diff --git a/rnacounter/draft_nocython.py b/rnacounter/draft_nocython.py
index 48a0350..5af59f0 100755
--- a/rnacounter/draft_nocython.py
+++ b/rnacounter/draft_nocython.py
@@ -400,7 +400,7 @@ def is_in(ftype,x,feat_id):
             # x is an exon: x == itself or x contains the piece
             # x is a piece: p == feat_id
 
-def estimate_expression_NNLS(ftype, pieces, ids, exons, norm_cst, stranded, weighted):
+def estimate_expression_NNLS(ftype, pieces, ids, exons, norm_cst, stranded):
     #--- Build the exons-transcripts structure matrix:
     # Lines are exons, columns are transcripts,
     # so that A[i,j]!=0 means "transcript Tj contains exon Ei".
@@ -412,11 +412,11 @@ def estimate_expression_NNLS(ftype, pieces, ids, exons, norm_cst, stranded, weig
             A[i,j] = 1. if is_in(ftype,p,f) else 0.
     #--- Build the exons RPKs vector
     E = asarray([p.rpk for p in pieces])
-    if weighted:
-        w = sqrt(asarray([p.length for p in pieces]))
-        W = diag(w)
-        A = dot(W,A)
-        E = multiply(E, w)
+    # Weights
+    w = sqrt(asarray([p.length for p in pieces]))
+    W = diag(w)
+    A = dot(W,A)
+    E = multiply(E, w)
     #--- Solve for transcripts RPK
     T,rnorm = nnls(A,E)
     #-- Same for antisense if stranded protocol
@@ -520,7 +520,6 @@ def process_chunk(ckexons, sam, chrom, options):
     threshold = options['threshold']
     fraglength = options['fraglength']
     exon_cutoff = options['exon_cutoff']
-    weighted = True
 
     #--- Regroup occurrences of the same exon from a different transcript
     exons = []
@@ -547,7 +546,7 @@ def process_chunk(ckexons, sam, chrom, options):
         for p in pieces + exons:
             p.transcripts = set(replace[t] for t in p.transcripts)
         for t,main in replace.iteritems():
-            if t!=main: synonyms.setdefault(main, set()).add(t)
+            synonyms.setdefault(main, set()).add(t)
     transcript_ids = sorted(t2p.keys())  # sort to have the same order in all outputs from same gtf
 
     #--- Count reads in each piece
@@ -590,37 +589,35 @@ def process_chunk(ckexons, sam, chrom, options):
     if 1 in types:
         method = methods.get(1,1)
         if method == 1:
-            transcripts = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded,weighted)
+            transcripts = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
         elif method == 0:
             transcripts = estimate_expression_raw("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
         for i,trans in enumerate(transcripts):
             trans.rpk = correct_fraglen_bias(trans.rpk, trans.length, fraglength)
-            syns = synonyms.get(trans.name, [])
+            syns = sorted(synonyms.get(trans.name, []))
             toadd = []
             for synonym in syns:
-                syns2 = set(syns)
-                syns2.remove(synonym)
-                syns2.add(trans.name)
-                toadd.append(GenomicObject(name=synonym, length=trans.length,
-                        rpk=trans.rpk, rpk_anti=trans.rpk_anti, count=trans.count, count_anti=trans.count_anti,
-                        chrom=trans.chrom, start=trans.start, end=trans.end,
-                        gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
-                        synonyms=','.join(syns2), ftype="transcript"))
+                if synonym != trans.name:
+                    toadd.append(GenomicObject(name=synonym, length=trans.length,
+                            rpk=trans.rpk, rpk_anti=trans.rpk_anti, count=trans.count, count_anti=trans.count_anti,
+                            chrom=trans.chrom, start=trans.start, end=trans.end,
+                            gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
+                            synonyms=','.join(syns), ftype="transcript"))
             toadd.sort(key=attrgetter('start','end'))
             transcripts = transcripts[:i+1] + toadd + transcripts[i+1:]
-            trans.synonyms = ','.join(syns) if len(syns)>0 else '.'
+            trans.synonyms = ','.join(syns) if len(syns)>1 else '.'
     # Genes - 0
     if 0 in types:
         method = methods.get(0,0)
         if method == 0:
             genes = estimate_expression_raw("gene",pieces,gene_ids,exons,norm_cst,stranded)
         elif method == 1:
-            genes = estimate_expression_NNLS("gene",pieces,gene_ids,exons,norm_cst,stranded,weighted)
+            genes = estimate_expression_NNLS("gene",pieces,gene_ids,exons,norm_cst,stranded)
         elif method == 2:
             if 1 in types and methods.get(1) == 1:
                 genes = genes_from_transcripts(transcripts)
             else:
-                transcripts2 = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded,weighted)
+                transcripts2 = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
                 genes = genes_from_transcripts(transcripts2)
                 transcripts2 = []
         for gene in genes:
@@ -632,7 +629,7 @@ def process_chunk(ckexons, sam, chrom, options):
             exons2 = pieces[:]  # !
         elif method == 1:
             exon_ids = [p.name for p in exons]
-            exons2 = estimate_expression_NNLS("exon",pieces,exon_ids,exons,norm_cst,stranded,weighted)
+            exons2 = estimate_expression_NNLS("exon",pieces,exon_ids,exons,norm_cst,stranded)
     # Introns - 3
     if 3 in types and intron_pieces:
         method = methods.get(3,0)
@@ -640,7 +637,7 @@ def process_chunk(ckexons, sam, chrom, options):
             introns2 = intron_pieces[:]   # !
         elif method == 1:
             intron_ids = [e.name for e in introns]
-            introns2 = estimate_expression_NNLS("intron",intron_pieces,intron_ids,introns,norm_cst,stranded,weighted)
+            introns2 = estimate_expression_NNLS("intron",intron_pieces,intron_ids,introns,norm_cst,stranded)
 
     print_output(output, genes,transcripts,exons2,introns2, threshold,stranded)
 
diff --git a/rnacounter/rnacounter.c b/rnacounter/rnacounter.c
index 03e298e..3a582bf 100644
--- a/rnacounter/rnacounter.c
+++ b/rnacounter/rnacounter.c
@@ -897,7 +897,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":573
+/* "rnacounter/rnacounter.pyx":572
  * 
  * 
  * def process_chunk(list ckexons,object sam,str chrom,dict options):             # <<<<<<<<<<<<<<
@@ -910,7 +910,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk {
 };
 
 
-/* "rnacounter/rnacounter.pyx":604
+/* "rnacounter/rnacounter.pyx":602
  *             exon0.transcripts.add(gr.transcripts.pop())
  *         exons.append(exon0)
  *     gene_ids = sorted(set(e.gene_id for e in exons))             # <<<<<<<<<<<<<<
@@ -926,7 +926,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":605
+/* "rnacounter/rnacounter.pyx":603
  *         exons.append(exon0)
  *     gene_ids = sorted(set(e.gene_id for e in exons))
  *     exon_names = sorted(set(e.name for e in exons))             # <<<<<<<<<<<<<<
@@ -942,7 +942,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":625
+/* "rnacounter/rnacounter.pyx":623
  * 
  *     #--- Count reads in each piece
  *     lastend = max(e.end for e in exons)             # <<<<<<<<<<<<<<
@@ -958,7 +958,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":719
+/* "rnacounter/rnacounter.pyx":715
  * 
  * 
  * def print_output(output, genes,transcripts,exons,introns, threshold,stranded):             # <<<<<<<<<<<<<<
@@ -971,7 +971,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output {
 };
 
 
-/* "rnacounter/rnacounter.pyx":843
+/* "rnacounter/rnacounter.pyx":839
  *     sys.exit(1)
  * 
  * def parse_args(args):             # <<<<<<<<<<<<<<
@@ -984,7 +984,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args {
 };
 
 
-/* "rnacounter/rnacounter.pyx":855
+/* "rnacounter/rnacounter.pyx":851
  *     # will be mixed in the output stream. Split the output using the last field ("Type").
  *     args['--type'] = [x.lower() for x in args['--type'].split(',')]
  *     if not all(x in ["genes","transcripts","exons","introns"] for x in args['--type']):             # <<<<<<<<<<<<<<
@@ -1001,7 +1001,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":868
+/* "rnacounter/rnacounter.pyx":864
  *     elif len(args['--type']) > 1:  # apply same method to all types
  *         args['--method'] = args['--method'] * len(args['--type'])
  *     if not all(x in ["raw","nnls","indirect-nnls"] for x in args['--method']):             # <<<<<<<<<<<<<<
@@ -1018,7 +1018,7 @@ struct __pyx_obj_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr {
 };
 
 
-/* "rnacounter/rnacounter.pyx":885
+/* "rnacounter/rnacounter.pyx":881
  *         except ValueError: errmsg("--exon_cutoff must be an integer.")
  * 
  *     options = dict((k.lstrip('-').lower(), v) for k,v in list(args.items()))             # <<<<<<<<<<<<<<
@@ -1729,7 +1729,7 @@ static CYTHON_INLINE double __pyx_f_10rnacounter_10rnacounter_fromRPK(double, do
 static CYTHON_INLINE double __pyx_f_10rnacounter_10rnacounter_correct_fraglen_bias(double, int, int); /*proto*/
 static int __pyx_f_10rnacounter_10rnacounter_count_reads(PyObject *, PyObject *, int, int); /*proto*/
 static CYTHON_INLINE int __pyx_f_10rnacounter_10rnacounter_is_in(PyObject *, struct __pyx_obj_10rnacounter_10rnacounter_GenomicObject *, PyObject *); /*proto*/
-static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyObject *, PyObject *, PyObject *, PyObject *, double, int, int); /*proto*/
+static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyObject *, PyObject *, PyObject *, PyObject *, double, int); /*proto*/
 static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_raw(PyObject *, PyObject *, PyObject *, PyObject *, double, int); /*proto*/
 static PyObject *__pyx_f_10rnacounter_10rnacounter_genes_from_transcripts(PyObject *); /*proto*/
 static CYTHON_INLINE PyObject *__pyx_f_10rnacounter_10rnacounter_simplify(PyObject *); /*proto*/
@@ -1998,7 +1998,6 @@ static char __pyx_k_shell[] = "shell";
 static char __pyx_k_split[] = "split";
 static char __pyx_k_start[] = "start";
 static char __pyx_k_strip[] = "strip";
-static char __pyx_k_syns2[] = "syns2";
 static char __pyx_k_throw[] = "throw";
 static char __pyx_k_toadd[] = "toadd";
 static char __pyx_k_track[] = "track";
@@ -2079,7 +2078,6 @@ static char __pyx_k_rpk_anti[] = "rpk_anti";
 static char __pyx_k_stranded[] = "stranded";
 static char __pyx_k_synonyms[] = "synonyms";
 static char __pyx_k_type_map[] = "type_map";
-static char __pyx_k_weighted[] = "weighted";
 static char __pyx_k_alignment[] = "alignment";
 static char __pyx_k_annotname[] = "annotname";
 static char __pyx_k_antisense[] = "antisense";
@@ -2435,7 +2433,6 @@ static PyObject *__pyx_n_s_sum;
 static PyObject *__pyx_n_s_synonym;
 static PyObject *__pyx_n_s_synonyms;
 static PyObject *__pyx_n_s_syns;
-static PyObject *__pyx_n_s_syns2;
 static PyObject *__pyx_n_s_sys;
 static PyObject *__pyx_n_s_t;
 static PyObject *__pyx_n_s_t2p;
@@ -2467,7 +2464,6 @@ static PyObject *__pyx_n_s_usage_string;
 static PyObject *__pyx_n_s_v;
 static PyObject *__pyx_n_s_values;
 static PyObject *__pyx_n_s_wb;
-static PyObject *__pyx_n_s_weighted;
 static PyObject *__pyx_n_s_write;
 static PyObject *__pyx_n_s_x;
 static PyObject *__pyx_n_s_zeros;
@@ -12047,12 +12043,12 @@ static CYTHON_INLINE int __pyx_f_10rnacounter_10rnacounter_is_in(PyObject *__pyx
 /* "rnacounter/rnacounter.pyx":438
  * 
  * 
- * cdef list estimate_expression_NNLS(str ftype,list pieces,list ids,list exons,double norm_cst,             # <<<<<<<<<<<<<<
- *                                    bint stranded,bint weighted):
+ * cdef list estimate_expression_NNLS(str ftype,list pieces,list ids,list exons,double norm_cst,bint stranded):             # <<<<<<<<<<<<<<
  *     """Infer gene/transcript expression from exons RPK. Takes GenomicObject instances *pieces*
+ *     and returns for each feature ID in *ids* an instance of *ftype* with the
  */
 
-static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyObject *__pyx_v_ftype, PyObject *__pyx_v_pieces, PyObject *__pyx_v_ids, PyObject *__pyx_v_exons, double __pyx_v_norm_cst, int __pyx_v_stranded, int __pyx_v_weighted) {
+static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyObject *__pyx_v_ftype, PyObject *__pyx_v_pieces, PyObject *__pyx_v_ids, PyObject *__pyx_v_exons, double __pyx_v_norm_cst, int __pyx_v_stranded) {
   int __pyx_v_n;
   int __pyx_v_m;
   int __pyx_v_flen;
@@ -12137,7 +12133,7 @@ static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyOb
   __pyx_pybuffernd_w.data = NULL;
   __pyx_pybuffernd_w.rcbuffer = &__pyx_pybuffer_w;
 
-  /* "rnacounter/rnacounter.pyx":454
+  /* "rnacounter/rnacounter.pyx":453
  *     cdef GenomicObject p
  *     cdef list exs, feats
  *     n = len(pieces)             # <<<<<<<<<<<<<<
@@ -12146,12 +12142,12 @@ static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyOb
  */
   if (unlikely(__pyx_v_pieces == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_1 = PyList_GET_SIZE(__pyx_v_pieces); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyList_GET_SIZE(__pyx_v_pieces); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_n = __pyx_t_1;
 
-  /* "rnacounter/rnacounter.pyx":455
+  /* "rnacounter/rnacounter.pyx":454
  *     cdef list exs, feats
  *     n = len(pieces)
  *     m = len(ids)             # <<<<<<<<<<<<<<
@@ -12160,25 +12156,25 @@ static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyOb
  */
   if (unlikely(__pyx_v_ids == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_1 = PyList_GET_SIZE(__pyx_v_ids); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyList_GET_SIZE(__pyx_v_ids); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_m = __pyx_t_1;
 
-  /* "rnacounter/rnacounter.pyx":456
+  /* "rnacounter/rnacounter.pyx":455
  *     n = len(pieces)
  *     m = len(ids)
  *     A = zeros((n,m))             # <<<<<<<<<<<<<<
  *     for i,p in enumerate(pieces):
  *         for j,f in enumerate(ids):
  */
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+  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
-  __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
   __Pyx_GIVEREF(__pyx_t_4);
@@ -12197,22 +12193,22 @@ static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyOb
     }
   }
   if (!__pyx_t_5) {
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+    __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_6);
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-    __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   }
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_t_7 = ((PyArrayObject *)__pyx_t_2);
   {
     __Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12228,13 +12224,13 @@ static PyObject *__pyx_f_10rnacounter_10rnacounter_estimate_expression_NNLS(PyOb
       }
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-    /* "rnacounter/rnacounter.pyx":479
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_7 = PySet_Pop(__pyx_v_gr->transcripts); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "rnacounter/rnacounter.pyx":653
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-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "rnacounter/rnacounter.pyx":662
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "rnacounter/rnacounter.pyx":663
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-      /* "rnacounter/rnacounter.pyx":664
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+        PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
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+        __pyx_t_6 = __pyx_f_10rnacounter_10rnacounter_genes_from_transcripts(__pyx_v_transcripts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_1 = __pyx_f_10rnacounter_10rnacounter_genes_from_transcripts(__pyx_v_transcripts2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "rnacounter/rnacounter.pyx":702
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-  __pyx_t_15 = __pyx_t_16;
+  __pyx_t_3 = (__pyx_v_intron_pieces != Py_None) && (PyList_GET_SIZE(__pyx_v_intron_pieces) != 0);
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-    /* "rnacounter/rnacounter.pyx":709
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-    /* "rnacounter/rnacounter.pyx":712
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-      /* "rnacounter/rnacounter.pyx":710
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-      /* "rnacounter/rnacounter.pyx":713
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-    /* "rnacounter/rnacounter.pyx":792
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-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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-        if (__pyx_t_7) {
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-          __Pyx_XDECREF_SET(__pyx_v_partition_minus, ((PyObject*)__pyx_t_5));
-          __pyx_t_5 = 0;
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-            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __Pyx_GOTREF(__pyx_t_2);
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-            PyTuple_SET_ITEM(__pyx_t_1, 0+__pyx_t_16, __pyx_t_2);
-            __Pyx_GIVEREF(__pyx_t_2);
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-            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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-              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_2 = NULL;
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+            __pyx_t_3 = PyTuple_New(4+__pyx_t_17); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
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  */
-  __pyx_tuple__30 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__30 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__30);
   __Pyx_GIVEREF(__pyx_tuple__30);
 
-  /* "rnacounter/rnacounter.pyx":504
+  /* "rnacounter/rnacounter.pyx":503
  *     frpk_anti = fcount_anti = 0.0
  *     for i,f in enumerate(ids):
  *         exs = sorted([e for e in exons if is_in(ftype,e,f)], key=attrgetter('start','end'))             # <<<<<<<<<<<<<<
  *         inner = [p for p in pieces if (len(p.gene_id.split('|'))==1 and is_in(ftype,p,f))]
  *         if len(inner)==0:
  */
-  __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__31);
   __Pyx_GIVEREF(__pyx_tuple__31);
 
-  /* "rnacounter/rnacounter.pyx":505
+  /* "rnacounter/rnacounter.pyx":504
  *     for i,f in enumerate(ids):
  *         exs = sorted([e for e in exons if is_in(ftype,e,f)], key=attrgetter('start','end'))
  *         inner = [p for p in pieces if (len(p.gene_id.split('|'))==1 and is_in(ftype,p,f))]             # <<<<<<<<<<<<<<
  *         if len(inner)==0:
  *             flen = 0
  */
-  __pyx_tuple__32 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__32 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__32);
   __Pyx_GIVEREF(__pyx_tuple__32);
 
-  /* "rnacounter/rnacounter.pyx":520
+  /* "rnacounter/rnacounter.pyx":519
  *                 chrom=exs[0].chrom, start=exs[0].start, end=exs[len(exs)-1].end,
  *                 gene_id=exs[0].gene_id, gene_name=exs[0].gene_name, strand=exs[0].strand))
  *     feats.sort(key=attrgetter('start','end'))             # <<<<<<<<<<<<<<
  *     return feats
  * 
  */
-  __pyx_tuple__33 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__33 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__33);
   __Pyx_GIVEREF(__pyx_tuple__33);
 
-  /* "rnacounter/rnacounter.pyx":530
+  /* "rnacounter/rnacounter.pyx":529
  *     cdef int glen
  *     genes = []
  *     for k,group in itertools.groupby(transcripts, key=attrgetter("gene_id")):             # <<<<<<<<<<<<<<
  *         g = list(group)
  *         t0 = g[0]
  */
-  __pyx_tuple__34 = PyTuple_Pack(1, __pyx_n_s_gene_id); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__34 = PyTuple_Pack(1, __pyx_n_s_gene_id); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__34);
   __Pyx_GIVEREF(__pyx_tuple__34);
 
-  /* "rnacounter/rnacounter.pyx":547
+  /* "rnacounter/rnacounter.pyx":546
  * cdef inline str simplify(str name):
  *     """Removes duplicates in names of the form 'name1|name2', and sorts elements."""
  *     return '|'.join(sorted(set(name.split('|'))))             # <<<<<<<<<<<<<<
  * 
  * cdef dict filter_transcripts(dict t2p,int exon_cutoff):
  */
-  __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__35);
   __Pyx_GIVEREF(__pyx_tuple__35);
 
-  /* "rnacounter/rnacounter.pyx":560
+  /* "rnacounter/rnacounter.pyx":559
  *     structs = {}  # transcript structures, as tuples of exon ids
  *     replace = {} # too close transcripts
  *     for t,texons in sorted(t2p.items(), key=itemgetter(0)):             # <<<<<<<<<<<<<<
  *         structure = tuple([te.id for te in texons if te.length > exon_cutoff])
  *         structs.setdefault(structure, []).append(t)
  */
-  __pyx_tuple__36 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__36 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__36);
   __Pyx_GIVEREF(__pyx_tuple__36);
 
-  /* "rnacounter/rnacounter.pyx":598
+  /* "rnacounter/rnacounter.pyx":596
  *     #--- Regroup occurrences of the same exons from a different transcript
  *     exons = []
  *     for key,group in itertools.groupby(ckexons, attrgetter('name')):             # <<<<<<<<<<<<<<
  *         # ckexons are sorted by id because chrexons were sorted by chrom,start,end
  *         exon0 = next(group)
  */
-  __pyx_tuple__37 = PyTuple_Pack(1, __pyx_n_s_name); if (unlikely(!__pyx_tuple__37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__37 = PyTuple_Pack(1, __pyx_n_s_name); if (unlikely(!__pyx_tuple__37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__37);
   __Pyx_GIVEREF(__pyx_tuple__37);
 
-  /* "rnacounter/rnacounter.pyx":634
+  /* "rnacounter/rnacounter.pyx":632
  *         introns = []
  *         for tid,tpieces in sorted(t2p.items()):
  *             tpieces.sort(key=attrgetter('start','end'))             # <<<<<<<<<<<<<<
  *             introns.extend(complement(tid,tpieces))
  *         if introns:
  */
-  __pyx_tuple__38 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__38)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__38 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__38)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__38);
   __Pyx_GIVEREF(__pyx_tuple__38);
 
-  /* "rnacounter/rnacounter.pyx":640
+  /* "rnacounter/rnacounter.pyx":638
  *             intron_pieces = [ip for ip in intron_exon_pieces if \
  *                              # ip.length > exon_cutoff and \
  *                              not any([n in exon_names for n in ip.name.split('|')])]             # <<<<<<<<<<<<<<
  *             if intron_pieces:
  *                 lastend = max([intron.end for intron in introns])
  */
-  __pyx_tuple__39 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__39 = PyTuple_Pack(1, __pyx_kp_s__25); if (unlikely(!__pyx_tuple__39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__39);
   __Pyx_GIVEREF(__pyx_tuple__39);
 
-  /* "rnacounter/rnacounter.pyx":680
- *                         gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
- *                         synonyms=','.join(syns2)))
+  /* "rnacounter/rnacounter.pyx":676
+ *                             gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
+ *                             synonyms=','.join(syns)))
  *             toadd.sort(key=attrgetter('start','end'))             # <<<<<<<<<<<<<<
  *             transcripts = transcripts[:i+1] + toadd + transcripts[i+1:]
- *             trans.synonyms = ','.join(syns) if len(syns)>0 else '.'
+ *             trans.synonyms = ','.join(syns) if len(syns)>1 else '.'
  */
-  __pyx_tuple__41 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__41 = PyTuple_Pack(2, __pyx_n_s_start, __pyx_n_s_end); if (unlikely(!__pyx_tuple__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__41);
   __Pyx_GIVEREF(__pyx_tuple__41);
 
-  /* "rnacounter/rnacounter.pyx":742
+  /* "rnacounter/rnacounter.pyx":738
  *     # Index BAM if necessary
  *     if not os.path.exists(bamname+'.bai'):
  *         sys.stderr.write("BAM index not found. Indexing...")             # <<<<<<<<<<<<<<
  *         subprocess.check_call("samtools index %s" % bamname, shell=True)
  *         sys.stderr.write("...done.\n")
  */
-  __pyx_tuple__43 = PyTuple_Pack(1, __pyx_kp_s_BAM_index_not_found_Indexing); if (unlikely(!__pyx_tuple__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__43 = PyTuple_Pack(1, __pyx_kp_s_BAM_index_not_found_Indexing); if (unlikely(!__pyx_tuple__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__43);
   __Pyx_GIVEREF(__pyx_tuple__43);
 
-  /* "rnacounter/rnacounter.pyx":744
+  /* "rnacounter/rnacounter.pyx":740
  *         sys.stderr.write("BAM index not found. Indexing...")
  *         subprocess.check_call("samtools index %s" % bamname, shell=True)
  *         sys.stderr.write("...done.\n")             # <<<<<<<<<<<<<<
  * 
  *     # Open BAM. Get read length
  */
-  __pyx_tuple__44 = PyTuple_Pack(1, __pyx_kp_s_done); if (unlikely(!__pyx_tuple__44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__44 = PyTuple_Pack(1, __pyx_kp_s_done); if (unlikely(!__pyx_tuple__44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__44);
   __Pyx_GIVEREF(__pyx_tuple__44);
 
-  /* "rnacounter/rnacounter.pyx":792
+  /* "rnacounter/rnacounter.pyx":788
  *         chrom = exon.chrom
  *     if chrom == '':
  *         raise ValueError("Reference names in BAM do not correspond to that of the GTF.")             # <<<<<<<<<<<<<<
  *     lastchrom = chrom
  * 
  */
-  __pyx_tuple__45 = PyTuple_Pack(1, __pyx_kp_s_Reference_names_in_BAM_do_not_co); if (unlikely(!__pyx_tuple__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__45 = PyTuple_Pack(1, __pyx_kp_s_Reference_names_in_BAM_do_not_co); if (unlikely(!__pyx_tuple__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__45);
   __Pyx_GIVEREF(__pyx_tuple__45);
 
-  /* "rnacounter/rnacounter.pyx":809
+  /* "rnacounter/rnacounter.pyx":805
  *             chrom = exon.chrom
  *         if chrexons:
  *             chrexons.sort(key=attrgetter('start','end','name'))             # <<<<<<<<<<<<<<
  *             if options['stranded']:
  *                 chrexons_plus = [x for x in chrexons if x.strand == 1]
  */
-  __pyx_tuple__46 = PyTuple_Pack(3, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_name); if (unlikely(!__pyx_tuple__46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__46 = PyTuple_Pack(3, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_name); if (unlikely(!__pyx_tuple__46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__46);
   __Pyx_GIVEREF(__pyx_tuple__46);
 
-  /* "rnacounter/rnacounter.pyx":841
+  /* "rnacounter/rnacounter.pyx":837
  * def errmsg(message):
  *     sys.stderr.write('\n\t'+message + '\n\n')
  *     sys.exit(1)             # <<<<<<<<<<<<<<
  * 
  * def parse_args(args):
  */
-  __pyx_tuple__49 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_tuple__49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__49 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_tuple__49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__49);
   __Pyx_GIVEREF(__pyx_tuple__49);
 
-  /* "rnacounter/rnacounter.pyx":885
+  /* "rnacounter/rnacounter.pyx":881
  *         except ValueError: errmsg("--exon_cutoff must be an integer.")
  * 
  *     options = dict((k.lstrip('-').lower(), v) for k,v in list(args.items()))             # <<<<<<<<<<<<<<
  *     return options
  * 
  */
-  __pyx_tuple__50 = PyTuple_Pack(1, __pyx_kp_s__3); if (unlikely(!__pyx_tuple__50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__50 = PyTuple_Pack(1, __pyx_kp_s__3); if (unlikely(!__pyx_tuple__50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__50);
   __Pyx_GIVEREF(__pyx_tuple__50);
 
-  /* "rnacounter/rnacounter.pyx":845
+  /* "rnacounter/rnacounter.pyx":841
  * def parse_args(args):
  *     if args['--chromosomes'] is None: args['--chromosomes'] = []
  *     else: args['--chromosomes'] = args['--chromosomes'].split(',')             # <<<<<<<<<<<<<<
  * 
  *     if args['--format'].lower() not in ['gtf','bed']:
  */
-  __pyx_tuple__51 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__51 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__51);
   __Pyx_GIVEREF(__pyx_tuple__51);
 
-  /* "rnacounter/rnacounter.pyx":848
+  /* "rnacounter/rnacounter.pyx":844
  * 
  *     if args['--format'].lower() not in ['gtf','bed']:
  *         errmsg("FORMAT must be one of 'gtf' or 'bed'.")             # <<<<<<<<<<<<<<
  *     if (args['--format'].lower() == 'bed') and (args['--type'] != 'genes'):
  *         errmsg("BED input is not compatible with the '--type' option.")
  */
-  __pyx_tuple__52 = PyTuple_Pack(1, __pyx_kp_s_FORMAT_must_be_one_of_gtf_or_bed); if (unlikely(!__pyx_tuple__52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__52 = PyTuple_Pack(1, __pyx_kp_s_FORMAT_must_be_one_of_gtf_or_bed); if (unlikely(!__pyx_tuple__52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__52);
   __Pyx_GIVEREF(__pyx_tuple__52);
 
-  /* "rnacounter/rnacounter.pyx":850
+  /* "rnacounter/rnacounter.pyx":846
  *         errmsg("FORMAT must be one of 'gtf' or 'bed'.")
  *     if (args['--format'].lower() == 'bed') and (args['--type'] != 'genes'):
  *         errmsg("BED input is not compatible with the '--type' option.")             # <<<<<<<<<<<<<<
  * 
  *     # Type: one can actually give both as "-t genes,transcripts" but they
  */
-  __pyx_tuple__53 = PyTuple_Pack(1, __pyx_kp_s_BED_input_is_not_compatible_with); if (unlikely(!__pyx_tuple__53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__53 = PyTuple_Pack(1, __pyx_kp_s_BED_input_is_not_compatible_with); if (unlikely(!__pyx_tuple__53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__53);
   __Pyx_GIVEREF(__pyx_tuple__53);
 
-  /* "rnacounter/rnacounter.pyx":854
+  /* "rnacounter/rnacounter.pyx":850
  *     # Type: one can actually give both as "-t genes,transcripts" but they
  *     # will be mixed in the output stream. Split the output using the last field ("Type").
  *     args['--type'] = [x.lower() for x in args['--type'].split(',')]             # <<<<<<<<<<<<<<
  *     if not all(x in ["genes","transcripts","exons","introns"] for x in args['--type']):
  *         errmsg("TYPE must be one of 'genes', 'transcripts', 'exons' or 'introns'.")
  */
-  __pyx_tuple__54 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__54)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__54 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__54)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__54);
   __Pyx_GIVEREF(__pyx_tuple__54);
 
-  /* "rnacounter/rnacounter.pyx":856
+  /* "rnacounter/rnacounter.pyx":852
  *     args['--type'] = [x.lower() for x in args['--type'].split(',')]
  *     if not all(x in ["genes","transcripts","exons","introns"] for x in args['--type']):
  *         errmsg("TYPE must be one of 'genes', 'transcripts', 'exons' or 'introns'.")             # <<<<<<<<<<<<<<
  *     type_map = {'genes':0, 'transcripts':1, 'exons':2, 'introns':3}  # avoid comparing strings later
  *     args['--type'] = [type_map[x] for x in args['--type']]
  */
-  __pyx_tuple__55 = PyTuple_Pack(1, __pyx_kp_s_TYPE_must_be_one_of_genes_transc); if (unlikely(!__pyx_tuple__55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__55 = PyTuple_Pack(1, __pyx_kp_s_TYPE_must_be_one_of_genes_transc); if (unlikely(!__pyx_tuple__55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__55);
   __Pyx_GIVEREF(__pyx_tuple__55);
 
-  /* "rnacounter/rnacounter.pyx":862
+  /* "rnacounter/rnacounter.pyx":858
  *     # Same for methods. If given as a list, the length must be that of `--type`,
  *     # the method at index i will be applied to feature type at index i.
  *     args['--method'] = [x.lower() for x in args['--method'].split(',')]             # <<<<<<<<<<<<<<
  *     if len(args['--method']) > 1:  # multiple methods given
  *         if not len(args['--method']) == len(args['--type']):
  */
-  __pyx_tuple__56 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__56 = PyTuple_Pack(1, __pyx_kp_s__40); if (unlikely(!__pyx_tuple__56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__56);
   __Pyx_GIVEREF(__pyx_tuple__56);
 
-  /* "rnacounter/rnacounter.pyx":865
+  /* "rnacounter/rnacounter.pyx":861
  *     if len(args['--method']) > 1:  # multiple methods given
  *         if not len(args['--method']) == len(args['--type']):
  *             errmsg("TYPE and METHOD arguments must have the same number of elements.")             # <<<<<<<<<<<<<<
  *     elif len(args['--type']) > 1:  # apply same method to all types
  *         args['--method'] = args['--method'] * len(args['--type'])
  */
-  __pyx_tuple__57 = PyTuple_Pack(1, __pyx_kp_s_TYPE_and_METHOD_arguments_must_h); if (unlikely(!__pyx_tuple__57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__57 = PyTuple_Pack(1, __pyx_kp_s_TYPE_and_METHOD_arguments_must_h); if (unlikely(!__pyx_tuple__57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__57);
   __Pyx_GIVEREF(__pyx_tuple__57);
 
-  /* "rnacounter/rnacounter.pyx":869
+  /* "rnacounter/rnacounter.pyx":865
  *         args['--method'] = args['--method'] * len(args['--type'])
  *     if not all(x in ["raw","nnls","indirect-nnls"] for x in args['--method']):
  *         errmsg("METHOD must be one of 'raw', 'nnls' or 'indirect-nnls'.")             # <<<<<<<<<<<<<<
  *     method_map = {'raw':0, 'nnls':1, "indirect-nnls":2}  # avoid comparing strings later
  *     args['--method'] = [method_map[x] for x in args['--method']]
  */
-  __pyx_tuple__58 = PyTuple_Pack(1, __pyx_kp_s_METHOD_must_be_one_of_raw_nnls_o); if (unlikely(!__pyx_tuple__58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__58 = PyTuple_Pack(1, __pyx_kp_s_METHOD_must_be_one_of_raw_nnls_o); if (unlikely(!__pyx_tuple__58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__58);
   __Pyx_GIVEREF(__pyx_tuple__58);
 
-  /* "rnacounter/rnacounter.pyx":875
+  /* "rnacounter/rnacounter.pyx":871
  *     for k,v in args['--method'].items():
  *         if v == 2 and k != 0:
  *             errmsg("'indirect-nnls' method can only be applied to type 'genes'.")             # <<<<<<<<<<<<<<
  * 
  *     try: args['--threshold'] = float(args['--threshold'])
  */
-  __pyx_tuple__59 = PyTuple_Pack(1, __pyx_kp_s_indirect_nnls_method_can_only_b); if (unlikely(!__pyx_tuple__59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__59 = PyTuple_Pack(1, __pyx_kp_s_indirect_nnls_method_can_only_b); if (unlikely(!__pyx_tuple__59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__59);
   __Pyx_GIVEREF(__pyx_tuple__59);
 
-  /* "rnacounter/rnacounter.pyx":878
+  /* "rnacounter/rnacounter.pyx":874
  * 
  *     try: args['--threshold'] = float(args['--threshold'])
  *     except ValueError: errmsg("--threshold must be numeric.")             # <<<<<<<<<<<<<<
  *     try: args['--fraglength'] = int(args['--fraglength'])
  *     except ValueError: errmsg("FRAGLENGTH must be an integer.")
  */
-  __pyx_tuple__60 = PyTuple_Pack(1, __pyx_kp_s_threshold_must_be_numeric); if (unlikely(!__pyx_tuple__60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__60 = PyTuple_Pack(1, __pyx_kp_s_threshold_must_be_numeric); if (unlikely(!__pyx_tuple__60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__60);
   __Pyx_GIVEREF(__pyx_tuple__60);
 
-  /* "rnacounter/rnacounter.pyx":880
+  /* "rnacounter/rnacounter.pyx":876
  *     except ValueError: errmsg("--threshold must be numeric.")
  *     try: args['--fraglength'] = int(args['--fraglength'])
  *     except ValueError: errmsg("FRAGLENGTH must be an integer.")             # <<<<<<<<<<<<<<
  *     if args['--exon_cutoff']:
  *         try: args['--exon_cutoff'] = int(args['--exon_cutoff'])
  */
-  __pyx_tuple__61 = PyTuple_Pack(1, __pyx_kp_s_FRAGLENGTH_must_be_an_integer); if (unlikely(!__pyx_tuple__61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__61 = PyTuple_Pack(1, __pyx_kp_s_FRAGLENGTH_must_be_an_integer); if (unlikely(!__pyx_tuple__61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__61);
   __Pyx_GIVEREF(__pyx_tuple__61);
 
-  /* "rnacounter/rnacounter.pyx":883
+  /* "rnacounter/rnacounter.pyx":879
  *     if args['--exon_cutoff']:
  *         try: args['--exon_cutoff'] = int(args['--exon_cutoff'])
  *         except ValueError: errmsg("--exon_cutoff must be an integer.")             # <<<<<<<<<<<<<<
  * 
  *     options = dict((k.lstrip('-').lower(), v) for k,v in list(args.items()))
  */
-  __pyx_tuple__62 = PyTuple_Pack(1, __pyx_kp_s_exon_cutoff_must_be_an_integer); if (unlikely(!__pyx_tuple__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__62 = PyTuple_Pack(1, __pyx_kp_s_exon_cutoff_must_be_an_integer); if (unlikely(!__pyx_tuple__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__62);
   __Pyx_GIVEREF(__pyx_tuple__62);
 
@@ -28880,74 +28796,74 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(__pyx_tuple__74);
   __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(2, 0, 19, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":573
+  /* "rnacounter/rnacounter.pyx":572
  * 
  * 
  * def process_chunk(list ckexons,object sam,str chrom,dict options):             # <<<<<<<<<<<<<<
  *     """Distribute counts across transcripts and genes of a chunk *ckexons*
  *     of non-overlapping exons."""
  */
-  __pyx_tuple__76 = PyTuple_Pack(58, __pyx_n_s_ckexons, __pyx_n_s_sam, __pyx_n_s_chrom, __pyx_n_s_options, __pyx_n_s_method, __pyx_n_s_lastend, __pyx_n_s_fraglength, __pyx_n_s_exon_cutoff, __pyx_n_s_i, __pyx_n_s_exon0, __pyx_n_s_gr, __pyx_n_s_p, __pyx_n_s_e, __pyx_n_s_gene, __pyx_n_s_trans, __pyx_n_s_exons, __pyx_n_s_exons2, __pyx_n_s_introns, __pyx_n_s_introns2, __pyx_n_s_genes, __pyx_n_s_transcripts, __pyx_n_s_exon_names, __pyx_n_s_transcript_ids, __pyx_n_s_gene_ids, __pyx_n_s_pieces, __pyx_n_s_tpieces, __pyx_n_s_types, __pyx_n_s_t2p, __pyx_n_s_methods, __pyx_n_s_t, __pyx_n_s_tid, __pyx_n_s_stranded, __pyx_n_s_weighted, __pyx_n_s_norm_cst, __pyx_n_s_threshold, __pyx_n_s_output, __pyx_n_s_key, __pyx_n_s_group, __pyx_n_s_synonyms, __pyx_n_s_replace, __pyx_n_s_main_2, __pyx_n_s_ckreads, __pyx_n_s_intron_pieces, __pyx_n_s_intron_exon_pieces, __pyx_n_s_ip, __pyx_n_s_syns, __pyx_n_s_toadd, __pyx_n_s_synonym, __pyx_n_s_syns2, __pyx_n_s_transcripts2, __pyx_n_s_exon_ids, __pyx_n_s_intron_ids, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_n, __pyx_n_s_intron); if (unlikely(!__pyx_tuple__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__76 = PyTuple_Pack(56, __pyx_n_s_ckexons, __pyx_n_s_sam, __pyx_n_s_chrom, __pyx_n_s_options, __pyx_n_s_method, __pyx_n_s_lastend, __pyx_n_s_fraglength, __pyx_n_s_exon_cutoff, __pyx_n_s_i, __pyx_n_s_exon0, __pyx_n_s_gr, __pyx_n_s_p, __pyx_n_s_e, __pyx_n_s_gene, __pyx_n_s_trans, __pyx_n_s_exons, __pyx_n_s_exons2, __pyx_n_s_introns, __pyx_n_s_introns2, __pyx_n_s_genes, __pyx_n_s_transcripts, __pyx_n_s_exon_names, __pyx_n_s_transcript_ids, __pyx_n_s_gene_ids, __pyx_n_s_pieces, __pyx_n_s_tpieces, __pyx_n_s_types, __pyx_n_s_syns, __pyx_n_s_t2p, __pyx_n_s_methods, __pyx_n_s_synonyms, __pyx_n_s_t, __pyx_n_s_tid, __pyx_n_s_synonym, __pyx_n_s_stranded, __pyx_n_s_norm_cst, __pyx_n_s_threshold, __pyx_n_s_output, __pyx_n_s_key, __pyx_n_s_group, __pyx_n_s_replace, __pyx_n_s_main_2, __pyx_n_s_ckreads, __pyx_n_s_intron_pieces, __pyx_n_s_intron_exon_pieces, __pyx_n_s_ip, __pyx_n_s_toadd, __pyx_n_s_transcripts2, __pyx_n_s_exon_ids, __pyx_n_s_intron_ids, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_n, __pyx_n_s_intron); if (unlikely(!__pyx_tuple__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__76);
   __Pyx_GIVEREF(__pyx_tuple__76);
-  __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 58, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 573, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 56, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 572, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":719
+  /* "rnacounter/rnacounter.pyx":715
  * 
  * 
  * def print_output(output, genes,transcripts,exons,introns, threshold,stranded):             # <<<<<<<<<<<<<<
  *     igenes = filter(lambda x:x.count > threshold, genes)
  *     itranscripts = filter(lambda x:x.count > threshold, transcripts)
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-  __pyx_tuple__78 = PyTuple_Pack(14, __pyx_n_s_output, __pyx_n_s_genes, __pyx_n_s_transcripts, __pyx_n_s_exons, __pyx_n_s_introns, __pyx_n_s_threshold, __pyx_n_s_stranded, __pyx_n_s_igenes, __pyx_n_s_itranscripts, __pyx_n_s_iexons, __pyx_n_s_iintrons, __pyx_n_s_f, __pyx_n_s_towrite, __pyx_n_s_x); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__78 = PyTuple_Pack(14, __pyx_n_s_output, __pyx_n_s_genes, __pyx_n_s_transcripts, __pyx_n_s_exons, __pyx_n_s_introns, __pyx_n_s_threshold, __pyx_n_s_stranded, __pyx_n_s_igenes, __pyx_n_s_itranscripts, __pyx_n_s_iexons, __pyx_n_s_iintrons, __pyx_n_s_f, __pyx_n_s_towrite, __pyx_n_s_x); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__78);
   __Pyx_GIVEREF(__pyx_tuple__78);
-  __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 719, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 715, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":739
+  /* "rnacounter/rnacounter.pyx":735
  * 
  * 
  * def rnacounter_main(bamname, annotname, options):             # <<<<<<<<<<<<<<
  *     # Index BAM if necessary
  *     if not os.path.exists(bamname+'.bai'):
  */
-  __pyx_tuple__81 = PyTuple_Pack(25, __pyx_n_s_bamname, __pyx_n_s_annotname, __pyx_n_s_options, __pyx_n_s_sam, __pyx_n_s_nhead, __pyx_n_s_annot, __pyx_n_s__80, __pyx_n_s_header, __pyx_n_s_parse, __pyx_n_s_chromosomes, __pyx_n_s_gtf_ftype, __pyx_n_s_chrom, __pyx_n_s_exon, __pyx_n_s_row, __pyx_n_s_lastchrom, __pyx_n_s_chrexons, __pyx_n_s_chrexons_plus, __pyx_n_s_chrexons_minus, __pyx_n_s_partition_plus, __pyx_n_s_a, __pyx_n_s_b, __pyx_n_s_partition_minus, __pyx_n_s_partition, __pyx_n_s_c, __pyx_n_s_x); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__81 = PyTuple_Pack(25, __pyx_n_s_bamname, __pyx_n_s_annotname, __pyx_n_s_options, __pyx_n_s_sam, __pyx_n_s_nhead, __pyx_n_s_annot, __pyx_n_s__80, __pyx_n_s_header, __pyx_n_s_parse, __pyx_n_s_chromosomes, __pyx_n_s_gtf_ftype, __pyx_n_s_chrom, __pyx_n_s_exon, __pyx_n_s_row, __pyx_n_s_lastchrom, __pyx_n_s_chrexons, __pyx_n_s_chrexons_plus, __pyx_n_s_chrexons_minus, __pyx_n_s_partition_plus, __pyx_n_s_a, __pyx_n_s_b, __pyx_n_s_partition_minus, __pyx_n_s_partition, __pyx_n_s_c, __pyx_n_s_x); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__81);
   __Pyx_GIVEREF(__pyx_tuple__81);
-  __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 735, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":836
+  /* "rnacounter/rnacounter.pyx":832
  * 
  * 
  * def usage_string():             # <<<<<<<<<<<<<<
  *     return __doc__
  * 
  */
-  __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 832, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":839
+  /* "rnacounter/rnacounter.pyx":835
  *     return __doc__
  * 
  * def errmsg(message):             # <<<<<<<<<<<<<<
  *     sys.stderr.write('\n\t'+message + '\n\n')
  *     sys.exit(1)
  */
-  __pyx_tuple__84 = PyTuple_Pack(1, __pyx_n_s_message); if (unlikely(!__pyx_tuple__84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__84 = PyTuple_Pack(1, __pyx_n_s_message); if (unlikely(!__pyx_tuple__84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__84);
   __Pyx_GIVEREF(__pyx_tuple__84);
-  __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 835, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "rnacounter/rnacounter.pyx":843
+  /* "rnacounter/rnacounter.pyx":839
  *     sys.exit(1)
  * 
  * def parse_args(args):             # <<<<<<<<<<<<<<
  *     if args['--chromosomes'] is None: args['--chromosomes'] = []
  *     else: args['--chromosomes'] = args['--chromosomes'].split(',')
  */
-  __pyx_tuple__86 = PyTuple_Pack(11, __pyx_n_s_args, __pyx_n_s_type_map, __pyx_n_s_method_map, __pyx_n_s_k, __pyx_n_s_v, __pyx_n_s_options, __pyx_n_s_x, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__86 = PyTuple_Pack(11, __pyx_n_s_args, __pyx_n_s_type_map, __pyx_n_s_method_map, __pyx_n_s_k, __pyx_n_s_v, __pyx_n_s_options, __pyx_n_s_x, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__86);
   __Pyx_GIVEREF(__pyx_tuple__86);
-  __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 843, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_RefNannyFinishContext();
   return 0;
   __pyx_L1_error:;
@@ -29089,31 +29005,31 @@ PyMODINIT_FUNC PyInit_rnacounter(void)
   if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 623; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_print_output;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr;
-  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0;
   __pyx_ptype_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr = &__pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr;
   /*--- Type import code ---*/
@@ -29398,76 +29314,76 @@ PyMODINIT_FUNC PyInit_rnacounter(void)
   __Pyx_GIVEREF(__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":573
+  /* "rnacounter/rnacounter.pyx":572
  * 
  * 
  * def process_chunk(list ckexons,object sam,str chrom,dict options):             # <<<<<<<<<<<<<<
  *     """Distribute counts across transcripts and genes of a chunk *ckexons*
  *     of non-overlapping exons."""
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_7process_chunk, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_7process_chunk, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_process_chunk, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_process_chunk, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":719
+  /* "rnacounter/rnacounter.pyx":715
  * 
  * 
  * def print_output(output, genes,transcripts,exons,introns, threshold,stranded):             # <<<<<<<<<<<<<<
  *     igenes = filter(lambda x:x.count > threshold, genes)
  *     itranscripts = filter(lambda x:x.count > threshold, transcripts)
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_9print_output, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_9print_output, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_print_output, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_print_output, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":739
+  /* "rnacounter/rnacounter.pyx":735
  * 
  * 
  * def rnacounter_main(bamname, annotname, options):             # <<<<<<<<<<<<<<
  *     # Index BAM if necessary
  *     if not os.path.exists(bamname+'.bai'):
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_11rnacounter_main, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_11rnacounter_main, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_rnacounter_main, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_rnacounter_main, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":836
+  /* "rnacounter/rnacounter.pyx":832
  * 
  * 
  * def usage_string():             # <<<<<<<<<<<<<<
  *     return __doc__
  * 
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_13usage_string, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_13usage_string, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_usage_string, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_usage_string, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":839
+  /* "rnacounter/rnacounter.pyx":835
  *     return __doc__
  * 
  * def errmsg(message):             # <<<<<<<<<<<<<<
  *     sys.stderr.write('\n\t'+message + '\n\n')
  *     sys.exit(1)
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_15errmsg, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_15errmsg, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_errmsg, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_errmsg, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "rnacounter/rnacounter.pyx":843
+  /* "rnacounter/rnacounter.pyx":839
  *     sys.exit(1)
  * 
  * def parse_args(args):             # <<<<<<<<<<<<<<
  *     if args['--chromosomes'] is None: args['--chromosomes'] = []
  *     else: args['--chromosomes'] = args['--chromosomes'].split(',')
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_17parse_args, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10rnacounter_10rnacounter_17parse_args, NULL, __pyx_n_s_rnacounter_rnacounter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_parse_args, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_parse_args, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
   /* "rnacounter/rnacounter.pyx":1
diff --git a/rnacounter/rnacounter.pyx b/rnacounter/rnacounter.pyx
index abd8446..dfc5f97 100644
--- a/rnacounter/rnacounter.pyx
+++ b/rnacounter/rnacounter.pyx
@@ -435,8 +435,7 @@ cdef inline bint is_in(str ftype,GenomicObject x,str feat_id):
             # x is a piece: p == feat_id
 
 
-cdef list estimate_expression_NNLS(str ftype,list pieces,list ids,list exons,double norm_cst,
-                                   bint stranded,bint weighted):
+cdef list estimate_expression_NNLS(str ftype,list pieces,list ids,list exons,double norm_cst,bint stranded):
     """Infer gene/transcript expression from exons RPK. Takes GenomicObject instances *pieces*
     and returns for each feature ID in *ids* an instance of *ftype* with the
     appropriate count and RPK attributes set.
@@ -459,11 +458,11 @@ cdef list estimate_expression_NNLS(str ftype,list pieces,list ids,list exons,dou
             if is_in(ftype,p,f): A[i,j] = 1.
     #--- Build the exons scores vector
     E = array([p.rpk for p in pieces])
-    if weighted:
-        w = sqrt(array([p.length for p in pieces]))
-        W = diag(w)
-        A = dot(W,A)
-        E = multiply(E, w)
+    # Weights
+    w = sqrt(array([p.length for p in pieces]))
+    W = diag(w)
+    A = dot(W,A)
+    E = multiply(E, w)
     #--- Solve for RPK
     T,rnorm = nnls(A,E)
     #-- Same for antisense if stranded protocol
@@ -550,11 +549,11 @@ cdef dict filter_transcripts(dict t2p,int exon_cutoff):
     """*t2p* is a map {transcriptID: [exon pieces]}.
     Find transcripts that differ from others by exon parts of less than
     one read length."""
-    cdef dict seen, replace
+    cdef dict structs, replace
     cdef str t, main
     cdef list texons, tlist
     cdef GenomicObject te
-    cdef tuple filtered_ids, f
+    cdef tuple filtered_ids, f, structure
     structs = {}  # transcript structures, as tuples of exon ids
     replace = {} # too close transcripts
     for t,texons in sorted(t2p.items(), key=itemgetter(0)):
@@ -577,10 +576,10 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
     cdef GenomicObject exon0, gr, p, e, gene, trans
     cdef list exons, exons2, introns, introns2, genes, transcripts
     cdef list exon_names, transcript_ids, gene_ids
-    cdef list pieces, tpieces, types
-    cdef dict t2p, methods
-    cdef str t, tid
-    cdef bint stranded, weighted
+    cdef list pieces, tpieces, types, syns
+    cdef dict t2p, methods, synonyms
+    cdef str t, tid, synonym
+    cdef bint stranded
     cdef double norm_cst, threshold
 
     norm_cst = options['normalize']
@@ -591,7 +590,6 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
     threshold = options['threshold']
     fraglength = options['fraglength']
     exon_cutoff = options['exon_cutoff']
-    weighted = True  # WNNLS switch !
 
     #--- Regroup occurrences of the same exons from a different transcript
     exons = []
@@ -618,7 +616,7 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
         for p in pieces + exons:
             p.transcripts = set([replace[t] for t in p.transcripts])
         for t,main in replace.items():
-            if t!=main: synonyms.setdefault(main, set()).add(t)
+            synonyms.setdefault(main, set()).add(t)
     transcript_ids = sorted(t2p.keys())  # sort to have the same order in all outputs from same gtf
 
     #--- Count reads in each piece
@@ -661,37 +659,35 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
     if 1 in types:
         method = methods.get(1,1)
         if method == 1:
-            transcripts = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded,weighted)
+            transcripts = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
         elif method == 0:
             transcripts = estimate_expression_raw("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
         for i,trans in enumerate(transcripts):
             trans.rpk = correct_fraglen_bias(trans.rpk, trans.length, fraglength)
-            syns = synonyms.get(trans.name, [])
+            syns = sorted(list(synonyms.get(trans.name, [])))
             toadd = []
             for synonym in syns:
-                syns2 = set(syns)
-                syns2.remove(synonym)
-                syns2.add(trans.name)
-                toadd.append(GenomicObject(name=synonym, length=trans.length, ftype="transcript",
-                        rpk=trans.rpk, rpk_anti=trans.rpk_anti, count=trans.count, count_anti=trans.count_anti,
-                        chrom=trans.chrom, start=trans.start, end=trans.end,
-                        gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
-                        synonyms=','.join(syns2)))
+                if synonym != trans.name:
+                    toadd.append(GenomicObject(name=synonym, length=trans.length, ftype="transcript",
+                            rpk=trans.rpk, rpk_anti=trans.rpk_anti, count=trans.count, count_anti=trans.count_anti,
+                            chrom=trans.chrom, start=trans.start, end=trans.end,
+                            gene_id=trans.gene_id, gene_name=trans.gene_name, strand=trans.strand,
+                            synonyms=','.join(syns)))
             toadd.sort(key=attrgetter('start','end'))
             transcripts = transcripts[:i+1] + toadd + transcripts[i+1:]
-            trans.synonyms = ','.join(syns) if len(syns)>0 else '.'
+            trans.synonyms = ','.join(syns) if len(syns)>1 else '.'
     # Genes - 0
     if 0 in types:
         method = methods.get(0,0)
         if method == 0:
             genes = estimate_expression_raw("gene",pieces,gene_ids,exons,norm_cst,stranded)
         elif method == 1:
-            genes = estimate_expression_NNLS("gene",pieces,gene_ids,exons,norm_cst,stranded,weighted)
+            genes = estimate_expression_NNLS("gene",pieces,gene_ids,exons,norm_cst,stranded)
         elif method == 2:
             if 1 in types and methods.get(1) == 1:
                 genes = genes_from_transcripts(transcripts)
             else:
-                transcripts2 = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded,weighted)
+                transcripts2 = estimate_expression_NNLS("transcript",pieces,transcript_ids,exons,norm_cst,stranded)
                 genes = genes_from_transcripts(transcripts2)
                 transcripts2 = []
         for gene in genes:
@@ -703,7 +699,7 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
             exons2 = pieces[:]  # !
         elif method == 1:
             exon_ids = [p.name for p in exons]
-            exons2 = estimate_expression_NNLS("exon",pieces,exon_ids,exons,norm_cst,stranded,weighted)
+            exons2 = estimate_expression_NNLS("exon",pieces,exon_ids,exons,norm_cst,stranded)
     # Introns - 3
     if 3 in types and intron_pieces:
         method = methods.get(3,0)
@@ -711,7 +707,7 @@ def process_chunk(list ckexons,object sam,str chrom,dict options):
             introns2 = intron_pieces[:]   # !
         elif method == 1:
             intron_ids = [p.name for p in introns]
-            introns2 = estimate_expression_NNLS("intron",intron_pieces,intron_ids,introns,norm_cst,stranded,weighted)
+            introns2 = estimate_expression_NNLS("intron",intron_pieces,intron_ids,introns,norm_cst,stranded)
 
     print_output(output, genes,transcripts,exons2,introns2, threshold,stranded)
 
diff --git a/setup.py b/setup.py
index 421c42d..3d58541 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@ def readme():
 ]
 
 setup(name='rnacounter',
-    version='1.4.2',
+    version='1.5',
     description='Estimate abundances of genomic features from read densities',
     long_description=readme(),
     classifiers=[