From cbcd3e17d28a3c0eab2ce610a17758b029778b8e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 15 Nov 2017 10:50:19 +0000
Subject: [PATCH] JAL-2835 take all CSQ fields; catch invalid field match
 patterns

---
 src/jalview/io/vcf/VCFLoader.java |   29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 960615a..2847bd7 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -1,14 +1,5 @@
 package jalview.io.vcf;
 
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import htsjdk.variant.vcf.VCFHeaderLineCount;
-import htsjdk.variant.vcf.VCFHeaderLineType;
-import htsjdk.variant.vcf.VCFInfoHeaderLine;
-
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Dna;
 import jalview.api.AlignViewControllerGuiI;
@@ -37,6 +28,16 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+import htsjdk.variant.vcf.VCFHeaderLineCount;
+import htsjdk.variant.vcf.VCFHeaderLineType;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
 
 /**
  * A class to read VCF data (using the htsjdk) and add variants as sequence
@@ -56,7 +57,7 @@ public class VCFLoader
 
   private static final String DEFAULT_VCF_FIELDS = "AF,AC*";
 
-  private static final String DEFAULT_VEP_FIELDS = "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
+  private static final String DEFAULT_VEP_FIELDS = ".*";// "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
 
   /*
    * keys to fields of VEP CSQ consequence data
@@ -156,7 +157,7 @@ public class VCFLoader
     al = alignment;
 
     // map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
-    assemblyMappings = new HashMap<String, Map<int[], int[]>>();
+    assemblyMappings = new HashMap<>();
   }
 
   /**
@@ -420,7 +421,13 @@ public class VCFLoader
     String[] tokens = pref.split(",");
     for (String token : tokens)
     {
+      try
+      {
       patterns.add(Pattern.compile(token.toUpperCase()));
+      } catch (PatternSyntaxException e)
+      {
+        System.err.println("Invalid pattern ignored: " + token);
+      }
     }
     return patterns;
   }
-- 
1.7.10.2