A bug regarding command line parameter parsing conflict.

[ashesmt0310]

Describe the bug
In the class CommandLineParserForJuicer.java (which inherits from CommandLineParser.java), the line addBooleanOption('j', "cpu"); overrides the parent class’s definition of addIntegerOption('j', "threads");. This conflict causes the -j short option to be interpreted as a boolean flag (for "cpu") instead of an integer parameter (for "threads"), ​resulting in failure to set the thread count correctly.

To Reproduce
RUN "./scripts/common/juicer_tools apa -j 1 ./work/aligned/inter_30.hic ./work/aligned/inter_30_loops/merged_loops.bedpe ./apa_results"

Expected behavior
The -j or --threads option should accept an integer value (e.g., -j 4) to set the number of CPU threads. The thread pool should initialize successfully with the specified thread count.
But currently, it can only be avoided through the form of --threads 4.

Screenshots
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-03-13T06:35:49,742] [Globals.java:138] [main] Development mode is enabled
Usage: juicer_tools apa [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosomes] [-k NONE/VC/VC_SQRT/KR] [-q corner_width] [-e include_inter_chr] [-u save_all_data] <hicFile(s)>

Desktop (please complete the following information):

• OS: Ubuntu 22.04.5 LTS
• Version: juicer-1.6-0

Additional context
Add any other context about the problem here.