Fix bug where nonlinear_dist is not being properly enabled

mkirsche · Aug 10, 2021 · 6249550 · 6249550
1 parent 93b073d
commit 6249550
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Showing 7 changed files with 4 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 
 JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
 
-Version 1.1.3
+Version 1.1.4
 
 This tool is used to merge structural variants (SVs) across samples.  Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values.  Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
 

diff --git a/jasmine.jar b/jasmine.jar
diff --git a/jasmine_igv.jar b/jasmine_igv.jar
diff --git a/jasmine_iris.jar b/jasmine_iris.jar
diff --git a/jasmine_split.jar b/jasmine_split.jar
diff --git a/src/Settings.java b/src/Settings.java
@@ -78,7 +78,7 @@ public class Settings {
 	static void usage()
 	{
 		System.out.println();
-		System.out.println("Jasmine version 1.1.3");
+		System.out.println("Jasmine version 1.1.4");
 		System.out.println("Usage: jasmine [args]");
 		System.out.println("  Example: jasmine file_list=filelist.txt out_file=out.vcf");
 		System.out.println();
@@ -185,7 +185,7 @@ static void parseArgs(String[] args) throws Exception
 	{
 		if(args.length == 1 && (args[0].equalsIgnoreCase("--version") || args[0].equalsIgnoreCase("-v")))
 		{
-			System.out.println("Jasmine version 1.1.3");
+			System.out.println("Jasmine version 1.1.4");
 			System.exit(0);
 		}
 		if(args.length == 0)

diff --git a/src/VariantInput.java b/src/VariantInput.java
@@ -187,7 +187,7 @@ else if(Settings.PER_SAMPLE_DISTS != null && Settings.PER_SAMPLE_DISTS.length >
 		}
 
 		// Next, check if there is a length-based threshold
-		else if(Settings.MAX_DIST_LINEAR > 0)
+		else if(Settings.USE_LINEAR_THRESHOLD && Settings.MAX_DIST_LINEAR > 0)
 		{
 			maxDist = (int)(Settings.MAX_DIST_LINEAR * Math.abs(entry.getLength()) + 0.5);
 			if(Settings.MAX_DIST_SET)