#!/usr/bin/env perl -w
use strict;

our ($samplename, $bam_file, $variant_file, $aligned_length_thh, $ERDS_dir, $mq_thh, $exp_pct, $num_state, $ref_file, $ref_fai_file, $win_size_del, $win_size_dup, $sample_dir, $script_dir, $sd_dir, $log_dir, $rc_dir, $cnv_dir, $gcbin_dir, $samtools, $max_mq, $read_length, $min_det_size, $sd_win_size, $ins_pem, $gap_events, $low_scan_ratio, $pem_pairs, $low_pem_pairs, $rcp_rate, $clip_len, $clip_spt_pem, $clip_spt_npem, $softclip_check_thh, $large_pem, $small_pem, $CIAGR_length);
our (@chr, @normal_chr);
my $parameter_sample=$ARGV[0];
my $functions=$ARGV[1];
require "$parameter_sample";
require "$functions";
for(my $j=0; $j<=$#normal_chr; $j++){
    my $chr=$normal_chr[$j];
	system("perl $script_dir/hmm.pl $parameter_sample $functions $chr");
}
