Merge branch 'release/v1.1.1'

milaboratory · Sep 10, 2015 · 14428c2 · 14428c2
2 parents 75ab7ac + 7b49b91
commit 14428c2
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Showing 5 changed files with 19 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -11,5 +11,6 @@
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 *.iml
+.idea/
 target
 src/main/java/com/milaboratory/mitools/parsers
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,9 @@
 
+MiTools 1.1.1 (11 Sep 2015)
+========================
+
+
+
 MiTools 1.1 (21 Aug 2015)
 ========================
 

diff --git a/pom.xml b/pom.xml
@@ -19,7 +19,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mitools</artifactId>
-    <version>1.1</version>
+    <version>1.1.1</version>
     <packaging>jar</packaging>
     <name>MiTools</name>
     <url>http://milaboratory.com/</url>
@@ -120,6 +120,11 @@
             <artifactId>jcommander</artifactId>
             <version>1.30</version>
         </dependency>
+        <dependency>
+            <groupId>cc.redberry</groupId>
+            <artifactId>pipe</artifactId>
+            <version>0.9.4</version>
+        </dependency>
     </dependencies>
 
     <properties>

diff --git a/src/main/java/com/milaboratory/mitools/cli/MergeAction.java b/src/main/java/com/milaboratory/mitools/cli/MergeAction.java
@@ -46,7 +46,8 @@ public class MergeAction implements Action {
     @Override
     public void go(ActionHelper helper) throws Exception {
         final MismatchOnlyPairedReadMerger merger = new MismatchOnlyPairedReadMerger(actionParameters.overlap,
-                actionParameters.similarity);
+                actionParameters.similarity, MismatchOnlyPairedReadMerger.DEFAULT_MAX_SCORE_VALUE,
+                !actionParameters.sameStrand);
 
         long total = 0, overlapped = 0;
         try (PairedFastqReader reader = new PairedFastqReader(actionParameters.getR1(), actionParameters.getR2());
@@ -151,6 +152,10 @@ public static final class MergingParameters extends ActionParameters {
                 names = {"-d", "--discard-header"})
         boolean discardHeader;
 
+        @Parameter(description = "Assume that reads are on the same strand (opposite of raw Illumina reads orientation).",
+                names = {"-ss", "--same-strand"})
+        boolean sameStrand;
+
         @Parameter(description = "Minimal overlap.",
                 names = {"-p", "--overlap"}, validateWith = PositiveInteger.class)
         int overlap = 15;

diff --git a/src/main/java/com/milaboratory/mitools/merger/MismatchOnlyPairedReadMerger.java b/src/main/java/com/milaboratory/mitools/merger/MismatchOnlyPairedReadMerger.java
@@ -31,7 +31,7 @@
 
 public final class MismatchOnlyPairedReadMerger implements Processor<PairedRead, PairedReadMergingResult>,
         java.io.Serializable {
-    public static final int DEFAULT_MAX_SCORE_VALUE = 45;
+    public static final int DEFAULT_MAX_SCORE_VALUE = 50;
     final int minOverlap;
     final double maxMismatchesPart;
     final int maxScoreValue;