Dont sort samples when merging VCFs

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -16,10 +16,8 @@
 package org.labkey.sequenceanalysis;
 
 import htsjdk.samtools.SAMException;
-import htsjdk.tribble.AbstractFeatureReader;
-import htsjdk.tribble.FeatureReader;
 import htsjdk.tribble.TribbleException;
-import htsjdk.variant.vcf.VCFCodec;
+import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
@@ -5115,13 +5113,13 @@ public ApiResponse execute(OutputFilesForm form, BindException errors) throws Ex
             return new ApiSimpleResponse(ret);
         }
 
-        public List<String> getSamplesForVcf(File vcf) throws IOException
+        public List<String> getSamplesForVcf(File vcf)
         {
-            try (FeatureReader reader = AbstractFeatureReader.getFeatureReader(vcf.getPath(), new VCFCodec(), false))
+            try (VCFFileReader reader = new VCFFileReader(vcf))
             {
-                VCFHeader header = (VCFHeader)reader.getHeader();
+                VCFHeader header = reader.getFileHeader();
 
-                return header.getSampleNamesInOrder();
+                return header.getGenotypeSamples();
             }
         }
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -384,14 +384,6 @@ public static File processVCF(File input, Integer libraryId, JobContext ctx, Res
         {
             ctx.getLogger().info("Starting to run: " + stepCtx.getProvider().getLabel());
 
-            //To debug sample name issue:
-            try (VCFFileReader reader = new VCFFileReader(input))
-            {
-                VCFHeader header = reader.getFileHeader();
-                ctx.getLogger().info("Total samples: " + header.getSampleNamesInOrder().size());
-                ctx.getLogger().info("Sample names: " + StringUtils.join(header.getSampleNamesInOrder(), ","));
-            }
-
             ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running: " + stepCtx.getProvider().getLabel());
             stepIdx++;
 
@@ -441,14 +433,6 @@ public static File processVCF(File input, Integer libraryId, JobContext ctx, Res
                 ctx.getJob().getLogger().info("passing variants: " + getVCFLineCount(currentVCF, ctx.getJob().getLogger(), true));
                 ctx.getJob().getLogger().debug("index exists: " + (new File(currentVCF.getPath() + ".tbi")).exists());
 
-                //To debug sample name issue:
-                try (VCFFileReader reader = new VCFFileReader(input))
-                {
-                    VCFHeader header = reader.getFileHeader();
-                    ctx.getLogger().debug("Total samples in output: " + header.getSampleNamesInOrder().size());
-                    ctx.getLogger().debug("Sample names in output: " + StringUtils.join(header.getSampleNamesInOrder(), ","));
-                }
-
                 try
                 {
                     SequenceAnalysisService.get().ensureVcfIndex(currentVCF, ctx.getJob().getLogger(), true);

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

@@ -77,7 +77,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         try (VCFFileReader reader = new VCFFileReader(inputVCF); VariantContextWriter writer = builder.build())
         {
             VCFHeader header = reader.getFileHeader();
-            List<String> samples = header.getSampleNamesInOrder();
+            List<String> samples = header.getGenotypeSamples();
             List<String> remappedSamples = new ArrayList<>();
 
             int totalRenamed = 0;

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

@@ -462,9 +462,9 @@ public static File combineVcfs(List<File> files, ReferenceGenome genome, File ou
 
                 if (samples.isEmpty())
                 {
-                    samples.addAll(header.getSampleNamesInOrder());
+                    samples.addAll(header.getGenotypeSamples());
                 }
-                else if (!samples.equals(header.getSampleNamesInOrder()))
+                else if (!samples.equals(header.getGenotypeSamples()))
                 {
                     throw new IllegalArgumentException("Samples list different between VCF headers!  Encountered for: " + x.getPath());
                 }