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# itd_test.sh
# Author: Chin-Chen Pan
# Directore, General and Surgical Pathology
# Professor, attending pathologist
# Department of Pathology and Laboratory Medicine
# Taipei Veterans General Hospital
# TAIWAN
# Version 1.2.2
# Date: Nov 12, 2018

[Introduction]

itd_test.sh is a shell script to run Genomon-ITDetector with multithreading.

[Before running]

1. Prepare exome_test.config. The file contains four words in one line. No other words and lines are allowed.

	/path/to/programs /path/to/inputfile /path/to/outputfile thread_number

	ex1: 
	/home/user_name	/media/user_name/disk1/input /home/user_name/output 8

	ex2:
        ~  ~/input ~/output 8

2. Install Genomon-ITDetector according to https://github.com/ken0-1n/Genomon-ITDetector to /path/to/programs/Genomon-ITDetector-master.

3. Copy config.tmp to /path/to/programs/Genomon-ITDetector-master.

4. The script uses the files produced from exome_test.sh.

[RUNNING]

Syntax:  sh itd_test.sh samplename -options
	
	options:
 		-spb: keep splitted bam for further use
 		-kt: keep temporary files
 		-s: shutdown after finished


	ex1:
	  sh itd_test.sh test1 -spb -s
Source: README, updated 2018-11-12