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Dear @altanturkoglu , My apologies for the very late reply and thank you for reporting this issue. I'm not sure why this error arises at first glance, it seems related...

Hi Zach, Sorry for the late reply I was away with very limited access to the internet... # About the gene anchor indices They are obtained via the IMGT *gapped*...

Dear Zhou, Regarding your first question: sadly I currently do not have access to any IgH mouse dataset, and would not have the time to build a model myself... Regarding...

Hi @jeremycfd ! For now it is not quite possible to do so, and the --ntCDR3 option only accept sequences CDR3 nt sequences without knowledge of the associated V/J. Of...

You mean the alignment threshold? It makes perfect sense to lower the alignment score threshold since the number of observable genomic nucleotides is much lower on CDR3 than full read...

Following up on this: I've automated the decrease in alignment threshold for V and J when the `--ntCDR3` option is used (and set them to 0 since the alignment offsets...

Dear Adam, I'll try and reply quickly and further edit my answer for more clarity. About (1): 1) There might be slight differences due to differences in the scoring scheme....

Dear Adam, My apologies I just realized I had not answered your second round of questions. # About the `infer` command ## About models There is indeed no model for...

Dear Adam, I have finished editing my previous response in order to answer the rest of your questions. Concerning this new batch of questions: >One issue (on computational performance) is...

Hi Thomas, Thanks for taking the time to produce such a detailed bug report! I highly appreciate it This indeed seems to be a real segfault issue, valgrind points to...