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 73be7de..0000000 Binary files a/tests/integration/.config.sh.swp and /dev/null differ 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 5543e3f..0000000 Binary files a/tests/integration/.test_non_deterministic_behavior.sh.swp and /dev/null differ diff --git a/tests/integration/.tests_integration.sh.swp b/tests/integration/.tests_integration.sh.swp deleted file mode 100644 index 4530efb..0000000 Binary files a/tests/integration/.tests_integration.sh.swp and /dev/null differ 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