supp_reads becomes max support reads

svreader/Annotate.py

@@ -40,6 +40,10 @@ class AnnotatedRecord(object):
     def pos(self):
         return self.record.pos
 
+    @property
+    def start(self):
+        return self.record.pos
+
     @property
     def chrom(self):
         return self.record.chrom
@@ -48,6 +52,10 @@ class AnnotatedRecord(object):
     def stop(self):
         return self.record.stop
 
+    @property
+    def end(self):
+        return self.record.stop
+
     @property
     def svtype(self):
         return self._sv_type
@@ -72,7 +80,7 @@ class AnnotatedRecord(object):
         return sum([s.isVariant for s in self.samples])
 
     def variant_read_support(self):
-        return sum([s.AltSupport() for s in self.samples])
+        return max([s.AltSupport() for s in self.samples])
 
     def qual(self):
         return sum([s.SQ_score() for s in self.samples if s.isVariant])
@@ -84,7 +92,7 @@ class AnnotatedRecord(object):
         supp_reads = self.variant_read_support()
         num_supp_samples = self.num_variant_samples()
         try:
-            self.record.info['SUPP_READS'] = supp_reads
+            self.record.info['MAX_SUPP_READS'] = supp_reads
             self.record.info['NUM_SUPP_SAMPLES'] = num_supp_samples
         except KeyError:
             eprint("SUPP_READS or NUM_SUPP_SAMPLES absent from record info keys")
@@ -130,7 +138,6 @@ class AnnotatedRecordSample(object):
 class VCFReader(SVReader):
 
     def __init__(self, file_name, sv_to_report=None):
-<<<<<<< HEAD
         super(VCFReader, self).__init__(file_name)
         self.filename = file_name
         self.sv_to_report = sv_to_report
@@ -165,8 +172,8 @@ class VCFReader(SVReader):
     def add_metadata(self):
         self.addInfo("SOURCEID", 1, "String",
                      "The source sv identifier")
-        self.addInfo("SUPP_READS", 1, "Integer",
-                     "Number of supporting reads")
+        self.addInfo("MAX_SUPP_READS", 1, "Integer",
+                     "Max number of supporting reads")
         self.addInfo("NUM_SUPP_SAMPLES", 1, "Integer",
                      "Number of supporting samples")
         self.addFilter("LOWSUPPORT",

svreader/pindel.py

@@ -284,7 +284,7 @@ class PindelRecord(SVRecord):
 
     @property
     def sv_len(self):
-        return self.__svlen
+        return self.__sv_len
 
     def addbatch2Id(self, batch=None):
         if batch: