Michael Meuleman

As you can see in src/java/HMMR_ATAC/MAIN_HMMR_Driver line 134 ```// printHMMRTracks = p.getPrintHMMRTracks(); ```, the printing option is currently commented out, you would have to manually undo this in the code...

The internal samtools dependency is using a reader implementation that has been [deprecated](https://www.javadoc.io/doc/com.github.samtools/htsjdk/1.136/htsjdk/samtools/SAMFileReader.html) for years and does not seem to support .csi index files. The dependency should be update to...

You can simply add ```stopAfterModel = p.getStopAfterModel();``` to src/java/HMMR_ATAC/MAIN_HMMR_Driver main() somewhere at the start.

> I git clone https://github.com/LiuLabUB/HMMRATAC,and make both these code edits but don't know how to rebuild the jar,could you offer me some advice? Thank you foy your help! I would...

> Hi,Mikxox,I just wonder how I install this version of HMMRATAC ,I install the liulab-HMMRATAC with conda,but it seems that this version is not in the conda list Best meilin...