--- a
+++ b/singlecellmultiomics/fragment/scartrace.py
@@ -0,0 +1,67 @@
+from singlecellmultiomics.utils.sequtils import reverse_complement
+from singlecellmultiomics.fragment import Fragment
+
+class ScarTraceFragment(Fragment):
+    """
+    Fragment definition for ScarTrace
+    """
+
+    def __init__(self, reads,scartrace_r1_primers=None, **kwargs):
+        Fragment.__init__(self, reads,  **kwargs)
+        self.scartrace_r1_primers = scartrace_r1_primers
+        assert scartrace_r1_primers is not None, 'please supply primer sequences'
+
+    # remove the set_umi function
+    def set_umi(self, **kwargs):
+        pass
+
+    def is_valid(self):
+        """ Check if R1 starts with the defined primers and if R2 and R1 are mapped
+
+        Returns:
+            bool
+        """
+        if not self.has_R1() or not self.has_R2():
+            if not self.has_R1():
+                self.set_meta('fr','no_R1', as_set=True)
+            if not self.has_R2():
+                self.set_meta('fr','no_R2', as_set=True)
+            return False
+
+        if self[0].is_unmapped or self[1].is_unmapped:
+            self.set_meta('fr','unmapped_mate', as_set=True)
+            return False
+
+        r1_seq = self.get_R1().seq
+
+        if self.get_R1().is_reverse:
+            r1_seq = reverse_complement(r1_seq)
+
+        if any( r1_seq.startswith(primer) for primer in self.scartrace_r1_primers ):
+            # Good
+            return True
+
+        self.set_meta('fr','primer_not_matching', as_set=True)
+        # Bad
+        return False
+
+
+
+
+    # Replace the equality function
+    def __eq__(self, other):  # other can also be a Molecule!
+        # Make sure fragments map to the same strand, cheap comparisons
+        if self.sample != other.sample:
+            return False
+
+        if self.strand != other.strand:
+            return False
+
+        if min(abs(self.span[1] -
+                   other.span[1]), abs(self.span[2] -
+                                       other.span[2])) > self.assignment_radius:
+            return False
+
+        # Sample matches and starting position is within the defined span
+        # radius
+        return True