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Describe the bug When running MACS3 in HMMRATAC mode, using the --save-digested flag writes the short signal to all four signal tracks.
To Reproduce Use the --save-digested flag and then run diff on the resulting files.
diff
Additional context The problem is here: https://github.com/macs3-project/MACS/blob/429f8f8b0114974b168900ba17d96467c27b550f/MACS3/Commands/hmmratac_cmd.py#L158C1-L170C21
Solution The index of digested_atac_signals was mistakenly set to 0 in all four cases. The following block:
digested_atac_signals
if options.save_digested: fhd = open(short_bdgfile,"w") digested_atac_signals[ 0 ].write_bedGraph(fhd, "short","short") fhd.close() fhd = open(mono_bdgfile,"w") digested_atac_signals[ 0 ].write_bedGraph(fhd, "mono","mono") fhd.close() fhd = open(di_bdgfile,"w") digested_atac_signals[ 0 ].write_bedGraph(fhd, "di","di") fhd.close() fhd = open(tri_bdgfile,"w") digested_atac_signals[ 0 ].write_bedGraph(fhd, "tri","tri") fhd.close()
should actually be:
if options.save_digested: fhd = open(short_bdgfile,"w") digested_atac_signals[ 0 ].write_bedGraph(fhd, "short","short") fhd.close() fhd = open(mono_bdgfile,"w") digested_atac_signals[ 1 ].write_bedGraph(fhd, "mono","mono") fhd.close() fhd = open(di_bdgfile,"w") digested_atac_signals[ 2 ].write_bedGraph(fhd, "di","di") fhd.close() fhd = open(tri_bdgfile,"w") digested_atac_signals[ 3 ].write_bedGraph(fhd, "tri","tri") fhd.close()
The text was updated successfully, but these errors were encountered:
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Describe the bug
When running MACS3 in HMMRATAC mode, using the --save-digested flag writes the short signal to all four signal tracks.
To Reproduce
Use the --save-digested flag and then run
diff
on the resulting files.Additional context
The problem is here:
https://github.com/macs3-project/MACS/blob/429f8f8b0114974b168900ba17d96467c27b550f/MACS3/Commands/hmmratac_cmd.py#L158C1-L170C21
Solution
The index of
digested_atac_signals
was mistakenly set to 0 in all four cases. The following block:should actually be:
The text was updated successfully, but these errors were encountered: