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mufreq.threshold instead of mufreq.treshold
sequenzatools instead of sequenza_tools
In non-seqz mode, the code was not preserving semantic column labels. It was reshuffling columns to match the internal format expected by downstream numeric indexing. How headers looked: [1] "SampleID" "Chromosome" "Start_position" "End_position" [5] "total_cn" "A_cn" "B_cn" "ploidy" [9] "V9" "V10" Column 7 was copying the original A_cn. Should not generate process downstream, but for consistency's sake, changed
Result can be used in future scar_score() runs in non-seqz mode
…ore.R This would be the case if seqz step has been run previously and interrupted
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mufreq.threshold instead of mufreq.treshold