svreader/annotation.py

@@ -145,6 +145,7 @@ class AnnotateRecord(VCFRecord):
     def add_supporting_infos(self):
         supp_reads = self.variant_read_support()
         num_supp_samples = self.num_variant_samples()
+        #print(supp_reads, num_supp_samples)
         try:
             self.record.info['MAX_SUPP_READS'] = supp_reads
             self.record.info['NUM_SUPP_SAMPLES'] = num_supp_samples

svreader/lumpy.py

@@ -181,10 +181,15 @@ class LumpyReader(SVReader):
     def AreSamplesSpecified(self):
         return 1
 
+    # def getOrderedSamples(self):
+    #     if not hasattr(self.vcf_reader, "samples"):
+    #         return []
+    #     return self.vcf_reader.samples
+
     def getOrderedSamples(self):
-        if not hasattr(self.vcf_reader, "samples"):
-            return []
-        return self.vcf_reader.samples
+        samples = self.vcf_reader.header.samples
+        sample_names = [sample.rsplit('.')[0] for sample in samples]
+        return sample_names
 
     def SpecificFilterPass(self, record):
         # First try after sensibility analysis with Mathieu
@@ -219,4 +224,5 @@ class LumpyWriter(SVWriter):
         if self._isopen:
             self.vcf_writer.close()
         else:  # nothing was written
+            # Make sure appropriate samples are added to the vcf
             self._dumpemptyvcf()