#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

# configuration file stuff
my %config;
my $dirname = dirname(__FILE__);
my $tool_dir = shift @ARGV;

if(not -e "$tool_dir/dedup_realign_bam.loc"){
  system("cp $dirname/tool-data/dedup_realign_bam.loc $tool_dir/dedup_realign_bam.loc");
}
open CONFIG, '<', "$tool_dir/dedup_realign_bam.loc";
while(<CONFIG>){
  next if $_ =~ /^#/;
  (my $key, my $value) = split(/\s+/, $_);
  $config{$key} = $value;
}
close CONFIG;

@ARGV > 4 or die "Usage: $0 <output log> <reference.fa> <temporary directory> <deduped_realigned.bam> <input1.bam> [input2.bam] ...\n";

my $log = shift @ARGV;
my $ref = $config{"dbs_dir"} . shift @ARGV;
my $tmpdir = shift @ARGV;
my $outfile = shift @ARGV;
$SIG{__DIE__} = $SIG{INT} = $SIG{HUP} = $SIG{TERM} = $SIG{ABRT} = \&cleanup;
if(@ARGV > 1){
  system ("merge_bam_headers $log $tmpdir/tmp$$.headers.sam ".join(" ", @ARGV))>>8 and die "merge_bam_headers failed with exit status ", ($?>>8), ", please check the log\n";
  system("samtools merge -h $tmpdir/tmp$$.headers.sam $tmpdir/tmp$$.bam ".join(" ", @ARGV)." 2>> $log")>>8 and die "Samtools merge failed with exit status ", ($?>>8), ", please check the log\n";
  system("samtools flagstat $tmpdir/tmp$$.bam > $outfile.before_dedup.flagstat.txt");
  system("samtools rmdup $tmpdir/tmp$$.bam $tmpdir/tmp$$.rmdup.bam 2>> $log")>>8 and die "Samtools rmdup failed with exit status ", ($?>>8), ", please check the log\n";
  unlink "$tmpdir/tmp$$.bam";
}
else{
  system("samtools flagstat $ARGV[0] > $outfile.before_dedup.flagstat.txt");
  system("samtools rmdup $ARGV[0] $tmpdir/tmp$$.rmdup.bam 2>> $log")>>8 and die "Samtools rmdup failed with exit status ", ($?>>8), ", please check the log\n";
}
die "Samtools rmdup did not generate the expected output file" if not -e "$tmpdir/tmp$$.rmdup.bam";
die "Samtools generated a blank output file" if -z "$tmpdir/tmp$$.rmdup.bam";
system "samtools index $tmpdir/tmp$$.rmdup.bam";
system "java -Xmx4G -jar $dirname/GenomeAnalysisTK.jar -I $tmpdir/tmp$$.rmdup.bam -R $ref -T RealignerTargetCreator -o $tmpdir/tmp$$.rmdup.gatk_realigner.intervals 2>> $log";
die "GATK did not generate the expected intervals file" if not -e "$tmpdir/tmp$$.rmdup.gatk_realigner.intervals";
system "java -Xmx4G -jar $dirname/GenomeAnalysisTK.jar -I $tmpdir/tmp$$.rmdup.bam -R $ref -T IndelRealigner -targetIntervals $tmpdir/tmp$$.rmdup.gatk_realigner.intervals -o $outfile 2>> $log";
die "GATK did not generate the expected realigned BAM output file" if not -e $outfile;
die "GATK generated a blank output file" if -z $outfile;
my $outfile_bai = $outfile;
$outfile_bai =~ s/\.bam$/.bai/;
if(not -e $outfile_bai){
  if(not -e "$outfile.bai"){
    system "samtools index $outfile";
  }
  system "cp $outfile.bai $outfile_bai";
}
else{
  system "cp $outfile_bai $outfile.bai"; # some tools expect name.bai, some expect name.bam.bai, so provide both
}
&cleanup;

sub cleanup{
  print STDERR @_;
  unlink "$tmpdir/$tmpdir/tmp$$.headers.sam";
  unlink "$tmpdir/tmp$$.bam";
  unlink "$tmpdir/tmp$$.rmdup.bam";
  unlink "$tmpdir/tmp$$.rmdup.bam.bai";
  unlink "$tmpdir/tmp$$.rmdup.gatk_realigner.intervals";
}