Version 1.5.6

Author: pcingola

VarDict

@@ -4,7 +4,7 @@ plugins {
     id 'jacoco'
 }
 
-version = '1.5.5'
+version = '1.5.6'
 
 repositories { 
     mavenCentral() 
@@ -65,4 +65,4 @@ test {
     useTestNG()
 }
 
-applicationDistribution.from('VarDict/teststrandbias.R','VarDict/testsomatic.R','VarDict/var2vcf_valid.pl','VarDict/var2vcf_paired.pl').into('bin')
+applicationDistribution.from('VarDict/teststrandbias.R','VarDict/testsomatic.R','VarDict/var2vcf_valid.pl','VarDict/var2vcf_paired.pl').into('bin')

build.gradle

@@ -17,19 +17,21 @@ for i in $(seq 1 $N); do
 	echo "Running VarDict Perl: $i / $N"
 	time $VARDICTPERL \
 			-G $REF_GENOME \
-			-f 0.001 -N abc \
-			-b $COLO20 $UNMAPPED_FLAG \
-			-c 1 -S 2 -E 3 -g 4 \
+			-f 0.001 \
+			-N abc \
+			-b $COLO20 \
+			$UNMAPPED_FLAG \
 			$REGION \
 		| sort \
 		> $DIR_OUTPUT/vardictColo20.perl.$i.txt
 
  	echo "Running VarDict Java: $i / $N"
  	time $VARDICTJAVA \
  			-G $REF_GENOME \
- 			-f 0.001 -N abc \
- 			-b $COLO20 $UNMAPPED_FLAG \
- 			-c 1 -S 2 -E 3 -g 4 \
+ 			-f 0.001 \
+			-N abc \
+ 			-b $COLO20 \
+			$UNMAPPED_FLAG \
  			$REGION \
  	| sort \
  	> $DIR_OUTPUT/vardictColo20.java.$i.txt