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Description
Main command
version: hicexplorer==3.7.3 (micromamba install)
chicViewpoint -m 3_hicmatrices/*_matrix.h5 \
--averageContactBin 5 --range 1000000 1000000 \
-rp <reference_points.bed> \
-bmf 4_background_model/bg.txt \
--outFileName 5_calc_all_interactions/all_interactions.ugenes.hdf5 --fixateRange 500000 --threads 30
Problem
If the -rp
parameter is a BED file, it hangs if the 4th column is not unique:
e.g. A reference point bed file with these entries will hang indefinitely with 100% CPU for several days until killed.
11 108810997 108811117 Axin2
11 108919925 108920044 Axin2
16 45044224 45044344 Btla
16 45044616 45044736 Btla
8 107329854 107329974 Cdh1
e.g.2 A reference point bed file with these entries will run near instantly without problems:
11 108810997 108811117 Axin2-1
11 108919925 108920044 Axin2-2
16 45044224 45044344 Btla-1
16 45044616 45044736 Btla-2
8 107329854 107329974 Cdh1-1
(generated via awk '{gmap[$4] = gmap[$4] + 1; print $0"-"gmap[$4];}' <original_rp.bed>
)
I think a small bit of text that mentions this in the help text of the --referencePoints
parameter would be enough
Cheers!
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