illumina paired end files may have 1:N:0 and 2:N:0 #38
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Description
Add a new "if" in utilities.get_reformatted_identifiers function
Using the regular expression r'\d+:N:\d+:(?=[A|T|C|G])' to get the issue part of sequence label.
And then just delete it.
Related Issue
I found some users alway get zero file of two paired files [issue1]
(https://forum.biobakery.org/t/paired-end-data-results-in-unpaired-output/928/2) [issue2]
(https://forum.biobakery.org/t/no-reads-in-the-final-output-files-created/3419).
I also have that issue, my sequence label was like
R1: @A00456:506:H5GC2DSXY:1:1101:6027:1000 1:N:0:CAACACAG+CAAGGTAC
R2: @A00456:506:H5GC2DSXY:1:1101:6027:1000 2:N:0:CAACACAG+CAAGGTAC
So. in old "get_reformatted_identifiers adding" "#0/1" and "#0/2" not solving this issue. and I just delete the part. it worked.
Screenshots (if appropriate):