From 4567ee2f18f8c16ce6800ec7f888638bd4fe731a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 2 Oct 2017 18:52:23 +0100
Subject: [PATCH] JAL-2738 code tidy up, null checks &c

---
 src/jalview/io/vcf/VCFLoader.java |   29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 89b1d2a..8dab1d6 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -181,7 +181,7 @@ public class VCFLoader
       /*
        * note offset of CSQ ALLELE_NUM field if it is declared
        */
-      findAlleleNumberFieldIndex();
+      locateCsqFields();
 
       // check if reference is wrt assembly19 (GRCh37)
       // todo may need to allow user to specify reference assembly?
@@ -239,15 +239,20 @@ public class VCFLoader
   }
 
   /**
-   * If the CSQ INFO header declares that ALLELE_NUM is included in the data,
-   * record its (pipe-delimited) offset in each (comma-delimited) consequence
-   * block; CSQ fields are declared in the CSQ INFO Description e.g.
+   * Records the position of fields for ALLELE_NUM and Feature defined in the
+   * CSQ INFO header (if there is one). CSQ fields are declared in the CSQ INFO
+   * Description e.g.
    * <p>
    * Description="Consequence ...from ... VEP. Format: Allele|Consequence|...
    */
-  protected void findAlleleNumberFieldIndex()
+  protected void locateCsqFields()
   {
     VCFInfoHeaderLine csqInfo = header.getInfoHeaderLine(CSQ);
+    if (csqInfo == null)
+    {
+      return;
+    }
+
     String desc = csqInfo.getDescription();
     if (desc != null)
     {
@@ -303,7 +308,6 @@ public class VCFLoader
         /*
          * nucleotide-to-nucleotide mapping e.g. transcript to CDS
          */
-        // TODO no DBRef to CDS is added to transcripts
         List<SequenceFeature> features = seq.getFeatures()
                 .getPositionalFeatures(SequenceOntologyI.SEQUENCE_VARIANT);
         for (SequenceFeature sf : features)
@@ -689,8 +693,17 @@ public class VCFLoader
        * these may be per alternate allele (INFO[key].Number = 'A') 
        * or per allele including reference (INFO[key].Number = 'R') 
        */
-      VCFHeaderLineCount number = header.getInfoHeaderLine(key)
-              .getCountType();
+      VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(key);
+      if (infoHeader == null)
+      {
+        /*
+         * can't be sure what data belongs to this allele, so
+         * play safe and don't take any
+         */
+        continue;
+      }
+
+      VCFHeaderLineCount number = infoHeader.getCountType();
       int index = altAlelleIndex;
       if (number == VCFHeaderLineCount.R)
       {
-- 
1.7.10.2