error running sequenza.extract

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Issue #7 resolved
huilei xu created an issue

Hi,

unittest was successful. However when I run on my real samples, it shows the error message after Collecting CG inforomation is done:

library(sequenza) Warning messages: 1: replacing previous import by ‘squash::colorgram’ when loading ‘sequenza’ 2: replacing previous import by ‘squash::makecmap’ when loading ‘sequenza’ test <- sequenza.extract('my.seqz.gz') Collecting CG inforomation ....................................................................................................................................................................................................................................................................................................................................................................................................................................................... done

Processing 1: Error in data.frame(base.count = as.integer(n.base.mut), maj.base.freq = as.numeric(max.freqs[, : arguments imply differing number of rows: 1962, 235

Comments (1)

  1. Francesco Favero

    resolving #7. utations.R: Filter out ambiguous variants that pass the mufreq treshold but do not have a genotype (eg, when the variant base is also present in the normal sample at low frequency)

    → <<cset a649833df5eb>>

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