Add index information for sample declaration

src/ng6/sample.py

@@ -22,13 +22,14 @@ class Sample(object):
     
     AVAILABLE_TYPES = ["pe", "se", "ose", "ope", "mp"]
     
-    def __init__(self, sample_id, reads1, reads2 = None, name = None, description = None, type = None, 
+    def __init__(self, sample_id, reads1, reads2 = None,index = None, name = None, description = None, type = None, 
                  insert_size = None, species = None, nb_sequences = None, full_size = None, id = None ):
         self.sample_id = sample_id
         self.name = name
         self.description = description
         self.reads1 = reads1
         self.reads2 = reads2
+        self.index = index
         self.insert_size = insert_size
         self.nb_sequences = nb_sequences
         self.full_size = full_size
@@ -42,6 +43,9 @@ class Sample(object):
         if isinstance(reads2, str) :
             self.reads2 = [reads2]
             
+        if isinstance(index, str) :
+            self.index = [index]
+        
         if self.type is None:
             if self.reads2 :
                 self.type = self.AVAILABLE_TYPES[0]
@@ -94,12 +98,13 @@ class Sample(object):
             raise UnsavedRunError()
     
     def __str__(self, *args, **kwargs):
-        return "sid={sid}; name={name}; desc={desc}; r1={r1}; r2={r2}; insize={insize}; nbs={nbs}; fsize={fsize}; spec={spec}; t={t}".format(
+        return "sid={sid}; name={name}; desc={desc}; r1={r1}; r2={r2}; i={i}; insize={insize}; nbs={nbs}; fsize={fsize}; spec={spec}; t={t}".format(
         sid = self.sample_id or '',
         name = self.name or '',
         desc = self.description or '',
         r1 = self.reads1 or [],
         r2 = self.reads2 or [],
+        i = self.index or [],
         insize = self.insert_size or '',
         nbs = self.nb_sequences or '',
         fsize = self.full_size or '',