Fix tool_consensus.py

src/tool_consensus.py

@@ -33,7 +33,7 @@ for key in nuc_to_iupac.keys():
 def consensus_iupac(alignment,threshold):
 	summary_align = AlignInfo.SummaryInfo(alignment)
 	nb_reads = len(summary_align.get_column(0))
-	align_size=len(alignment[1].seq)
+	align_size=len(alignment[0].seq)
 	letters=summary_align._get_all_letters()
 	seq=""
 	#Run the alignment column by column
@@ -103,7 +103,7 @@ def consensus_iupac(alignment,threshold):
 def consensus(alignment,threshold):
 	summary_align = AlignInfo.SummaryInfo(alignment)
 	nb_reads = len(summary_align.get_column(0))
-	align_size = len(alignment[1].seq)
+	align_size = len(alignment[0].seq)
 	letters = summary_align._get_all_letters()
 	letters = letters.replace('-','')
 	seq=""
@@ -149,7 +149,7 @@ def majority_consensus(alignment):
 	threshold=0.5
 	summary_align = AlignInfo.SummaryInfo(alignment)
 	nb_reads = len(summary_align.get_column(0))
-	align_size = len(alignment[1].seq)
+	align_size = len(alignment[0].seq)
 	seq=""
 
 	#Run the alignment column by column