diff --git a/src/alignment.r b/src/alignment.r
index d5f3e17..f4bbee4 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -1,27 +1,15 @@
 library(Biostrings)
 library(parallel)
 
-construct_hvr_sequence <- function(data) {
-  vdj_dataframe <- as.data.frame(data)
-  hvr_sequence <- paste(vdj_dataframe$v_sequence,
-    vdj_dataframe$d_sequence,
-    vdj_dataframe$j_sequence,
-    sep = ""
-  )
-  vdj_dataframe$hvr <- hvr_sequence
-  return(vdj_dataframe)
-}
-
 parse_data <- function(files) {
   reversed_sequences <- Biostrings::readQualityScaledDNAStringSet(files[1])
   sequences <- Biostrings::reverseComplement(reversed_sequences)
-  vdj_alignment <- read.csv(files[2])
-  vdj_dataframe <- construct_hvr_sequence(vdj_alignment)
+  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_dataframe))
+  return(list(sequences, vj_segments, vdj_metadata))
 }
 
 get_vj_sequence <- function(identifier, names, sequences) {
@@ -41,7 +29,7 @@ construct_full_sequences <- function(vdj_segments, metadata) {
     vdj_segments,
     FUN = get_vj_sequence
   )
-  full_sequence <- paste(v_sequences, metadata$hvr, j_sequences, sep = "")
+  full_sequence <- paste(v_sequences, metadata$junction, j_sequences, sep = "")
   return(Biostrings::DNAStringSet(full_sequence))
 }
 
@@ -64,11 +52,11 @@ perform_alignment <- function(sequences, vdj_segments, metadata) {
   return(sequence_alignment)
 }
 
-input_files <- c("data/curesim_sequence.fastq", "data/vdj_alignment.csv")
-data <- parse_data(input_files)
+input_files <- c("data/curesim_sequence.fastq", "data/vdj_metadata.csv")
+data <- parse_data(files = input_files)
 alignment <- perform_alignment(
   sequences = data[[1]],
   vdj_segments = data[[2]],
   metadata = data[[3]]
 )
-print(alignment)
+print(alignment)
\ No newline at end of file
diff --git a/src/repertoire.r b/src/repertoire.r
index cb60947..8904ad7 100644
--- a/src/repertoire.r
+++ b/src/repertoire.r
@@ -14,15 +14,11 @@ save_data <- function(data, reads) {
   Biostrings::writeXStringSet(data$sequence, "data/sequence.fasta")
   vdj_sequences <- data[-1]
   amplified_vdj <- vdj_sequences[rep(seq_len(nrow(vdj_sequences)), reads), ]
-  write.csv(amplified_vdj, "data/vdj_alignment.csv", row.names = FALSE)
+  write.csv(amplified_vdj, "data/vdj_metadata.csv", row.names = FALSE)
 }
 
 process_data <- function(repertoire, reads) {
-  columns <- c(
-    "sequence", "v_sequence_alignment",
-    "d_sequence_alignment", "j_sequence_alignment",
-    "v_call", "j_call"
-  )
+  columns <- c("sequence", "junction", "v_call", "j_call")
   data <- repertoire[, columns]
   dna_sequence <- Biostrings::DNAStringSet(data$sequence)
   data$sequence <- Biostrings::reverseComplement(dna_sequence)