Does the default value (-1) of "--maxCoverage" mean ALL or ALL - 1. (@4b2bb33)

PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

21 stars 21 forks source link

Does the default value (-1) of "--maxCoverage" mean ALL or ALL - 1. (@4b2bb33) #55

Open lemene opened 6 years ago

lemene commented 6 years ago

Hi, In ipdSummary.py(291), default value of "--maxCoverage" is assigned -1.

In KineticWorker.py(508), "--maxCoverage" is used as below

        if self.options.maxCoverage is not None:
            maxCov = self.options.maxCoverage
            for x in views:
                d = x['data']
                d = d[0:maxCov]
                x['data'] = d

d[0:maxCov] is d[0:-1], not include the last element.

I think it is more clear that "-1" mean all elements.