From e008a3892c05ac894020b6f3f40568a8338be4ec Mon Sep 17 00:00:00 2001
From: PolinaBevad <polina_bevad@epam.com>
Date: Wed, 16 Sep 2020 14:18:54 +0300
Subject: [PATCH 1/4] Updated integration tests to vcf 4.2

---
 VarDict                                       | 2 +-
 build.gradle                                  | 2 +-
 tests/integration/expected/vardict.paired.vcf | 4 ++--
 tests/integration/expected/vardict.simple.vcf | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/VarDict b/VarDict
index c74f0b1..cada98f 160000
--- a/VarDict
+++ b/VarDict
@@ -1 +1 @@
-Subproject commit c74f0b19efe1407cdb84a393f76eef13d0f12f17
+Subproject commit cada98faa51bdac56ca0f3891887e54b75943b5b
diff --git a/build.gradle b/build.gradle
index ce42236..b0c12d1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -4,7 +4,7 @@ plugins {
     id 'jacoco'
 }
 
-version = '1.8.1'
+version = '1.8.2'
 
 repositories { 
     mavenCentral() 
diff --git a/tests/integration/expected/vardict.paired.vcf b/tests/integration/expected/vardict.paired.vcf
index 53c133b..11416a5 100755
--- a/tests/integration/expected/vardict.paired.vcf
+++ b/tests/integration/expected/vardict.paired.vcf
@@ -1,5 +1,5 @@
-##fileformat=VCFv4.3
-##source=VarDict_v1.8.1
+##fileformat=VCFv4.2
+##source=VarDict_v1.8.2
 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
diff --git a/tests/integration/expected/vardict.simple.vcf b/tests/integration/expected/vardict.simple.vcf
index 383534e..fca6ce4 100755
--- a/tests/integration/expected/vardict.simple.vcf
+++ b/tests/integration/expected/vardict.simple.vcf
@@ -1,5 +1,5 @@
-##fileformat=VCFv4.3
-##source=VarDict_v1.8.1
+##fileformat=VCFv4.2
+##source=VarDict_v1.8.2
 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

From 35dcba623b346fc3561128b7bc442fa393efac4b Mon Sep 17 00:00:00 2001
From: Polina Bevad <polina_bevad@epam.com>
Date: Wed, 16 Sep 2020 14:36:32 +0300
Subject: [PATCH 2/4] Update Readme.md

Fixed description of variant filtering step.
---
 Readme.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Readme.md b/Readme.md
index b1a37c1..4a0a90d 100644
--- a/Readme.md
+++ b/Readme.md
@@ -250,7 +250,7 @@ The VarDictJava program follows the workflow:
    2. Find structural variants (optionally can be disabled by option `-U`).
    3. Realign some of the variants using realignment of insertions, deletions, large insertions, and large deletions using unaligned parts of reads 
    (soft-clipped ends). This step is optional and can be disabled using the `-k 0` switch.
-   4. Calculate statistics for the variant, filter out some bad ones, if any.
+   4. Apply variant filtering rules (hard filters) defined in [Variant filtering](Readme.md#VarFiltering). 
    5. Assign a type to each variant.
    6. Output variants in an intermediate internal format (tabular). Columns of the table are described in the Output Columns section.
 	 
@@ -301,7 +301,7 @@ String | Description
 ...^[0-9]+ | something followed by a deletion
 ...&amp;[ATGC]+ | for insertion/deletion variants followed by a matched sequence
 
-#### Variant Filtering
+#### <a name="VarFiltering"></a>Variant Filtering
 A variant appears in the output if it satisfies the following criteria (in this order). 
 If variant doesn't fit criteria on the step, it will be filtered out and the next steps won't be checked (except for the step 8, read the explanation below):
 1. Frequency of the variant exceeds the threshold set by the `-f` option (default = 1%).

From 18c6ac4783bb9bc0d8b025abf84942b4808b6ac6 Mon Sep 17 00:00:00 2001
From: Pablo Cingolani <pablo.e.cingolani@gmail.com>
Date: Wed, 16 Sep 2020 10:18:16 -0400
Subject: [PATCH 3/4] Project updated

---
 VarDict | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VarDict b/VarDict
index cada98f..f48bf3b 160000
--- a/VarDict
+++ b/VarDict
@@ -1 +1 @@
-Subproject commit cada98faa51bdac56ca0f3891887e54b75943b5b
+Subproject commit f48bf3b0b1c51bc4fd2e6db6b27a7db7f313c846

From 91cb74b0fbdae27a0aceaa22c05a91e4376f6150 Mon Sep 17 00:00:00 2001
From: Pablo Cingolani <pablo.e.cingolani@gmail.com>
Date: Wed, 16 Sep 2020 10:20:09 -0400
Subject: [PATCH 4/4] Updated changelog.txt

---
 changelog.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 7af477c..dc68047 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,3 +1,7 @@
+Version 1.8.2
+    - Update Readme.md
+    - Updated integration tests to vcf 4.2
+
 Version 1.8.1
     - Updated version.
     - Added validation of VCF files in integration tests. Fixed flag InDelLikely name in expected file and duplicated Bias filter. Updated submodule.