Bugfixes to GenotypeGVCFs when run using multple GVCFs

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -312,6 +312,8 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
             if (filesToProcess.size() > 1)
             {
                 inputVcf = combineInputs(ctx, filesToProcess, genomeId);
+                ctx.getFileManager().addIntermediateFile(inputVcf);
+                ctx.getFileManager().addIntermediateFile(new File(inputVcf.getPath() + ".tbi"));
             }
             else
             {
@@ -387,8 +389,13 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
 
         private File combineInputs(JobContext ctx, List<File> inputFiles, int genomeId) throws PipelineJobException
         {
-            // TODO: this should ultimately be expanded to include smarter merge with GenomicsDB
-            // Also consider allowing the input to be a folder with per-contig gVCFs
+            for (File f : inputFiles)
+            {
+                if (!GenotypeGVCFsWrapper.GVCF.isType(f))
+                {
+                    throw new PipelineJobException("If multiple inputs are used, all must be gVCFs: " + f.getName());
+                }
+            }
 
             String basename = getBasename(ctx);
             File combined = new File(ctx.getOutputDir(), basename + ".combined.gvcf.gz");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java

@@ -80,7 +80,7 @@ else if (inputFile.isDirectory())
         }
     }
 
-    private static FileType GVCF = new FileType(".g.vcf", FileType.gzSupportLevel.SUPPORT_GZ);
+    public static FileType GVCF = new FileType(Arrays.asList(".g.vcf", ".gvcf"), ".g.vcf", FileType.gzSupportLevel.SUPPORT_GZ);
 
     public static List<File> copyVcfsLocally(Collection<File> inputGVCFs, Collection<File> toDelete, File localWorkDir, Logger log, boolean isResume) throws PipelineJobException
     {