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LiuLabUB / HMMRATAC

HMMRATAC peak caller for ATAC-seq data
GNU General Public License v3.0
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BR: --modelonly true is ignored #73

Open angelosarmen opened 4 years ago

angelosarmen commented 4 years ago

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:

angelosarmen commented 3 years ago

Hi,

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

Thank you.

Mikxox commented 2 years ago

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