X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=7bf7791f2b5d98a916313b804098aa3d088e10e0;hb=e185cfd4324bf9e2277e25cfc280cc8a23e75360;hp=9831af7aa60fe6e27455d84eaba52d888b260c0b;hpb=1b0014839c94c711c09a94641ecb5036072bb5b3;p=jalview.git

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 9831af7..7bf7791 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -100,10 +100,12 @@ public class VCFLoader
    */
   private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY";
 
-  private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh38,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
+  private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh37,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
 
   private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
 
+  private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37
+
   /*
    * keys to fields of VEP CSQ consequence data
    * see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
@@ -263,7 +265,12 @@ public class VCFLoader
   public SequenceI loadVCFContig(String contig)
   {
     VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
-    String ref = headerLine == null ? null : headerLine.getValue();
+    if (headerLine == null)
+    {
+      Cache.log.error("VCF reference header not found");
+      return null;
+    }
+    String ref = headerLine.getValue();
     if (ref.startsWith("file://"))
     {
       ref = ref.substring(7);
@@ -282,7 +289,7 @@ public class VCFLoader
     }
     else
     {
-      System.err.println("VCF reference not found: " + ref);
+      Cache.log.error("VCF reference not found: " + ref);
     }
 
     return seq;
@@ -301,7 +308,7 @@ public class VCFLoader
     {
       VCFHeaderLine ref = header
               .getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
-      String reference = ref.getValue();
+      String reference = ref == null ? null : ref.getValue();
 
       setSpeciesAndAssembly(reference);
 
@@ -373,8 +380,13 @@ public class VCFLoader
    */
   protected void setSpeciesAndAssembly(String reference)
   {
+    if (reference == null)
+    {
+      Cache.log.error("No VCF ##reference found, defaulting to "
+              + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+      reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
+    }
     reference = reference.toLowerCase();
-    vcfSpecies = DEFAULT_SPECIES;
 
     /*
      * for a non-human species, or other assembly identifier,
@@ -397,6 +409,7 @@ public class VCFLoader
       }
     }
 
+    vcfSpecies = DEFAULT_SPECIES;
     prop = Cache.getProperty(VCF_SPECIES);
     if (prop != null)
     {
@@ -724,7 +737,7 @@ public class VCFLoader
     String species = seqCoords.getSpeciesId();
     String chromosome = seqCoords.getChromosomeId();
     String seqRef = seqCoords.getAssemblyId();
-    MapList map = seqCoords.getMap();
+    MapList map = seqCoords.getMapping();
 
     // note this requires the configured species to match that
     // returned with the Ensembl sequence; todo: support aliases?