UNCeqR_conf.pl.template

use Getopt::Long qw(GetOptionsFromArray);
Getopt::Long::Configure("pass_through");
my @ARGV2 = @ARGV;

my $version = "v0.2.1";

$header = <<END;
#UNCeqr (c) 2011-2015 Matthew D. Wilkerson.
END


@hisArgv = @ARGV;
GetOptionsFromArray(	
			\@hisArgv,
			'mode=s' => \$mode
			);



	#GLOBAL VARIABLES
	#arg with no initial value
	($rnaf,$tdnaf,$ndnaf,$preMinTumorCov,$startChr,$endChr,$maf,$sampId,$tumorLoose,$filterTumor,$testReg,$regionRestrict,$minTMapQ,$minTBaseQ,$maxNM,$maxIH,$trimEnd,$flagFilter,$st,$flagStrike,$minInNormFrac,$filterScript,$maxDepth,$mainProc,$resultsDir,$genomeFasta,$dense,$fastaWchr,$fastaWoChr,$tdnafChr,$ndnafChr,$rnafChr,$snpFile, $maxHomopolymer, $normalLoose,$mafEnd,$indelShadow,$verboseOut,$R,$Rscript,$R_LIBS_USER,$perlLib,	$normIndelShadowFrac,$trainNum,$medStart) = (("") x 200);
	#mode is passed

	#args with default value
	$preMinNormCov=5;
	$preMinTumorCov=5;
	$minInNormFrac=0.02;

	$maxNM=2;
	$maxIH=1;
	$minTBaseQ=20;
	$minTMapQ=20;
	$trimEnd=2;
	$maxDepth=10000;
	$maxHomopolymer=4;
	$normalLoose = "Y";
	$flagFilter=1; 
	$indelShadow=101;
	$normIndelShadowFrac=0.1;
	$verboseOut=0;

	$tdnafChr=$ndnafChr=$rnafChr="Y";
	$tdnaf = $ndnaf = $rnaf = "blank";

	$dnaOnly=0;
	$rnaOnly=0;

	$minNormCnt=5;
	$maxNormPlural=100;
	$minDnaTumorCnt=5;
	$maxDnaBias=0.01;
	$maxDnaStruckProp=0.75;
	$minRnaTumorCnt=5;
	$maxRnaBias=0.01;
	$maxRnaStruckProp=0.75;
	$trainNum=50000;
	$medStart = 1;
	
	$maxDnaTumorPluralProp=0.75;
	$maxRnaTumorPluralProp=0.75;

	$dense="Y";

        $annFlag=0;
	$pvCut = 0.001;	
	$regionRestrict="N";

	$snpFile = -1;



  $localPath = "[FULL PATH]/UNCeqR_vXXX";
  $st="$localPath/samtools-0.1.18_unceqr/samtools";
  $R="[FULL PATH]/bin/R";
  $Rscript="[FULL PATH]/Rscript";
  $R_LIBS_USER="";#[FULL PATH]/x86_64-unknown-linux-gnu-library/3.X.X/;
  $perlLib = "";#[FULL PATH]/site_perl/5.8.8/; 


if($mode eq "denovo"){

	$regionRestrict="Y";
	$flagFilter=5;
	$normalLoose="Y";
	$dense="Y";
	$maxDepth=10000; 
	$dnaOnly=0;
	$rnaOnly=0;
	$trainNum=50000; 
	$maxDnaTumorPluralProp=0.75;
	$maxRnaTumorPluralProp=0.75; 
	$maxRnaStruckProp=0.75;
	$maxDnaStruckProp=0.75;
	$maxRnaBias=0.01;
	$maxDnaBias=0.01;
	$indelShadow=101;
	$maxNormPlural=10;
	$minInNormFrac=0.02;
	$trimEnd=2; 
	$minTMapQ=20;
	$minTBaseQ=20;
	$maxNM=2;
	$maxIH=1;
	$minNormCnt=10;
	$preMinNormCov=10;
	$preMinTumorCov=5;
	$minDnaTumorCnt=5;
	$minRnaTumorCnt=5;
	$maxHomopolymer=4;
	$verboseOut=0;
	$annFlag=1;
	$pvCut = 0.25;	
	$medStart = 1;

}elsif($mode eq "interrogate"){
	#all data quality filtering is off
	#min normal depth 0
	#min tumor depth 1 

	$regionRestrict="N";
	$flagFilter=0;
	$normalLoose="Y";
	$dense="Y";
	$maxDepth=10000; 
	$dnaOnly=0;
	$rnaOnly=0;
	$trainNum=100; 
	$maxDnaTumorPluralProp=0;
	$maxRnaTumorPluralProp=0; 
	$maxRnaStruckProp=2;
	$maxDnaStruckProp=2;
	$maxRnaBias=0;
	$maxDnaBias=0;
	$indelShadow=0;
	$maxNormPlural=10;
	$minInNormFrac=2;  #should be 2 for ignore normal specimen; #take all alleles - 0
	$trimEnd=0; 
	$minTMapQ=0;
	$minTBaseQ=0;
	$maxNM=100000;
	$maxIH=100000;
	$minNormCnt=0;
	$preMinNormCov=0;
	$preMinTumorCov=1;
	$minDnaTumorCnt=1;
	$minRnaTumorCnt=1;
	$maxHomopolymer=100;
	$verboseOut=0;
	$annFlag=1;
	$pvCut = 100; #only print variants in test.csv; not matching reference.
	$medStart = 0;

}else{
  die "mode is undefined=$mode\n";
}



###
#get command line arguments
###
	GetOptionsFromArray(	
			\@ARGV2,
			#DATA
			'tumorRNA=s' => \$rnaf,
			'tumorDNA=s' => \$tdnaf,
			'normalDNA=s' => \$ndnaf,
			'normalDNAchr=s' => \$ndnafChr,
			'tumorRNAchr=s' => \$rnafChr,
			'tumorDNAchr=s' => \$tdnafChr,
			'fastaWchr:s' => \$fastaWchr,
			'fastaWoChr:s' => \$fastaWoChr,
			'resultsDir:s' => \$resultsDir,
			'regionsToQuery=s' =>\$posf, #this has to be sorted by chr,pos.  CHR order should be the same as index file and SNP files. must end with a comma
			'dense:s' => \$dense,
			'mainProc:s' => \$mainProc,
			'verboseOut:i' => \$verboseOut,
			'snpFile:s' => \$snpFile,  #this has to be sorted by chr,pos.  CHR order should be the same as index file and SNP files.
			'dnaOnly:i' => \$dnaOnly, 
			'rnaOnly:i' => \$rnaOnly, 
			'mode:s' => \$mode, 

			#alignment and base filtering
			'trimEnd:i' => \$trimEnd,
			'minTMapQ:i' => \$minTMapQ,
			'minTBaseQ:i' => \$minTBaseQ,
			'flagFilter:s' => \$flagFilter, 
			'maxIH:i' => \$maxIH,
			'maxNM:i' => \$maxNM, #maximum allowed number of mismatches
			'maxDepth:s' => \$maxDepth,
			'normalLoose:s' => \$normalLoose, #this refers to alignment criteria
			'maxHomopolymer:i' => \$maxHomopolymer,
                        'indelShadow:i' => \$indelShadow,
			'normIndelFrac:f' => \$normIndelFrac,
			'medStart:i' => \$medStart,

			#Genomic position
			'preMinNormCov=i' => \$preMinNormCov,
			'preMinTumorCov=i' => \$preMinTumorCov,
			'minInNormFrac=f' => \$minInNormFrac,
			'regionRestrict:s' => \$regionRestrict,

			#Usable data
			'minNormCnt:i' => \$minNormCnt,
			'maxNormPlural:i' => \$maxNormPlural,
			'minDnaTumorCnt:i' => \$minDnaTumorCnt,
			'maxDnaBias:f' => \$maxDnaBias,
			'maxDnaStruckProp:f' => \$maxDnaStruckProp,
			'minRnaTumorCnt:i' => \$minRnaTumorCnt,
			'maxRnaBias:f' => \$maxRnaBias,
			'maxRnaStruckProp:f' => \$maxRnaStruckProp,
			'trainNum:i' => \$trainNum,
			'maxDnaTumorPluralProp:f' => \$maxDnaTumorPluralProp,
			'maxRnaTumorPluralProp:f' => \$maxRnaTumorPluralProp,

			#prior mutation file specific (interrogation mode)
			'priorMutFile=s' => \$maf,
			'sampleId=s' => \$sampId,
			'laneFile=s' => \$laneFile,
			'mafEnd=s' => \$mafEnd,
 			'annFlag=s' => \$annFlag

			);

#prior mut file, then dense is N, regions to query off





TRUE;