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Crashes when chromosomes have no CpG sites

Status: Open.

#307 In smithlabcode/dnmtools;

· andrewdavidsmith opened on Nov 12, 2025

the interpretation of the amrfinder output

Status: Open.

#297 In smithlabcode/dnmtools;

· JJJelly77 opened on Sep 23, 2025

Blank output from dnmtools amrfinder

Status: Open.

#296 In smithlabcode/dnmtools;

· JJJelly77 opened on Sep 23, 2025

Merge and dnmtools hmr-rep

Status: Open.

#291 In smithlabcode/dnmtools;

· vagan21 opened on Aug 29, 2025

SAM file is not sorted ERROR even if the input file is sorted

Status: Open.

#260 In smithlabcode/dnmtools;

· YuanfengZhang opened on May 12, 2025

regions not sorted in file

Status: Open.

#257 In smithlabcode/dnmtools;

· JavenCao opened on Feb 14, 2025

Negative mean coverage returned by dnmtools pmd

Status: Open.

#255 In smithlabcode/dnmtools;

· zhoujt1994 opened on Dec 30, 2024

The hmr command fails when methylation levels are at extremes

bugSomething isn't workingSomething isn't working

Status: Open.

#251 In smithlabcode/dnmtools;

· andrewdavidsmith opened on Nov 17, 2024

Are there any parameters that need to be tuned for mapping WGBS data to repeat regions?

Status: Open.

#248 In smithlabcode/dnmtools;

· QianhuiWan opened on Oct 23, 2024

roi should check for input files before reporting any problems with arguments

good first issueGood for newcomersGood for newcomers

Status: Open.

#154 In smithlabcode/dnmtools;

· andrewdavidsmith opened on Sep 30, 2023

Keep non-CpG sites after sym command

Status: Open.

#139 In smithlabcode/dnmtools;

· natliang opened on Sep 15, 2023

mlml "error: chrom or pos mismatch in both files"

Status: Open.

#135 In smithlabcode/dnmtools;

· christianwake opened on Sep 12, 2023