
Related Issues (20)
- Load more than 1024 HMM files HOT 2
- Best way to Read in/Search Over Many Many HMMs? HOT 3
- Batch the hmmsearch output HOT 5
- `hmmscan` gets confused about short monotone sequences' alphabet. ( assumes `Amino`, actually `RNA`) HOT 7
- Scoring a set of sequences with HMM HOT 3
- Save the DigitalSequenceBlock as pickle HOT 6
- [Feature Request] Internally assigning Z for ```HMM``` class HOT 3
- cannot reproduce example for ```pyhmmer.hmmer.hmmsearch``` HOT 1
- Hmmsearch callback tqdm update HOT 4
- HMMSearch block and freeze HOT 5
- `pyhmmer.nhmmer` throws error when the number of FASTA seqs is larger than 64 HOT 2
- pyhmmer.hmmer.hmmsearch is always slower than using hmmsearch directly HOT 6
- Guess bit_cutoffs in hmmsearch
- Apply cutoffs for domains HOT 2
- [Question] What does does `included` and `reported` mean in pyhmmer.plan7.Hit? HOT 2
- [Bug] Pickling and unpickling an HMM object changes the cutoff values HOT 5
- [question] PyInfernal? HOT 3
- BUG: `plan7.HMM.validate()` fails to raise exceptions with ill formatted hmm profiles HOT 1
- Uninformative error when input hmm file contains profiles with different alphabets HOT 2
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