diff --git a/src/alignment.r b/src/alignment.r
index 25facbb..7175e86 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -1,36 +1,39 @@
 library(Biostrings)
 library(parallel)
 
-parse_data <- function(files) {
-  reversed_sequences <- Biostrings::readQualityScaledDNAStringSet(files[1])
+parse_data <- function(file) {
+  reversed_sequences <- Biostrings::readQualityScaledDNAStringSet(file)
   sequences <- Biostrings::reverseComplement(reversed_sequences)
-  vdj_metadata <- read.csv(files[2])
   vj_segments <- union(
     readRDS("data/v_segments.rds"),
     readRDS("data/j_segments_phe.rds")
   )
-  return(list(sequences, vj_segments, vdj_metadata))
+  return(list(sequences, vj_segments))
 }
 
-get_vj_sequence <- function(identifier, names, sequences) {
-  matches <- grep(names, pattern = identifier)
+match_id_sequence <- function(names, sequences, id) {
+  matches <- grep(names, pattern = id)
   row <- matches[1]
   return(as.character(sequences[row]))
 }
 
-construct_full_sequences <- function(vdj_segments, metadata) {
-  v_sequences <- lapply(metadata$v_call,
+get_vj_sequence <- function(sequences, names, vdj_segments) {
+  metadata <- unlist(strsplit(sequences, split = " "))
+  v_identifier <- metadata[2]
+  j_identifier <- metadata[3]
+  v_sequence <- match_id_sequence(names, vdj_segments, id = v_identifier)
+  j_sequence <- match_id_sequence(names, vdj_segments, id = j_identifier)
+  return(c(v_sequence, j_sequence))
+}
+
+fetch_vj_sequences <- function(vdj_segments, sequences) {
+  vj_sequences <- mclapply(names(sequences),
     names(vdj_segments),
     vdj_segments,
-    FUN = get_vj_sequence
+    FUN = get_vj_sequence,
+    mc.cores = detectCores()
   )
-  j_sequences <- lapply(metadata$j_call,
-    names(vdj_segments),
-    vdj_segments,
-    FUN = get_vj_sequence
-  )
-  full_sequence <- paste(v_sequences, metadata$junction, j_sequences, sep = "")
-  return(Biostrings::DNAStringSet(full_sequence))
+  return(c(vj_sequences[1], vj_sequences[2]))
 }
 
 align_sequence <- function(sequence, vdj_segment) {
@@ -38,25 +41,24 @@ align_sequence <- function(sequence, vdj_segment) {
     subject = sequence,
     pattern = vdj_segment,
     type = "global-local",
-    gapOpening = 1,
+    gapOpening = 1
   ))
 }
 
-perform_alignment <- function(sequences, vdj_segments, metadata) {
-  vj_sequences <- construct_full_sequences(vdj_segments, metadata)
-  sequence_alignment <- mcmapply(vj_sequences,
-    vdj_segments,
-    FUN = align_sequence,
-    mc.cores = detectCores()
+get_hvr_sequences <- function(sequences, vdj_segments) {
+  vj_sequences <- fetch_vj_sequences(vdj_segments, sequences)
+  v_alignment <- parallel::mcmapply(sequences,
+    vj_sequences[1],
+    FUN = align_sequence
+  )
+  j_alignment <- parallel::mcmapply(sequences,
+    vj_sequences[2],
+    FUN = align_sequence
   )
-  return(sequence_alignment)
 }
 
-input_files <- c("data/curesim_sequence.fastq", "data/vdj_metadata.csv")
-data <- parse_data(files = input_files)
-alignment <- perform_alignment(
+data <- parse_data(file = "data/curesim_sequence.fastq")
+hvr_sequences <- get_hvr_sequences(
   sequences = data[[1]],
-  vdj_segments = data[[2]],
-  metadata = data[[3]]
-)
-print(alignment)
\ No newline at end of file
+  vdj_segments = data[[2]]
+)
\ No newline at end of file