In GtcToVcf, set infinite values to missing ('.') in the VCF. (#1777)

In GtcToVcf, set infinite values to missing ('.') in the VCF. In VcfToAdpc, if value is a '?' (which was what had been encoded for infinite) treat as missing.
broadinstitute · Feb 17, 2022 · a03ed41 · a03ed41
1 parent 1d4dc0b
commit a03ed41
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diff --git a/src/main/java/picard/arrays/GtcToVcf.java b/src/main/java/picard/arrays/GtcToVcf.java
@@ -508,7 +508,7 @@ public Genotype getGenotype(final String sampleName,
     }
 
     public static String formatFloatForVcf(final float value) {
-        if (Float.isNaN(value)) {
+        if (Float.isNaN(value) || Float.isInfinite(value)) {
             return DOT;
         }
         return df.format(value);

diff --git a/src/main/java/picard/arrays/VcfToAdpc.java b/src/main/java/picard/arrays/VcfToAdpc.java
@@ -215,7 +215,7 @@ private int getUnsignedShortAttributeAsInt(final Genotype genotype, final String
 
     private Float getFloatAttribute(final Genotype genotype, final String key) {
         final Object value = genotype.getAnyAttribute(key);
-        if (value != null) {
+        if ((value != null) && (!value.equals("?"))) {
             return Float.parseFloat(value.toString());
         }
         return null;