Merge pull request #198 from BimberLab/23.3_fb_merge

Merge 22.11 into 23.3

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -77,6 +77,9 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs.add(inputVCF.getPath());
 
         plinkArgs.add("--make-bed");
+        
+        // Added since KING is designed for plink1.9. This avoids the "Too many first alleles as the major allele" error.
+        plinkArgs.add("--maj-ref");        
 
         boolean limitToChromosomes = getProvider().getParameterByName("limitToChromosomes").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, true);
         if (limitToChromosomes)

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java

@@ -338,6 +338,16 @@ public void exec(Results rs) throws SQLException
 
         //UCSC is a main source of chain files, so deal with their quirks:
         // https://genome.ucsc.edu/cgi-bin/hgGateway
+        if (refName.startsWith("chr0"))
+        {
+            // Allow chr01, chr1 -> 1
+            String toTest = refName.replaceFirst("chr0", "");
+            if (cachedReferences.containsKey(toTest))
+            {
+                return cachedReferences.get(toTest);
+            }
+        }
+
         if (refName.startsWith("chr"))
         {
             String toTest = refName.replaceFirst("chr", "");