Use annotated VCF as output

Author: bbimber

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

@@ -523,7 +523,9 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             getPipelineCtx().getLogger().warn("Consensus ambiguities from bcftools and lofreq did not match: " + bcfToolsConsensusNs + " / " + lofreqConsensusNs);
         }
 
-        output.addSequenceOutput(outputVcfSnpEff, "LoFreq: " + rs.getName(), CATEGORY, rs.getReadsetId(), null, referenceGenome.getGenomeId(), description);
+        output.addIntermediateFile(outputVcfSnpEff);
+        output.addIntermediateFile(new File(outputVcfSnpEff.getPath() + ".tbi"));
+        output.addSequenceOutput(loFreqAllVcf, "LoFreq: " + rs.getName(), CATEGORY, rs.getReadsetId(), null, referenceGenome.getGenomeId(), description);
         output.addSequenceOutput(coverageOut, "Depth of Coverage: " + rs.getName(), "Depth of Coverage", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
         output.addSequenceOutput(consensusFastaLoFreq, "Consensus: " + rs.getName(), "Viral Consensus Sequence", rs.getReadsetId(), null, referenceGenome.getGenomeId(), description);