reformat segments.txt and Y lim on genome_view

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Issue #2 resolved
Rajesh Patidar created an issue

Hi, Could you please add quote=FALSE to avoid printing quotes in the segments.txt file, this is causing problems when I have "chr" in chromosome names. also would it be possible to add "#" in the header chromosome column name? so that it could be directly used in bedtools for intersect etc..

Is there a way to fix the upper limit in genome view? sometime you get a small segment maybe a telomere with very high copy gain >20 and the whole plot looks ugly, if there could be a parameter to set the upper limit to say 6, everything above 6 should be plotted at 6 and plot will look much better.

Thanks for such a good tool. Rajesh

Comments (2)

  1. Francesco Favero

    Hi Rajesh,

    I'm cleaning up the package for a newer version, it's a good point yours. I'll take care in the following release.

    Best

    Francesco

  2. Francesco Favero

    fixed in the cleanup branch; the file can't start with # as a proper .bed file for compatibility issues with post-process conmpatibility

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