From 2e10a6fecd42d530a49e3a1ae370835fae6cbfa7 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Mon, 26 Dec 2016 18:07:12 +0300
Subject: [PATCH 01/19] Next development cycle v2.0.4

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 3e7973c7d..b26c4413e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>2.0.3</version>
+    <version>2.0.4-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

From 0e3ccf5e78052e01110dece4a8cfc256f75b0d8c Mon Sep 17 00:00:00 2001
From: Stanislav Poslavsky <stvlpos@mail.ru>
Date: Thu, 12 Jan 2017 18:19:11 +0300
Subject: [PATCH 02/19] feature extractors work

---
 pom.xml                                       |  2 +-
 .../mixcr/export/FeatureExtractors.java       | 62 +++++++++++++++----
 .../mixcr/export/FieldExtractorsTest.java     |  1 +
 3 files changed, 51 insertions(+), 14 deletions(-)

diff --git a/pom.xml b/pom.xml
index b26c4413e..3271c07b2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,7 @@
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.2.4</version>
+            <version>1.2.5-SNAPSHOT</version>
         </dependency>
 
         <dependency>
diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
index 246e0b6eb..cedeb9f11 100644
--- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
+++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -8,10 +8,7 @@
 import com.milaboratory.core.sequence.TranslationParameters;
 import com.milaboratory.mixcr.basictypes.VDJCHit;
 import com.milaboratory.mixcr.basictypes.VDJCObject;
-import io.repseq.core.GeneFeature;
-import io.repseq.core.GeneType;
-import io.repseq.core.ReferencePoints;
-import io.repseq.core.VDJCGene;
+import io.repseq.core.*;
 
 import static com.milaboratory.mixcr.export.FieldExtractors.NULL;
 
@@ -32,7 +29,14 @@ static abstract class WithHeader extends FieldWithParameters<VDJCObject, GeneFea
 
         void validate(GeneFeature[] features) {
             if (features.length == 2 && !features[1].contains(features[0]))
-                throw new IllegalArgumentException(String.format("%s: Base feature %s does not contain relative feature %s", command, features[1], features[0]));
+                throw new IllegalArgumentException(String.format("%s: Base feature %s does not contain relative feature %s",
+                        command, GeneFeature.encode(features[1]), GeneFeature.encode(features[0])));
+            for (GeneFeature feature : features)
+                if (feature.getGeneType() == null)
+                    throw new IllegalArgumentException(String.format("%s: Gene feature %s covers several gene types " +
+                            "(not possible to select corresponding alignment)", command, GeneFeature.encode(feature)));
+
+            //todo bigfeature nofloating bounds
         }
 
         private String header0(String[] prefixes, GeneFeature[] features) {
@@ -94,23 +98,41 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
             GeneFeature bigGeneFeature = parameters[parameters.length - 1];
 
             GeneType geneType = bigGeneFeature.getGeneType();
+            assert geneType != null;
+
             VDJCHit hit = object.getBestHit(geneType);
 
             if (hit == null)
                 return "-";
 
             GeneFeature alignedFeature = hit.getAlignedFeature();
-            if (!alignedFeature.contains(smallGeneFeature))
-                return "-";
+//            if (!alignedFeature.contains(smallGeneFeature))
+//                return "-";
 
             VDJCGene gene = hit.getGene();
-            ReferencePoints partitioning = gene.getPartitioning();
-            if (!partitioning.isAvailable(bigGeneFeature))
+            ReferencePoints germlinePartitioning = gene.getPartitioning();
+            if (!germlinePartitioning.isAvailable(bigGeneFeature))
+                return "-";
+
+            Range smallTargetRage = germlinePartitioning.getRelativeRange(alignedFeature, smallGeneFeature);
+            if (smallTargetRage == null)
+                for (int i = 0; i < object.numberOfTargets(); i++) {
+                    SequencePartitioning pt = object.getPartitionedTarget(i).getPartitioning();
+                    Range range = pt.getRange(smallGeneFeature);
+                    if (range == null)
+                        continue;
+                    Alignment<NucleotideSequence> alignment = object.getBestHit(geneType).getAlignment(i);
+                    smallTargetRage = alignment.convertToSeq1Range(range);
+                    if (smallTargetRage != null)
+                        break;
+                }
+
+            if (smallTargetRage == null)
                 return "-";
 
-            Range smallTargetRage = partitioning.getRelativeRange(alignedFeature, smallGeneFeature);
+            GeneFeature intersection = GeneFeature.intersection(bigGeneFeature, alignedFeature);
 
-            for (int i = 0; i < hit.numberOfTargets(); i++) {
+            for (int i = 0; i < hit.numberOfTargets(); ++i) {
                 Alignment<NucleotideSequence> alignment = hit.getAlignment(i);
 
                 if (alignment == null || !alignment.getSequence1Range().contains(smallTargetRage))
@@ -118,13 +140,27 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
 
                 Mutations<NucleotideSequence> mutations = alignment.getAbsoluteMutations().extractRelativeMutationsForRange(smallTargetRage);
                 if (parameters.length == 2) {
-                    int shift = partitioning.getRelativePosition(bigGeneFeature, smallGeneFeature.getFirstPoint());
+                    int shift = object.getPartitionedTarget(i).getPartitioning().getRelativePosition(intersection, smallGeneFeature.getFirstPoint());
                     if (shift < 0)
                         continue;
+
+                    int offset = germlinePartitioning.getRelativePosition(bigGeneFeature, intersection.getFirstPoint());
+                    if (offset < 0)
+                        throw new RuntimeException();
+
+                    shift += offset;
                     mutations = mutations.move(shift);
+
+//                    int shift = germlinePartitioning.getRelativePosition(bigGeneFeature, smallGeneFeature.getFirstPoint());
+//                    if (shift < 0)
+//                        continue;
+//                    mutations = mutations.move(shift);
+//                    mutations = mutations.extractRelativeMutationsForRange(bigRange);
+//                    if (mutations == null)
+//                        continue;
                 }
 
-                return convert(mutations, gene.getFeature(bigGeneFeature), object.getFeature(smallGeneFeature).getSequence(), partitioning.getTranslationParameters(bigGeneFeature));
+                return convert(mutations, gene.getFeature(bigGeneFeature), object.getFeature(smallGeneFeature).getSequence(), germlinePartitioning.getTranslationParameters(bigGeneFeature));
             }
             return "-";
         }
diff --git a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java
index 940a028dd..2ef5a7a2c 100644
--- a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java
+++ b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java
@@ -31,6 +31,7 @@
 import com.milaboratory.mixcr.basictypes.Clone;
 import com.milaboratory.mixcr.basictypes.VDJCAlignments;
 import com.milaboratory.mixcr.basictypes.VDJCObject;
+import com.milaboratory.mixcr.cli.Main;
 import com.milaboratory.mixcr.cli.Util;
 import io.repseq.core.GeneType;
 import org.junit.Ignore;

From 04d7cb1397712c36f5140dc2d041746594fb96bc Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Thu, 12 Jan 2017 19:39:28 +0300
Subject: [PATCH 03/19] Feature extraction fix WIP

---
 .../basictypes/VDJCAlignmentsFormatter.java   | 25 +++++++++++++++++--
 .../mixcr/export/FeatureExtractors.java       | 25 ++++++++++++-------
 2 files changed, 39 insertions(+), 11 deletions(-)

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
index 12bcd57c9..2cdf4012c 100644
--- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
+++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
@@ -113,6 +113,20 @@ public boolean accept(SequencePartitioning object) {
             return object.isAvailable(ReferencePoint.VEnd) && object.getPosition(ReferencePoint.VEnd) != object.getPosition(ReferencePoint.VEndTrimmed);
         }
     };
+    public static final Filter<SequencePartitioning> IsDPLeft = new Filter<SequencePartitioning>() {
+        @Override
+        public boolean accept(SequencePartitioning object) {
+            return object.isAvailable(ReferencePoint.DBegin) && object.getPosition(ReferencePoint.DBegin) != object.getPosition(ReferencePoint.DBeginTrimmed);
+        }
+    };
+    public static final Filter<SequencePartitioning> IsDPRight = new Filter<SequencePartitioning>() {
+        @Override
+        public boolean accept(SequencePartitioning object) {
+            return object.isAvailable(ReferencePoint.DEnd) && object.getPosition(ReferencePoint.DEnd) != object.getPosition(ReferencePoint.DEndTrimmed);
+        }
+    };
+    public static final Filter<SequencePartitioning> NotDPLeft = FilterUtil.not(IsDPLeft);
+    public static final Filter<SequencePartitioning> NotDPRight = FilterUtil.not(IsDPRight);
     public static final Filter<SequencePartitioning> NotVP = FilterUtil.not(IsVP);
 
 
@@ -130,8 +144,15 @@ public boolean accept(SequencePartitioning object) {
             pd(ReferencePoint.VEndTrimmed, "V>", -1, NotVP),
             pd(ReferencePoint.VEnd, "V><VP", IsVP),
             pd(ReferencePoint.VEndTrimmed, "VP>", -1, IsVP),
-            pd(ReferencePoint.DBeginTrimmed, "<D"),
-            pd(ReferencePoint.DEndTrimmed, "D>", -1),
+
+            pd(ReferencePoint.DBeginTrimmed, "<D", NotDPLeft),
+            pd(ReferencePoint.DBegin, "DP><D", IsDPLeft),
+            pd(ReferencePoint.DBeginTrimmed, "<DP", IsDPLeft),
+
+            pd(ReferencePoint.DEndTrimmed, "D>", -1, NotDPRight),
+            pd(ReferencePoint.DEnd, "D><DP", IsDPRight),
+            pd(ReferencePoint.DEndTrimmed, "DP>", IsDPRight),
+
             pd(ReferencePoint.JBeginTrimmed, "<J"),
             pd(ReferencePoint.CDR3End, "CDR3><FR4"),
             pd(ReferencePoint.FR4End, "FR4>", -1),
diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
index cedeb9f11..2eeb793d1 100644
--- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
+++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -130,7 +130,7 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
             if (smallTargetRage == null)
                 return "-";
 
-            GeneFeature intersection = GeneFeature.intersection(bigGeneFeature, alignedFeature);
+            GeneFeature intersectionBigAligned = GeneFeature.intersection(bigGeneFeature, alignedFeature);
 
             for (int i = 0; i < hit.numberOfTargets(); ++i) {
                 Alignment<NucleotideSequence> alignment = hit.getAlignment(i);
@@ -138,17 +138,23 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
                 if (alignment == null || !alignment.getSequence1Range().contains(smallTargetRage))
                     continue;
 
-                Mutations<NucleotideSequence> mutations = alignment.getAbsoluteMutations().extractRelativeMutationsForRange(smallTargetRage);
+                Mutations<NucleotideSequence> mutations;
                 if (parameters.length == 2) {
-                    int shift = object.getPartitionedTarget(i).getPartitioning().getRelativePosition(intersection, smallGeneFeature.getFirstPoint());
-                    if (shift < 0)
+                    mutations = alignment.getAbsoluteMutations().extractAbsoluteMutationsForRange(smallTargetRage);
+
+                    ReferencePoint baIntersectionBegin = intersectionBigAligned.getFirstPoint();
+
+                    int referencePosition = germlinePartitioning.getRelativePosition(alignedFeature, baIntersectionBegin);
+                    int bigFeaturePosition = germlinePartitioning.getRelativePosition(bigGeneFeature, baIntersectionBegin);
+
+                    if (bigFeaturePosition < 0 || referencePosition < 0)
                         continue;
 
-                    int offset = germlinePartitioning.getRelativePosition(bigGeneFeature, intersection.getFirstPoint());
-                    if (offset < 0)
-                        throw new RuntimeException();
+                    int shift = bigFeaturePosition - referencePosition;
+
+                    if (shift < 0)
+                        mutations = mutations.getRange(Mutations.pabs(mutations.firstMutationWithPosition(-shift)), mutations.size());
 
-                    shift += offset;
                     mutations = mutations.move(shift);
 
 //                    int shift = germlinePartitioning.getRelativePosition(bigGeneFeature, smallGeneFeature.getFirstPoint());
@@ -158,7 +164,8 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
 //                    mutations = mutations.extractRelativeMutationsForRange(bigRange);
 //                    if (mutations == null)
 //                        continue;
-                }
+                } else
+                    mutations = alignment.getAbsoluteMutations().extractRelativeMutationsForRange(smallTargetRage);
 
                 return convert(mutations, gene.getFeature(bigGeneFeature), object.getFeature(smallGeneFeature).getSequence(), germlinePartitioning.getTranslationParameters(bigGeneFeature));
             }

From 4e23297b24c8099959411ec703d86b02f0fa3b7c Mon Sep 17 00:00:00 2001
From: Stanislav Poslavsky <stvlpos@mail.ru>
Date: Mon, 30 Jan 2017 14:10:45 +0300
Subject: [PATCH 04/19] minor fix for export when fields are given in the file

---
 .../java/com/milaboratory/mixcr/cli/ActionExportParameters.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java
index bb94d734e..d174012a3 100644
--- a/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java
+++ b/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java
@@ -195,6 +195,7 @@ public static ArrayList<FieldExtractor> parseFile(OutputMode outputMode, Class c
             String line;
             while ((line = reader.readLine()) != null) {
                 line = line.trim();
+                line = line.replace("\"", "");
                 if (!line.isEmpty())
                     options.addAll(Arrays.asList(line.split(" ")));
             }

From dce8757f9af6f1001306d948da7b6c23355f8ef8 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Mon, 30 Jan 2017 15:32:54 +0300
Subject: [PATCH 05/19] CHANGELOG

---
 CHANGELOG_CURRENT | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
index e69de29bb..4f38ea9a5 100644
--- a/CHANGELOG_CURRENT
+++ b/CHANGELOG_CURRENT
@@ -0,0 +1,3 @@
+Fix for NPE in `-nMutations ...` `-aaMutations ...`
+Correct visualization of D gene P segments in exportAlignmentsPretty
+minor: Fix for error in export when fields are given in the file
\ No newline at end of file

From f9d11976539aada6f91240a57189c87c4bbfa515 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Mon, 30 Jan 2017 16:14:52 +0300
Subject: [PATCH 06/19] repseqio 1.2.5 release

---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 3271c07b2..1ae76cde0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -44,14 +44,14 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <milib.version>1.7</milib.version>
+        <milib.version>1.7.1</milib.version>
     </properties>
 
     <dependencies>
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.2.5-SNAPSHOT</version>
+            <version>1.2.5</version>
         </dependency>
 
         <dependency>

From 0fcaafdcd9fbe3843654318f3c477bdd7c37dc47 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Mon, 30 Jan 2017 16:51:20 +0300
Subject: [PATCH 07/19] Probable fix for problem with GeneFeature.intersection
 method.

---
 pom.xml                                                         | 2 +-
 .../java/com/milaboratory/mixcr/export/FeatureExtractors.java   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 1ae76cde0..f261c4c25 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,7 @@
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.2.5</version>
+            <version>1.2.6-SNAPSHOT</version>
         </dependency>
 
         <dependency>
diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
index 2eeb793d1..67d3ab537 100644
--- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
+++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -130,7 +130,7 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
             if (smallTargetRage == null)
                 return "-";
 
-            GeneFeature intersectionBigAligned = GeneFeature.intersection(bigGeneFeature, alignedFeature);
+            GeneFeature intersectionBigAligned = GeneFeature.intersectionStrict(bigGeneFeature, alignedFeature);
 
             for (int i = 0; i < hit.numberOfTargets(); ++i) {
                 Alignment<NucleotideSequence> alignment = hit.getAlignment(i);

From c369a103a08664d89164859bc66210d11234ac6a Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Tue, 31 Jan 2017 17:13:09 +0300
Subject: [PATCH 08/19] Fix for exception in default exportClones.

---
 .../mixcr/export/FeatureExtractors.java             | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
index 67d3ab537..40a9ded14 100644
--- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
+++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -31,10 +31,6 @@ void validate(GeneFeature[] features) {
             if (features.length == 2 && !features[1].contains(features[0]))
                 throw new IllegalArgumentException(String.format("%s: Base feature %s does not contain relative feature %s",
                         command, GeneFeature.encode(features[1]), GeneFeature.encode(features[0])));
-            for (GeneFeature feature : features)
-                if (feature.getGeneType() == null)
-                    throw new IllegalArgumentException(String.format("%s: Gene feature %s covers several gene types " +
-                            "(not possible to select corresponding alignment)", command, GeneFeature.encode(feature)));
 
             //todo bigfeature nofloating bounds
         }
@@ -92,6 +88,15 @@ static abstract class MutationsExtractor extends WithHeader {
             super(command, description, nArgs, hPrefix, sPrefix);
         }
 
+        @Override
+        void validate(GeneFeature[] features) {
+            super.validate(features);
+            for (GeneFeature feature : features)
+                if (feature.getGeneType() == null)
+                    throw new IllegalArgumentException(String.format("%s: Gene feature %s covers several gene types " +
+                            "(not possible to select corresponding alignment)", command, GeneFeature.encode(feature)));
+        }
+
         @Override
         protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
             GeneFeature smallGeneFeature = parameters[0];

From af7eec6e65ac91a75d46d17f8ea7dfc1dd0bd4ec Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:07:27 +0300
Subject: [PATCH 09/19] Prepare for travis-ci

---
 .gitmodules |  3 +++
 .travis.yml | 19 +++++++++++++++++++
 repseqio    |  1 +
 3 files changed, 23 insertions(+)
 create mode 100644 .travis.yml
 create mode 160000 repseqio

diff --git a/.gitmodules b/.gitmodules
index e69de29bb..6e4efa51e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "repseqio"]
+	path = repseqio
+	url = https://github.com/repseqio/repseqio.git
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 000000000..7b739c0b1
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,19 @@
+language: java
+
+sudo: false
+
+git:
+  submodules: false
+
+before_install:
+  - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
+  - git submodule update --init --recursive
+  - cd repseqio/milib && mvn clean install -DskipTests && cd ..
+  - mvn clean install -DskipTests && cd ..
+
+jdk:
+  - openjdk7
+
+cache:
+  directories:
+  - $HOME/.m2
\ No newline at end of file
diff --git a/repseqio b/repseqio
new file mode 160000
index 000000000..199a917a8
--- /dev/null
+++ b/repseqio
@@ -0,0 +1 @@
+Subproject commit 199a917a81c2f9faf89802f4ad359c1c58946b30

From 4e195bb4648b2f4b3569dd8d9be0d9d398c99f2a Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:10:53 +0300
Subject: [PATCH 10/19] Bump.

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 7b739c0b1..308771fb1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,4 +16,4 @@ jdk:
 
 cache:
   directories:
-  - $HOME/.m2
\ No newline at end of file
+  - $HOME/.m2

From ccacdd6e4fa788dbc6f749014b43ee0a0b044454 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:17:27 +0300
Subject: [PATCH 11/19] Batch-mode submodule build.

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 308771fb1..10c0dc31e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,8 +8,8 @@ git:
 before_install:
   - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
   - git submodule update --init --recursive
-  - cd repseqio/milib && mvn clean install -DskipTests && cd ..
-  - mvn clean install -DskipTests && cd ..
+  - cd repseqio/milib && mvn clean install -DskipTests -B && cd ..
+  - mvn clean install -DskipTests -B && cd ..
 
 jdk:
   - openjdk7

From 2ae00d1e430dfb020e6bd61da1bc7ac2ac96c72f Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:27:28 +0300
Subject: [PATCH 12/19] Test output cleanup. Cache of repseqio .cache folder.

---
 .travis.yml                                                   | 1 +
 .../partialassembler/PartialAlignmentsAssemblerTest.java      | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 10c0dc31e..8b5b8da4f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,3 +17,4 @@ jdk:
 cache:
   directories:
   - $HOME/.m2
+  - ./repseqio/.cache
diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
index a78082fae..70b022cf8 100644
--- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
+++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
@@ -250,8 +250,8 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr
             try (final VDJCAlignmentsReader reader = inputAlignments.resultReader()) {
                 assembler.searchOverlaps(reader);
             }
-            assembler.writeReport(new ReportHelper(System.out));
-            System.out.println("\n");
+            //assembler.writeReport(new ReportHelper(System.out));
+            //System.out.println("\n");
         }
 
 

From 86aed5ba7ac7119c51e9d13506c52264cfe099a5 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:30:48 +0300
Subject: [PATCH 13/19] toprev

---
 .travis.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8b5b8da4f..9fbf327bf 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,8 +8,11 @@ git:
 before_install:
   - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
   - git submodule update --init --recursive
+  - rm -rf ./repseqio/.cache
+  - mv .cache ./repseqio/.cache
   - cd repseqio/milib && mvn clean install -DskipTests -B && cd ..
   - mvn clean install -DskipTests -B && cd ..
+  - mv ./repseqio/.cache .cache
 
 jdk:
   - openjdk7
@@ -17,4 +20,4 @@ jdk:
 cache:
   directories:
   - $HOME/.m2
-  - ./repseqio/.cache
+  - .cache

From 24f10437e167045611f5a5e8c02c535f6c459dd3 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:47:09 +0300
Subject: [PATCH 14/19] To previous.

---
 .../partialassembler/PartialAlignmentsAssemblerTest.java    | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
index 70b022cf8..e4d82f3a5 100644
--- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
+++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java
@@ -8,7 +8,6 @@
 import com.milaboratory.core.sequence.SequenceBuilder;
 import com.milaboratory.core.sequence.SequenceQuality;
 import com.milaboratory.mixcr.basictypes.*;
-import com.milaboratory.mixcr.cli.ReportHelper;
 import com.milaboratory.mixcr.util.RunMiXCR;
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
 import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets;
@@ -214,9 +213,8 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr
         params.alignerParameters.setAllowPartialAlignments(true);
 
         final RunMiXCR.AlignResult inputAlignments = RunMiXCR.align(params);
-        inputAlignments.report.writeReport(new ReportHelper(System.out));
-        System.out.println("\n");
-
+        //inputAlignments.report.writeReport(new ReportHelper(System.out));
+        //System.out.println("\n");
 
         for (VDJCAlignments al : inputAlignments.alignments) {
             for (GeneType gt : GeneType.VJC_REFERENCE) {

From 895ef450d23d63e2caa4eb9673f30b39efa23ed2 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 14:49:34 +0300
Subject: [PATCH 15/19] Travis CI Build Status

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 139f212a4..c12871e5f 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/milaboratory/mixcr.svg)](https://travis-ci.org/milaboratory/mixcr)
+
 ## Overview
 
 MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data.

From c307eeec4edb572c273565f2e818f673525477fa Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 15:17:06 +0300
Subject: [PATCH 16/19] Build script.

---
 build.sh | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100755 build.sh

diff --git a/build.sh b/build.sh
new file mode 100755
index 000000000..59ad4a494
--- /dev/null
+++ b/build.sh
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+# Linux readlink -f alternative for Mac OS X
+function readlinkUniversal() {
+    targetFile=$1
+
+    cd `dirname $targetFile`
+    targetFile=`basename $targetFile`
+
+    # iterate down a (possible) chain of symlinks
+    while [ -L "$targetFile" ]
+    do
+        targetFile=`readlink $targetFile`
+        cd `dirname $targetFile`
+        targetFile=`basename $targetFile`
+    done
+
+    # compute the canonicalized name by finding the physical path 
+    # for the directory we're in and appending the target file.
+    phys_dir=`pwd -P`
+    result=$phys_dir/$targetFile
+    echo $result
+}
+
+os=`uname`
+delta=100
+
+dir=""
+
+case $os in
+    Darwin)
+        dir=$(dirname "$(readlinkUniversal "$0")")
+    ;;
+    Linux)
+        dir="$(dirname "$(readlink -f "$0")")"
+    ;;
+    FreeBSD)
+        dir=$(dirname "$(readlinkUniversal "$0")")    
+    ;;
+    *)
+       echo "Unknown OS."
+       exit 1
+    ;;
+esac
+
+if [[ ! -f ${dir}/repseqio/milib/pom.xml ]];
+then
+  echo "Please init git submodules. Try:"
+  echo "git submodule update --init --recursive"
+  exit 1
+fi
+
+function error_exit {
+    echo -e "$1"
+    exit "${2:-1}"
+}
+
+GREEN='\033[0;32m'
+RED='\033[0;31m'
+NC='\033[0m' # No Color
+
+echo "Building MiLib."
+cd ${dir}/repseqio/milib
+mvn clean install -DskipTests -B || error_exit "${RED}Problem building MiLib!${NC}" 1
+
+echo "Building RepSeq.IO util/lib"
+cd ${dir}/repseqio
+mvn clean install -DskipTests -B || error_exit "${RED}Problem building RepSeq.IO util!${NC}" 1
+
+echo "Building MiXCR."
+cd ${dir}
+mvn clean install -DskipTests -B || error_exit "${RED}Problem building MiXCR util!${NC}" 1
+
+echo -e "${GREEN}Build successfull!${NC}"
+echo "The following is the output of \"mixcr -v\" command:"
+${dir}/mixcr -v || error_exit "${RED}Something went wrong!${NC}" 1
+echo -e "${GREEN}Everything seems OK!${NC}"
+echo ""
+echo "Add mixcr script from this folder to your PATH variable or add symlink to your bin folder."
+echo ""
+echo "MiXCR is free for Academic use. For commertial use please contact licensing@milaboratory.com ."
+echo ""
+echo "If you discover bugs or have any questions, contact us at https://github.com/milaboratory/mixcr/issues ."

From e8134b72f7f11519ef12296216dd01b764d211fe Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 15:23:34 +0300
Subject: [PATCH 17/19] Build instructions.

---
 README.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/README.md b/README.md
index c12871e5f..59fef64e7 100644
--- a/README.md
+++ b/README.md
@@ -44,6 +44,27 @@ For more details see documentation.
 
 Detailed documentation can be found at https://mixcr.readthedocs.io/
 
+## Build
+
+Dependancy:
+
+- Maven 3 (https://maven.apache.org/)
+
+To build MiXCR from source:
+
+- Refresh git submodules
+
+  ```
+  git submodule update --init --recursive
+  ```
+  
+- Run build script. First build may take several minuties to download sequences for built-in V/D/J/C gene libraries from NCBI.
+
+  ```
+  ./build.sh
+  ```
+  
+
 ## License
 
 Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail

From 6d8d63fbe4345e0edcc535279deba3095698e573 Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 15:36:23 +0300
Subject: [PATCH 18/19] Repseqio 1.2.6 release version.

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index f261c4c25..238120ef1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,7 @@
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.2.6-SNAPSHOT</version>
+            <version>1.2.6</version>
         </dependency>
 
         <dependency>

From 04140fb88e627b081d5124afe0188a8579f152de Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Sat, 4 Feb 2017 15:39:38 +0300
Subject: [PATCH 19/19] Release v2.0.4

---
 CHANGELOG         | 8 ++++++++
 CHANGELOG_CURRENT | 3 ---
 pom.xml           | 2 +-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index 4ed7d17fe..23727c437 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,12 @@
 
+MiXCR 2.0.4 ( 4 Feb 2017)
+========================
+
+-- Fix for NPE in `-nMutations ...` `-aaMutations ...`
+-- Correct visualization of D gene P segments in exportAlignmentsPretty
+-- minor: Fix for error in export when fields are given in the file
+
+
 MiXCR 2.0.3 (26 Dec 2016)
 ========================
 
diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
index 4f38ea9a5..e69de29bb 100644
--- a/CHANGELOG_CURRENT
+++ b/CHANGELOG_CURRENT
@@ -1,3 +0,0 @@
-Fix for NPE in `-nMutations ...` `-aaMutations ...`
-Correct visualization of D gene P segments in exportAlignmentsPretty
-minor: Fix for error in export when fields are given in the file
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 238120ef1..f228e010b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>