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CIGAR operations out of range after splice junction correction #16
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Hi Matt, |
Update: I was able to find an example in some data I had of a noisy read that triggered a possibly related problem during non canonical splice junction correction. I fixed the problem and added more tests. The patch will be included in v2.0.2. Hope this helps! |
Hi Dana, Thanks! The patch fixed that issue. Sorry to bother you again, but I found another bug that I was hoping you could take a look at. I'm not sure if it's related to the problem you found, so I thought I'd post it here. I'm finding that after correcting noncanonical splice junctions, some transcripts have all of their canonical splice junctions shifted by 1 bp. I've attached an example of an affected transcript here. The issue appears when correcting with respect to either the gencode reference junctions or a set of junctions from Illumina sequencing of the same sample. Please let me know if you can't reproduce and I can share the gencode file I'm using. Thanks, Matt |
Hi Matt, |
Hi Matt, |
Hi,
Since the update in #14 to update transcripts after correcting splice junctions, I get the following error. I think there may be a bug in the
rescueNoncanonicalJunction
function, which results in a CIGAR string incompatible with the sequence (i.e. more match/insert/sub operations than there are characters in the sequence), but I haven't been able to trace the exact source of the error. Could you please look into it if you have the chance?Thanks!
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