BR: --modelonly true is ignored

[angelosarmen]

Describe the bug Setting --modelonly true is ignored.

To Reproduce

java -jar HMMRATAC_V1.2.10_exe.jar -b 65283_treat_rep1.chr22.20to30MB.bam -i 65283_treat_rep1.chr22.20to30MB.bam.bai -g hg19.chr22.genome --modelonly true

Expected behavior I would expect HMMRATAC to quit after generating NA.model.

Actual behavior Viterbi still runs and files NA_peaks.gappedPeak and NA_summits.bed are generated.

System:

• OS: Mac OSX
• Java 8 Update 231 build 11
• HMMRATAC Version 1.2.10

[angelosarmen]

Hi,

May I kindly remind you to take a look at this.

Thank you.

[Mikxox]

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