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pileupCaller: cannot parse read base string whith reference skip #29

Closed mscbig closed 1 year ago

mscbig commented 1 year ago

Hello, PileupCaller throw an exception when there's a reference skip symbol (> or <) in the pileup file. 

pileupCaller: cannot parse read base string >aaaaAAAA
error, called at src/SequenceFormats/Pileup.hs:75:23 in sequence-formats-1.6.3-Xy3K9C32ph8qkWXesYeWT:SequenceFormats.Pileup
stschiff commented 1 year ago

Oops... that's one I've never encountered. OK, will need to add that.

stschiff commented 1 year ago

So, I'm finally looking into this, and I am not sure whether there is really a symbol > in the documentation of the Pileup Format. I look here (https://samtools.sourceforge.net/pileup.shtml) and I can't find it. Did you generate this with samtools mpileup?

stschiff commented 1 year ago

Ah, nevermind, found it: http://www.htslib.org/doc/samtools-mpileup.html#Pileup_Format

stschiff commented 1 year ago

Sorry that I never reported back here, but this has been resolved in v1.5.3.