Parse Floats from GtcToVcf in VcfToAdpc (#1436)

* remove comma from floats from GtcToVcf * Add test for NORMX and NORMY over 1000
broadinstitute · Dec 9, 2019 · a3021a7 · a3021a7
1 parent 0c82cd4
commit a3021a7
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Showing 3 changed files with 3 additions and 10 deletions.
diff --git a/src/main/java/picard/arrays/GtcToVcf.java b/src/main/java/picard/arrays/GtcToVcf.java
@@ -74,7 +74,6 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -166,14 +165,8 @@ public class GtcToVcf extends CommandLineProgram {
 
     private static ReferenceSequenceFile refSeq;
 
-    private static final DecimalFormat df = new DecimalFormat();
-
     private static final String DOT = ".";
 
-    static {
-        df.setMaximumFractionDigits(3);
-    }
-
     @Override
     protected boolean requiresReference() {
         return true;
@@ -480,7 +473,7 @@ public static String formatFloatForVcf(final float value) {
         if (Float.isNaN(value)) {
             return DOT;
         }
-        return df.format(value);
+        return Float.toString(value);
     }
 
     /**

diff --git a/src/main/java/picard/arrays/VcfToAdpc.java b/src/main/java/picard/arrays/VcfToAdpc.java
@@ -43,7 +43,6 @@
 import picard.cmdline.StandardOptionDefinitions;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 

diff --git a/testdata/picard/arrays/illumina/Test.gtc_records.csv b/testdata/picard/arrays/illumina/Test.gtc_records.csv
@@ -1,4 +1,5 @@
 139,3304,3,0.9317507,0.008933085,1.1312464,1.1401795,0.99497294,1.0,-0.02116632
 655,1941,0,0.09023222,0.14054315,0.67860323,0.8191464,0.86998993,0.7306291,0.36733368
 1645,278,1,0.60272825,0.42509562,0.07603522,0.5011308,0.11267817,0.0,-0.34964624
-2243,1889,2,0.92726856,0.5817963,0.6338157,1.2156119,0.5272261,0.5384257,-0.103277266
+2243,1889,2,0.92726856,0.5817963,0.6338157,1.2156119,0.5272261,0.5384257,-0.103277266
+141,2005,2,0.9317507,1290.3258096018144,1612.9033,1.1401795,0.99497294,1.0,-0.02116632