diff --git a/src/alignment.r b/src/alignment.r
index 7175e86..63b161a 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -11,22 +11,22 @@ parse_data <- function(file) {
   return(list(sequences, vj_segments))
 }
 
-match_id_sequence <- function(names, sequences, id) {
+match_id_sequence <- function(names, vdj_segments, id) {
   matches <- grep(names, pattern = id)
   row <- matches[1]
-  return(as.character(sequences[row]))
+  return(as.character(vdj_segments[row]))
 }
 
-get_vj_sequence <- function(sequences, names, vdj_segments) {
-  metadata <- unlist(strsplit(sequences, split = " "))
-  v_identifier <- metadata[2]
-  j_identifier <- metadata[3]
+get_vj_sequence <- function(metadata, names, vdj_segments) {
+  id_elements <- unlist(strsplit(metadata, split = " "))
+  v_identifier <- id_elements[2]
+  j_identifier <- id_elements[3]
   v_sequence <- match_id_sequence(names, vdj_segments, id = v_identifier)
   j_sequence <- match_id_sequence(names, vdj_segments, id = j_identifier)
   return(c(v_sequence, j_sequence))
 }
 
-fetch_vj_sequences <- function(vdj_segments, sequences) {
+fetch_vj_sequences <- function(sequences, vdj_segments) {
   vj_sequences <- mclapply(names(sequences),
     names(vdj_segments),
     vdj_segments,
@@ -45,8 +45,9 @@ align_sequence <- function(sequence, vdj_segment) {
   ))
 }
 
+# TODO Extract CDR3
 get_hvr_sequences <- function(sequences, vdj_segments) {
-  vj_sequences <- fetch_vj_sequences(vdj_segments, sequences)
+  vj_sequences <- fetch_vj_sequences(sequences, vdj_segments)
   v_alignment <- parallel::mcmapply(sequences,
     vj_sequences[1],
     FUN = align_sequence