+ added some testcases
[qpalma.git] / scripts / PipelineHeuristic.py
index d4b92a8..e6e3a39 100644 (file)
@@ -247,13 +247,14 @@ class PipelineHeuristic:
 
          # forgot to do this
          if strand == '-':
-            pos = self.lt1.seqInfo.chromo_sizes[chr]-pos-self.read_size
+            #pos = self.lt1.seqInfo.chromo_sizes[chr]-pos-self.read_size
             unb_seq = reverse_complement(unb_seq)
 
          effective_len = len(unb_seq)
 
          genomicSeq_start  = pos
-         genomicSeq_stop   = pos+effective_len-1
+         #genomicSeq_stop   = pos+effective_len-1
+         genomicSeq_stop   = pos+effective_len
 
          start = cpu()
          #currentDNASeq, currentAcc, currentDon = get_seq_and_scores(chr,strand,genomicSeq_start,genomicSeq_stop,run['dna_flat_files'])