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KamilSJaron / smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data
Apache License 2.0
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quantile filtering does not take freq into account #153

Closed KamilSJaron closed 3 months ago

KamilSJaron commented 3 months ago

What did you do

Tell us about the problem. what is the version of the software you used (smudgeplot -v)? What was the input (possibly with a few example lines)? What is the command you run? What is the error output you get? And what you have expected to see instead?

E.g.

./exec/smudgeplot.py plot data/dicots/smu_files/daAchMill1.k31_ploidy.smu.txt -o data/dicots/alt_plots/daAchMill1 --alt_plot -q 0.5

does not work well. It should be a weighted quantile now using freq column of the smu files.

Posting so I won't worget to fix before release. These are the lines: https://github.com/KamilSJaron/smudgeplot/blob/master/exec/smudgeplot_plot.R#L57-L64