From 7749f4eb6c269e364853cb1b3e85cd02c462b330 Mon Sep 17 00:00:00 2001
From: Pablo Cingolani <pablo.e.cingolani@gmail.com>
Date: Fri, 5 Oct 2018 14:43:31 -0400
Subject: [PATCH] Version 1.5.6

---
 VarDict                                       |   2 +-
 build.gradle                                  |   4 +-
 tests/integration/.config.sh.swp              | Bin 12288 -> 0 bytes
 .../.test_non_deterministic_behavior.sh.swp   | Bin 12288 -> 0 bytes
 tests/integration/.tests_integration.sh.swp   | Bin 20480 -> 0 bytes
 .../test_non_deterministic_behavior.out       | 294 ++++++++++++++++++
 .../test_non_deterministic_behavior.sh        |  14 +-
 7 files changed, 305 insertions(+), 9 deletions(-)
 delete mode 100644 tests/integration/.config.sh.swp
 delete mode 100644 tests/integration/.test_non_deterministic_behavior.sh.swp
 delete mode 100644 tests/integration/.tests_integration.sh.swp
 create mode 100644 tests/integration/test_non_deterministic_behavior.out

diff --git a/VarDict b/VarDict
index 2e4380f..464d049 160000
--- a/VarDict
+++ b/VarDict
@@ -1 +1 @@
-Subproject commit 2e4380fb2cd8ab566434c4566d48545f8fda6020
+Subproject commit 464d04919253886cb1a7320390e9da75e9e18c3e
diff --git a/build.gradle b/build.gradle
index 1d2c805..0c46eff 100644
--- a/build.gradle
+++ b/build.gradle
@@ -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')
\ No newline at end of file
+applicationDistribution.from('VarDict/teststrandbias.R','VarDict/testsomatic.R','VarDict/var2vcf_valid.pl','VarDict/var2vcf_paired.pl').into('bin')
diff --git a/tests/integration/.config.sh.swp b/tests/integration/.config.sh.swp
deleted file mode 100644
index 73be7de937114d91faf4dec680c8d66da8e1be85..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12288
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kHVcYmq#thj05KO*HjqLu<Sz4ipscA$XKfaDq%7~lPX+ovH2?qr

diff --git a/tests/integration/.test_non_deterministic_behavior.sh.swp b/tests/integration/.test_non_deterministic_behavior.sh.swp
deleted file mode 100644
index 5543e3ff5ed75d33fd85f0112a1686f1b9aa958e..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12288
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diff --git a/tests/integration/.tests_integration.sh.swp b/tests/integration/.tests_integration.sh.swp
deleted file mode 100644
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GIT binary patch
literal 0
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diff --git a/tests/integration/test_non_deterministic_behavior.out b/tests/integration/test_non_deterministic_behavior.out
new file mode 100644
index 0000000..5b147d2
--- /dev/null
+++ b/tests/integration/test_non_deterministic_behavior.out
@@ -0,0 +1,294 @@
+Running VarDict Perl: 1 / 5
+Running VarDict Java: 1 / 5
+Running VarDict Perl: 2 / 5
+Running VarDict Java: 2 / 5
+Running VarDict Perl: 3 / 5
+Running VarDict Java: 3 / 5
+Running VarDict Perl: 4 / 5
+Running VarDict Java: 4 / 5
+Running VarDict Perl: 5 / 5
+Running VarDict Java: 5 / 5
+Differences:
+--------------------------------------------------------------------------------
+
+
+Difference 1-1 Perl:
+
+
+Difference 1-1 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 1-2 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+11c10
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 1-2 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 1-3 Perl:
+11c11
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 1-3 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 1-4 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+
+
+Difference 1-4 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 1-5 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+11c10
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 1-5 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 2-1 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+10c11
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 2-1 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 2-2 Perl:
+
+
+Difference 2-2 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 2-3 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+
+
+Difference 2-3 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 2-4 Perl:
+10c10
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 2-4 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 2-5 Perl:
+
+
+Difference 2-5 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 3-1 Perl:
+11c11
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 3-1 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 3-2 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+
+
+Difference 3-2 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 3-3 Perl:
+
+
+Difference 3-3 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 3-4 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+11c10
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 3-4 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 3-5 Perl:
+8,9c8
+< abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+---
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+
+
+Difference 3-5 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 4-1 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+
+
+Difference 4-1 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 4-2 Perl:
+10c10
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 4-2 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 4-3 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+10c11
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 4-3 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 4-4 Perl:
+
+
+Difference 4-4 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 4-5 Perl:
+10c10
+< abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 4-5 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 5-1 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+10c11
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 5-1 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 5-2 Perl:
+
+
+Difference 5-2 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 5-3 Perl:
+8c8,9
+< abc	chr20	chr20	61659444	61659444	A	G	23	17	4	0	15	2	A/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7778	0	0	2.000	2	4.4	14	18	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	0
+---
+> abc	chr20	chr20	61659444	61659444	A	AGAGGGGGCCGGTGGGGAGGGGGCCGGCGGGGAGTGGTTTGGTGGG	23	5	0	0	3	1	G/+45	0.2174	0;2	49.6	1	32.2	1	36.7	3.000	0.1579	0.1739	49	4.000	1	5.0	3	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	Insertion	0	5-0-0
+> abc	chr20	chr20	61659444	61659444	A	G	23	17	0	0	15	2	G/G	0.7391	0;2	26.2	1	33.9	1	48.4	4.667	0.7368	0	0	2.000	2	4.4	14	19	CGGTGGGGAGGGGCCGGTGG	GAGGGGGCCGGTGGGGAGGG	chr20:61659400-61659600	SNV	0	5-0-0
+
+
+Difference 5-3 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 5-4 Perl:
+10c10
+< abc	chr20	chr20	61659471	61659483	CGGGGAGTGGTTT	TGGGGGGGGGCCTGCAGGGAGGGGGCC	27	8	14	3	5	3	GCGGGGAGTGGTTT/+28	0.2963	2;2	38.0	1	37.3	1	52.4	16.000	0.4000	0.2963	0	0	0	1.0	8	20	GCCGGTGGGGAGGGGGCCGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+---
+> abc	chr20	chr20	61659481	61659483	TTT	GCC	13	6	3	1	3	3	TTT/GCC	0.4615	2;2	35.0	1	37.3	1	60.0	12.000	0.8571	0.3846	0	3.000	1	0.8	6	7	AGGGGGCCGGCGGGGAGTGG	GGTGGGGAGGAGGCTGGTGA	chr20:61659400-61659600	Complex	0	0
+
+
+Difference 5-4 Java:
+--------------------------------------------------------------------------------
+
+
+Difference 5-5 Perl:
+
+
+Difference 5-5 Java:
diff --git a/tests/integration/test_non_deterministic_behavior.sh b/tests/integration/test_non_deterministic_behavior.sh
index 17e12ad..0a51a39 100755
--- a/tests/integration/test_non_deterministic_behavior.sh
+++ b/tests/integration/test_non_deterministic_behavior.sh
@@ -17,9 +17,10 @@ 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
@@ -27,9 +28,10 @@ for i in $(seq 1 $N); do
  	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