Include FASTA reference in specHLA/samtools

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SpecHlaAnalysis.java

@@ -54,13 +54,20 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
     {
         AnalysisOutputImpl output = new AnalysisOutputImpl();
 
+        File gzippedFasta = referenceGenome.getWorkingFastaFileGzipped();
+        if (!gzippedFasta.exists())
+        {
+            throw new PipelineJobException("Missing file: " + gzippedFasta.getPath());
+        }
+
         File subsetBam = FileUtil.appendName(outputDir, FileUtil.getBaseName(inputBam) + ".subset.bam");
         SamtoolsRunner sr = new SamtoolsRunner(getWrapper().getLogger());
         sr.execute(Arrays.asList(
                 sr.getSamtoolsPath().getPath(),
                 "view",
                 "-h",
                 "-F", "12", //This selects pairs where either mate is mapped
+                "-T", gzippedFasta.getPath(),
                 "-o", subsetBam.getPath(),
                 inputBam.getPath()
         ));