Merge branch 'spikes/mungo' into features/JAL-1793VCF

Conflicts:
	src/jalview/ext/htsjdk/HtsContigDb.java
	src/jalview/io/vcf/VCFLoader.java
	test/jalview/ext/htsjdk/TestHtsContigDb.java
	test/jalview/io/vcf/VCFLoaderTest.java

diff --cc src/jalview/io/vcf/VCFLoader.java
index 20e3ccd,9addfaa..de2f18a
--- 1/src/jalview/io/vcf/VCFLoader.java
--- 2/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@@ -939,6 -1013,6 +1013,10 @@@ public class VCFLoade
    {
      String type = SequenceOntologyI.SEQUENCE_VARIANT;
  
++    /*
++     * could we associate Consequence data with this allele and feature (transcript)?
++     * if so, prefer the consequence term from that data
++     */
      if (csqAlleleFieldIndex == -1) // && snpEffAlleleFieldIndex == -1
      {
        /*
@@@ -947,14 -1021,10 +1025,6 @@@
        return type;
      }
  
--    /*
--     * can we associate Consequence data with this allele and feature (transcript)?
--     * if so, prefer the consequence term from that data
--     */
-     String consequence = getConsequenceForAlleleAndFeature(variant,
-             CSQ_FIELD,
-             altAlleleIndex, csqAlleleFieldIndex, csqAlleleNumberFieldIndex,
-             seq.getName().toLowerCase(), csqFeatureFieldIndex);
      if (consequence != null)
      {
        String[] csqFields = consequence.split(PIPE_REGEX);
@@@ -1163,36 -1235,21 +1243,20 @@@
  
    /**
     * Inspects CSQ data blocks (consequences) and adds attributes on the sequence
-    * feature for the current allele (and transcript if applicable)
+    * feature.
     * <p>
-    * Allele matching: if field ALLELE_NUM is present, it must match
-    * altAlleleIndex. If not present, then field Allele value must match the VCF
-    * Allele.
-    * <p>
-    * Transcript matching: if sequence name can be identified to at least one of
-    * the consequences' Feature values, then select only consequences that match
-    * the value (i.e. consequences for the current transcript sequence). If not,
-    * take all consequences (this is the case when adding features to the gene
-    * sequence).
+    * If <code>myConsequence</code> is not null, then this is the specific
+    * consequence data (pipe-delimited fields) that is for the current allele and
+    * transcript (sequence) being processed)
     * 
     * @param variant
-    * @param seq
     * @param sf
-    * @param altAlleleIndex
-    *          (0, 1..)
+    * @param myConsequence
     */
-   protected void addConsequences(VariantContext variant, SequenceI seq,
-           SequenceFeature sf, int altAlleleIndex)
+   protected void addConsequences(VariantContext variant, SequenceFeature sf,
+           String myConsequence)
    {
-     /*
-      * first try to identify the matching consequence
-      */
-     String myConsequence = getConsequenceForAlleleAndFeature(variant,
-             CSQ_FIELD, altAlleleIndex, csqAlleleFieldIndex,
-             csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
-             csqFeatureFieldIndex);
- 
      Object value = variant.getAttribute(CSQ_FIELD);
 -    // TODO if CSQ not present, try ANN (for SnpEff consequence data)?
  
      if (value == null || !(value instanceof List<?>))
      {