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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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supporting read ID not included in output #19

Closed charliechen912ilovbash closed 2 years ago

charliechen912ilovbash commented 2 years ago

I am using version 0.4.0, the *.nanomonsv.supporting_read.txt seems does not include any supporting read IDs. Version 0.2.0 did include the read IDs though.

jaesvi commented 2 years ago

Hi, I wanted to ask if there is any progress regarding this. Thanks.

friend1ws commented 2 years ago

Thank you very much. I will fix this problem in the next version, which will soon released.

jaesvi commented 2 years ago

Hi, congratulations on your publication. To follow-up on this issue, I see that in the publication you extract the SV-supporting reads and assign them to a specific Whatshap haplotag: Supporting reads for each SV were extracted and annotated using the haplotype tag in the WhatsHap results. Could you clarify how do you do this when Nanomonsv does not provide the SV-supporting reads? Thanks.

friend1ws commented 2 years ago

Thank you very much!. I think they used version 0.2.0, which generated supporting read files with read IDs. From version 0.4.0, somehow the read ID information disappeared... I have fixed this bug and the new release will be hopefully in a couple of days.

jaesvi commented 2 years ago

Ah that would explain, sorry. I had not tried nanomonsv before 0.4.0 . Thanks!

friend1ws commented 2 years ago

We have released v0.5.0, which should solve the above problem.

charliechen912ilovbash commented 2 years ago

Thanks! Could you also provide the example output at https://github.com/friend1ws/nanomonsv/tree/master/misc/example ?

jaesvi commented 2 years ago

Nice! How do you install the new version though? It is not (yet) on pip.

friend1ws commented 2 years ago

Sorry, we had some trouble pushing pypi. I think we fixed that. So please try. I am aware the current version still has several small problems and we will soon fix that.