fixed expected length, removed start sequence

dna_read.sh

@@ -179,7 +179,8 @@ then
 	call_function python3 "$consensus_script" "$clusters_frag_dir" "$consensus_path" $coded_frag_length
 
 else #ordered assembly
-	start_sequence=$(get_doc_param $container_path $document_index "start_sequence") #TODO remove start sequence -> use primers instead
+	start_primer=$(get_doc_param $container_path $document_index "start_primer")
+	stop_primer=$(get_doc_param $container_path $document_index "stop_primer")
 	
 	consensus_script="$project_dir"/sequencing_modules/reads_consensus.py
 	
@@ -187,10 +188,10 @@ else #ordered assembly
 	then
 		expected_length=$(($n_frag * $frag_length * 2)) # for a redundancy of 100%
 	else
-		expected_length=$(($n_frag * $frag_length -66 )) # primers are not expected
+		expected_length=$(($n_frag * $frag_length)) # primers are not expected but overhangs are (except on last fragments ->(-4))
 	fi
 	
-	call_function python3 "$consensus_script" -i "$sequenced_reads_path" -o "$consensus_path" -s "$start_sequence" -e "$expected_length"
+	call_function python3 "$consensus_script" -i "$sequenced_reads_path" -o "$consensus_path" --start $start_primer --stop $stop_primer -e $expected_length
 fi
 
 consensus_time=$(date +"%s")