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bcgsc / NanoSim

Nanopore sequence read simulator
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calculate head/tail lengths from the reference genome alignment #138

Closed SaberHQ closed 2 years ago

SaberHQ commented 2 years ago

In regards to an issue reported by @kmnip at #136 , I updated the head_align_tail_dist.py so that in "transcriptome" mode, head and tail lengths are calculated using reference genome alignment instead of reference transcriptome.

Although I did some tests on this, but it needs more benchmarking/analysis to make sure everything works well. I am kindly asking @cheny19 to take a look at it as well.

SaberHQ commented 2 years ago

Thank you @kmnip for your suggestions. I made another commit addressing your requested changes. I will be appreciated if you can review the code again and perform some benchmarking tasks. Cheers.

kmnip commented 2 years ago

@SaberHQ Looks good to me. I think we can merge this for now. We can optimize the code a bit more later!

SaberHQ commented 2 years ago

Thanks to another bug report by @kmnip , I adjusted the script to account for the strand of the alignment when calculating head and tail lengths. This is not specific to transcriptome mode, but also fixes the bug for genome mode as well. #