diff --git a/DESCRIPTION b/DESCRIPTION
index 0cef1b8..95e4147 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BIGr
 Title: Breeding Insight Genomics Functions for Polyploid and Diploid Species
-Version: 0.6.3
+Version: 0.7.0
 Authors@R: c(person(given='Alexander M.',
                     family='Sandercock',
                     email='sandercock.alex@gmail.com',
@@ -44,7 +44,7 @@ URL: https://github.com/Breeding-Insight/BIGr
 BugReports: https://github.com/Breeding-Insight/BIGr/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends: R (>= 4.4.0)
 biocViews:
 Imports: 
diff --git a/NAMESPACE b/NAMESPACE
index d47d95d..574981a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(dosage2vcf)
 export(dosage_ratios)
 export(filterMADC)
 export(filterVCF)
+export(fixMADC)
 export(flip_dosage)
 export(get_countsMADC)
 export(imputation_concordance)
@@ -40,6 +41,7 @@ importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(stats,cor)
 importFrom(stats,setNames)
+importFrom(tidyr,replace_na)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
diff --git a/NEWS.md b/NEWS.md
index 19d2509..e8f1b1c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# BIGr 0.7.0
+
+- Added a new function fixMADC to format raw MADC files with a user-supplied Chr and Pos file.
+
 # BIGr 0.6.3
 
 - Ignore tags when targets are indels
diff --git a/R/fixMADC.R b/R/fixMADC.R
new file mode 100644
index 0000000..2437f86
--- /dev/null
+++ b/R/fixMADC.R
@@ -0,0 +1,213 @@
+#' Fix MADC File Allele IDs
+#'
+#' Process raw MADC files to format and update the allele IDs with user supplied Chr and Pos information
+#'
+#' @details
+#' This function can process raw MADC files to update the Allele IDs and Clone IDs to the Chr_Pos format with a user supplied file.
+#' The output MADC will be the standard fixed allele ID format to support use in madc2vcf and BIGapp functions.
+#'
+#'@import dplyr
+#'@import stringr
+#'@importFrom tidyr replace_na
+#'@importFrom utils read.csv write.csv
+#'
+#'@param madc.file Path to the MADC file to be filtered
+#'@param marker.file Path to the three column marker ID file.
+#' - The first column is the existing list of unique CloneIDs (obtained from raw MADC CloneID),
+#'where each row is a unique CloneID.
+#' - The second column is the chromosome that the marker is located (ie Chr01). No special characters (*#_-!.) are permitted in the
+#' chromosome name.
+#' - The third column is the numeric position of the marker within the chromosome (ie 1234). No special characters (*#_-!.) are permitted.
+#'@param n.summary.columns (optional) Number of summary columns to remove from MADC file not including the first three. Otherwise, the columns will be automatically detected and removed.
+#'@param output.file Path to save the fixed allele ID MADC file (if NULL, data will not be saved)
+#'
+#'@return data.frame or saved csv file
+#'
+#'@examples
+#' #Example
+#'
+#' #Example MADC
+#' madc_file <- system.file("iris_DArT_MADC.csv", package="BIGr")
+#' marker_file <- system.file("iris_MADC_marker_file.csv", package="BIGr")
+#'
+#' #Fix the raw MADC file IDs to use the user provided Chr_Pos format
+#' fixedMADC_df <- fixMADC(madc.file = madc_file,
+#'                          marker.file = marker_file,
+#'                          n.summary.columns = NULL,
+#'                          output.file = NULL)
+#'
+#'
+#'
+#'@export
+fixMADC <- function(madc.file,
+                       marker.file,
+                       n.summary.columns = NULL,
+                       output.file = NULL) {
+
+
+  #Need to first inspect the first 7 rows of the MADC to see if it has been preprocessed or not
+  first_seven_rows <- read.csv(madc.file, header = FALSE, nrows = 7, colClasses = c(NA, "NULL"))
+
+  #Check if all entries in the first column are either blank or "*"
+  check_entries <- all(first_seven_rows[, 1] %in% c("", "*"))
+
+  #Check if the MADC file has the filler rows or is processed from updated fixed allele ID pipeline
+  if (check_entries) {
+    #Note: This assumes that the first 7 rows are placeholder info from DArT processing
+
+    #Read the madc file
+    filtered_df <- read.csv(madc.file, sep = ',', skip = 7, check.names = FALSE)
+
+    #Remove extra text after Ref and Alt (_001 or _002)
+    #filtered_df$AlleleID <- sub("\\|Ref_.*", "|Ref", filtered_df$AlleleID)
+    #filtered_df$AlleleID <- sub("\\|Alt_.*", "|Alt", filtered_df$AlleleID)
+
+  } else {
+
+    stop("This MADC file appears to already use fixed allele IDs and cannot be reprocessed with a raw-ID marker file.")
+
+    #Read the madc file
+    filtered_df <- read.csv(madc.file, sep = ',', check.names = FALSE)
+
+    #Remove extra text after Ref and Alt (_001 or _002)
+    #filtered_df$AlleleID <- sub("\\|Ref_.*", "|Ref", filtered_df$AlleleID)
+    #filtered_df$AlleleID <- sub("\\|Alt_.*", "|Alt", filtered_df$AlleleID)
+
+  }
+  #Check for extra columns
+  #Save the three columns for later adding to the output (currently unused)
+
+  if (!is.null(n.summary.columns)) {
+    #Remove the first n.summary.columns columns
+    if (n.summary.columns > 0) {
+      cols_to_remove <- 4:(3 + n.summary.columns)
+      filtered_df <- filtered_df[, -cols_to_remove, drop = FALSE]
+    }
+  }else{
+    rm.col <- c("ClusterConsensusSequence",
+                "CallRate", "OneRatioRef", "OneRatioSnp", "FreqHomRef", "FreqHomSnp",
+                "FreqHets", "PICRef", "PICSnp", "AvgPIC", "AvgCountRef", "AvgCountSnp","RatioAvgCountRefAvgCountSnp")
+
+    filtered_df <- filtered_df[, !(colnames(filtered_df) %in% rm.col)]
+  }
+
+  #Trim whitespace if present for some reason
+  filtered_df$CloneID <- trimws(as.character(filtered_df$CloneID))
+  filtered_df$AlleleID <- trimws(as.character(filtered_df$AlleleID))
+
+  #Read in the marker file
+  marker_file <- read.csv(marker.file, sep = ',', check.names = FALSE)
+
+  ### Verify marker file is formatted correctly ###
+
+  marker_file[,1] <- trimws(as.character(marker_file[,1]))
+  marker_file[,2] <- trimws(as.character(marker_file[,2]))
+  marker_file[,3] <- trimws(as.character(marker_file[,3]))
+
+  if (any(grepl("[*#_!.\\-]", marker_file[,3]))) {
+    stop("Special characters (*#_-!.) detected in the position column (column 3). Please review the marker file.")
+  }
+
+  if (!all(grepl("^[0-9]+$", marker_file[,3]))) {
+    stop("The position column (column 3) must be numeric. Please review the marker file.")
+  }
+
+  #Make marker IDs column and pad 0's for the position
+  marker_file$new_ID <- paste0(
+    marker_file[,2],
+    "_",
+    str_pad(marker_file[,3], width = 9, side = "left", pad = "0")
+  )
+
+  #Verify there are no duplicate IDs in the marker file
+  if (length(unique(marker_file[,1])) != length(marker_file[,1])) {
+    stop("There are duplicate marker IDs in the first column. Please review marker file.")
+  }
+
+  #Verify there are no duplicate position information
+  if (length(unique(marker_file$new_ID)) != length(marker_file$new_ID)) {
+    stop("There are duplicate Chr and Pos information where more than one marker has the same Chr_Pos. Please review the marker file.")
+  }
+
+  #Verify chromosome column (col 2) contains no special characters
+  if (any(grepl("[*#_!.\\-]", marker_file[,2]))) {
+    stop("Special characters (*#_-!.) detected in the chromosome column (column 2). Please review the marker file.")
+  }
+
+
+  ## Filtering
+
+  #Identify MADC CloneIDs not found in the marker file
+  missing_ids <- setdiff(filtered_df$CloneID, marker_file[,1])
+
+  if (length(missing_ids) > 0) {
+    warning(paste0(
+      length(missing_ids), " CloneID(s) in the MADC file were not found in the marker file and will be removed from the output:\n",
+      paste(missing_ids, collapse = "\n")
+    ))
+
+    # Remove unmatched IDs from MADC file
+    filtered_df <- filtered_df[filtered_df$CloneID %in% marker_file[,1], ]
+  }
+
+  ###Replace old IDs with new IDs
+
+  #Create a named lookup vector: old CloneID and AlleleID -> new_ID
+  id_lookup <- setNames(marker_file$new_ID, marker_file[,1])
+
+  filtered_df <- filtered_df %>%
+    mutate(
+      # Replace CloneID column directly via lookup
+      CloneID = id_lookup[CloneID],
+
+      # For AlleleID: extract the |suffix, replace the ID prefix, rejoin
+      AlleleID = {
+        old_id <- str_extract(AlleleID, "^[^|]+")
+        suffix  <- str_extract(AlleleID, "\\|.*$")
+        suffix  <- replace_na(suffix, "")  # Handle cases with no suffix
+        paste0(id_lookup[old_id], suffix)
+      }
+    )
+
+  ###Add the proper numbering suffix to allele IDs for unique IDs.
+  # |Ref    -> |Ref_0001
+  # |Alt    -> |Alt_0002
+  # |RefMatch -> numbered _0001, _0002, ... within each CloneID
+  # |AltMatch -> numbered _0001, _0002, ... within each CloneID
+
+  filtered_df <- filtered_df %>%
+    mutate(
+      .suffix_type = str_extract(AlleleID, "(?<=\\|)[^_]+$")
+    ) %>%
+    group_by(CloneID, .suffix_type) %>%
+    mutate(
+      AlleleID = case_when(
+        .suffix_type == "Ref" ~ paste0(str_remove(AlleleID, "\\|Ref$"), "|Ref_0001"),
+        .suffix_type == "Alt" ~ paste0(str_remove(AlleleID, "\\|Alt$"), "|Alt_0002"),
+        .suffix_type == "RefMatch" ~ paste0(
+          str_remove(AlleleID, "\\|RefMatch$"),
+          "|RefMatch_",
+          sprintf("%04d", row_number())
+        ),
+        .suffix_type == "AltMatch" ~ paste0(
+          str_remove(AlleleID, "\\|AltMatch$"),
+          "|AltMatch_",
+          sprintf("%04d", row_number())
+        ),
+        TRUE ~ AlleleID
+      )
+    ) %>%
+    ungroup() %>%
+    select(-.suffix_type)
+
+
+  #Save the output to disk if file name provided
+  if (!is.null(output.file)) {
+    message("Saving fixed MADC data to file")
+    write.csv(filtered_df, paste0(output.file,"_fixedID.csv"), row.names = FALSE)
+  } else {
+    message("No output file provided. Returning fixed MADC data.")
+    return(filtered_df)
+  }
+
+}
diff --git a/R/utils.R b/R/utils.R
index c280ad2..4f31798 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -6,7 +6,7 @@ utils::globalVariables(c(
   "ind", "ref", "row_name", "size", "snp",
   "CloneID", "Count", "qualifying_sites_count",
   "MarkerID", "SampleID", "Dosage",
-  "pos", "alt", "match_key"
+  "pos", "alt", "match_key", ".suffix_type"
 ))
 
 #' Convert GT format to numeric dosage
diff --git a/cran-comments.md b/cran-comments.md
index 2515e5b..858617d 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -3,7 +3,3 @@
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
-
-## Updates
-
-- The maintainer is the same as the previous release, but the email address has been updated.
diff --git a/inst/iris_MADC_marker_file.csv b/inst/iris_MADC_marker_file.csv
new file mode 100644
index 0000000..6ec0476
--- /dev/null
+++ b/inst/iris_MADC_marker_file.csv
@@ -0,0 +1,501 @@
+CloneID,Chr,Pos
+Chr1_0010,Chr1,10
+Chr1_0100,Chr1,100
+Chr4_0810,Chr4,810
+Chr4_0820,Chr4,820
+Chr4_0830,Chr4,830
+Chr4_0840,Chr4,840
+Chr4_0850,Chr4,850
+Chr5_0860,Chr5,860
+Chr5_0870,Chr5,870
+Chr5_0880,Chr5,880
+Chr5_0890,Chr5,890
+Chr5_0900,Chr5,900
+Chr1_0110,Chr1,110
+Chr5_0910,Chr5,910
+Chr5_0920,Chr5,920
+Chr5_0930,Chr5,930
+Chr5_0940,Chr5,940
+Chr5_0950,Chr5,950
+Chr5_0960,Chr5,960
+Chr5_0970,Chr5,970
+Chr5_0980,Chr5,980
+Chr5_0990,Chr5,990
+Chr5_1000,Chr5,1000
+Chr1_0120,Chr1,120
+Chr5_1010,Chr5,1010
+Chr5_1020,Chr5,1020
+Chr5_1030,Chr5,1030
+Chr5_1040,Chr5,1040
+Chr5_1050,Chr5,1050
+Chr5_1060,Chr5,1060
+Chr5_1070,Chr5,1070
+Chr5_1080,Chr5,1080
+Chr5_1090,Chr5,1090
+Chr5_1100,Chr5,1100
+Chr1_0130,Chr1,130
+Chr5_1110,Chr5,1110
+Chr5_1120,Chr5,1120
+Chr5_1130,Chr5,1130
+Chr5_1140,Chr5,1140
+Chr5_1150,Chr5,1150
+Chr5_1160,Chr5,1160
+Chr5_1170,Chr5,1170
+Chr5_1180,Chr5,1180
+Chr5_1190,Chr5,1190
+Chr5_1200,Chr5,1200
+Chr1_0140,Chr1,140
+Chr5_1210,Chr5,1210
+Chr5_1220,Chr5,1220
+Chr5_1230,Chr5,1230
+Chr5_1240,Chr5,1240
+Chr5_1250,Chr5,1250
+Chr5_1260,Chr5,1260
+Chr5_1270,Chr5,1270
+Chr5_1280,Chr5,1280
+Chr5_1290,Chr5,1290
+Chr5_1300,Chr5,1300
+Chr1_0150,Chr1,150
+Chr5_1310,Chr5,1310
+Chr5_1320,Chr5,1320
+Chr5_1330,Chr5,1330
+Chr5_1340,Chr5,1340
+Chr5_1350,Chr5,1350
+Chr5_1360,Chr5,1360
+Chr6_1370,Chr6,1370
+Chr6_1380,Chr6,1380
+Chr6_1390,Chr6,1390
+Chr6_1400,Chr6,1400
+Chr1_0160,Chr1,160
+Chr6_1410,Chr6,1410
+Chr6_1420,Chr6,1420
+Chr6_1430,Chr6,1430
+Chr6_1440,Chr6,1440
+Chr6_1450,Chr6,1450
+Chr6_1460,Chr6,1460
+Chr6_1470,Chr6,1470
+Chr6_1480,Chr6,1480
+Chr6_1490,Chr6,1490
+Chr6_1500,Chr6,1500
+Chr1_0170,Chr1,170
+Chr6_1510,Chr6,1510
+Chr6_1520,Chr6,1520
+Chr6_1530,Chr6,1530
+Chr6_1540,Chr6,1540
+Chr6_1550,Chr6,1550
+Chr6_1560,Chr6,1560
+Chr6_1570,Chr6,1570
+Chr6_1580,Chr6,1580
+Chr6_1590,Chr6,1590
+Chr6_1600,Chr6,1600
+Chr1_0180,Chr1,180
+Chr6_1610,Chr6,1610
+Chr6_1620,Chr6,1620
+Chr6_1630,Chr6,1630
+Chr6_1640,Chr6,1640
+Chr6_1650,Chr6,1650
+Chr6_1660,Chr6,1660
+Chr6_1670,Chr6,1670
+Chr6_1680,Chr6,1680
+Chr6_1690,Chr6,1690
+Chr6_1700,Chr6,1700
+Chr1_0190,Chr1,190
+Chr6_1710,Chr6,1710
+Chr6_1720,Chr6,1720
+Chr6_1730,Chr6,1730
+Chr6_1740,Chr6,1740
+Chr6_1750,Chr6,1750
+Chr6_1760,Chr6,1760
+Chr6_1770,Chr6,1770
+Chr6_1780,Chr6,1780
+Chr6_1790,Chr6,1790
+Chr6_1800,Chr6,1800
+Chr1_0020,Chr1,20
+Chr2_0010,Chr2,10
+Chr6_1810,Chr6,1810
+Chr6_1820,Chr6,1820
+Chr6_1830,Chr6,1830
+Chr6_1840,Chr6,1840
+Chr6_1850,Chr6,1850
+Chr6_1860,Chr6,1860
+Chr6_1870,Chr6,1870
+Chr6_1880,Chr6,1880
+Chr6_1890,Chr6,1890
+Chr6_1900,Chr6,1900
+Chr2_0020,Chr2,20
+Chr6_1910,Chr6,1910
+Chr6_1920,Chr6,1920
+Chr6_1930,Chr6,1930
+Chr6_1940,Chr6,1940
+Chr6_1950,Chr6,1950
+Chr6_1960,Chr6,1960
+Chr6_1970,Chr6,1970
+Chr6_1980,Chr6,1980
+Chr6_1990,Chr6,1990
+Chr6_2000,Chr6,2000
+Chr2_0030,Chr2,30
+Chr6_2010,Chr6,2010
+Chr6_2020,Chr6,2020
+Chr6_2030,Chr6,2030
+Chr7_2040,Chr7,2040
+Chr7_2050,Chr7,2050
+Chr7_2060,Chr7,2060
+Chr7_2070,Chr7,2070
+Chr7_2080,Chr7,2080
+Chr7_2090,Chr7,2090
+Chr7_2100,Chr7,2100
+Chr2_0040,Chr2,40
+Chr7_2110,Chr7,2110
+Chr7_2120,Chr7,2120
+Chr7_2130,Chr7,2130
+Chr7_2140,Chr7,2140
+Chr7_2150,Chr7,2150
+Chr7_2160,Chr7,2160
+Chr7_2170,Chr7,2170
+Chr7_2180,Chr7,2180
+Chr7_2190,Chr7,2190
+Chr7_2200,Chr7,2200
+Chr2_0050,Chr2,50
+Chr7_2210,Chr7,2210
+Chr7_2220,Chr7,2220
+Chr7_2230,Chr7,2230
+Chr7_2240,Chr7,2240
+Chr7_2250,Chr7,2250
+Chr7_2260,Chr7,2260
+Chr7_2270,Chr7,2270
+Chr7_2280,Chr7,2280
+Chr7_2290,Chr7,2290
+Chr7_2300,Chr7,2300
+Chr2_0060,Chr2,60
+Chr7_2310,Chr7,2310
+Chr7_2320,Chr7,2320
+Chr7_2330,Chr7,2330
+Chr7_2340,Chr7,2340
+Chr7_2350,Chr7,2350
+Chr7_2360,Chr7,2360
+Chr7_2370,Chr7,2370
+Chr7_2380,Chr7,2380
+Chr7_2390,Chr7,2390
+Chr7_2400,Chr7,2400
+Chr2_0070,Chr2,70
+Chr7_2410,Chr7,2410
+Chr7_2420,Chr7,2420
+Chr7_2430,Chr7,2430
+Chr7_2440,Chr7,2440
+Chr7_2450,Chr7,2450
+Chr7_2460,Chr7,2460
+Chr7_2470,Chr7,2470
+Chr7_2480,Chr7,2480
+Chr7_2490,Chr7,2490
+Chr7_2500,Chr7,2500
+Chr2_0080,Chr2,80
+Chr7_2510,Chr7,2510
+Chr7_2520,Chr7,2520
+Chr7_2530,Chr7,2530
+Chr7_2540,Chr7,2540
+Chr7_2550,Chr7,2550
+Chr7_2560,Chr7,2560
+Chr7_2570,Chr7,2570
+Chr7_2580,Chr7,2580
+Chr7_2590,Chr7,2590
+Chr7_2600,Chr7,2600
+Chr2_0090,Chr2,90
+Chr7_2610,Chr7,2610
+Chr7_2620,Chr7,2620
+Chr7_2630,Chr7,2630
+Chr7_2640,Chr7,2640
+Chr7_2650,Chr7,2650
+Chr7_2660,Chr7,2660
+Chr7_2670,Chr7,2670
+Chr7_2680,Chr7,2680
+Chr7_2690,Chr7,2690
+Chr7_2700,Chr7,2700
+Chr2_0100,Chr2,100
+Chr7_2710,Chr7,2710
+Chr7_2720,Chr7,2720
+Chr7_2730,Chr7,2730
+Chr7_2740,Chr7,2740
+Chr7_2750,Chr7,2750
+Chr7_2760,Chr7,2760
+Chr7_2770,Chr7,2770
+Chr7_2780,Chr7,2780
+Chr7_2790,Chr7,2790
+Chr7_2800,Chr7,2800
+Chr1_0030,Chr1,30
+Chr2_0110,Chr2,110
+Chr7_2810,Chr7,2810
+Chr7_2820,Chr7,2820
+Chr7_2830,Chr7,2830
+Chr7_2840,Chr7,2840
+Chr7_2850,Chr7,2850
+Chr7_2860,Chr7,2860
+Chr7_2870,Chr7,2870
+Chr7_2880,Chr7,2880
+Chr8_2890,Chr8,2890
+Chr8_2900,Chr8,2900
+Chr2_0120,Chr2,120
+Chr8_2910,Chr8,2910
+Chr8_2920,Chr8,2920
+Chr8_2930,Chr8,2930
+Chr8_2940,Chr8,2940
+Chr8_2950,Chr8,2950
+Chr8_2960,Chr8,2960
+Chr8_2970,Chr8,2970
+Chr8_2980,Chr8,2980
+Chr8_2990,Chr8,2990
+Chr8_3000,Chr8,3000
+Chr2_0130,Chr2,130
+Chr8_3010,Chr8,3010
+Chr8_3020,Chr8,3020
+Chr8_3030,Chr8,3030
+Chr8_3040,Chr8,3040
+Chr8_3050,Chr8,3050
+Chr8_3060,Chr8,3060
+Chr8_3070,Chr8,3070
+Chr8_3080,Chr8,3080
+Chr8_3090,Chr8,3090
+Chr8_3100,Chr8,3100
+Chr2_0140,Chr2,140
+Chr8_3110,Chr8,3110
+Chr8_3120,Chr8,3120
+Chr8_3130,Chr8,3130
+Chr8_3140,Chr8,3140
+Chr8_3150,Chr8,3150
+Chr8_3160,Chr8,3160
+Chr8_3170,Chr8,3170
+Chr8_3180,Chr8,3180
+Chr8_3190,Chr8,3190
+Chr8_3200,Chr8,3200
+Chr2_0150,Chr2,150
+Chr8_3210,Chr8,3210
+Chr8_3220,Chr8,3220
+Chr8_3230,Chr8,3230
+Chr8_3240,Chr8,3240
+Chr8_3250,Chr8,3250
+Chr8_3260,Chr8,3260
+Chr8_3270,Chr8,3270
+Chr8_3280,Chr8,3280
+Chr8_3290,Chr8,3290
+Chr8_3300,Chr8,3300
+Chr2_0160,Chr2,160
+Chr8_3310,Chr8,3310
+Chr8_3320,Chr8,3320
+Chr8_3330,Chr8,3330
+Chr8_3340,Chr8,3340
+Chr8_3350,Chr8,3350
+Chr8_3360,Chr8,3360
+Chr8_3370,Chr8,3370
+Chr8_3380,Chr8,3380
+Chr8_3390,Chr8,3390
+Chr8_3400,Chr8,3400
+Chr2_0170,Chr2,170
+Chr8_3410,Chr8,3410
+Chr8_3420,Chr8,3420
+Chr8_3430,Chr8,3430
+Chr8_3440,Chr8,3440
+Chr8_3450,Chr8,3450
+Chr8_3460,Chr8,3460
+Chr8_3470,Chr8,3470
+Chr8_3480,Chr8,3480
+Chr8_3490,Chr8,3490
+Chr8_3500,Chr8,3500
+Chr2_0180,Chr2,180
+Chr8_3510,Chr8,3510
+Chr8_3520,Chr8,3520
+Chr8_3530,Chr8,3530
+Chr8_3540,Chr8,3540
+Chr8_3550,Chr8,3550
+Chr8_3560,Chr8,3560
+Chr8_3570,Chr8,3570
+Chr8_3580,Chr8,3580
+Chr8_3590,Chr8,3590
+Chr8_3600,Chr8,3600
+Chr2_0190,Chr2,190
+Chr8_3610,Chr8,3610
+Chr8_3620,Chr8,3620
+Chr8_3630,Chr8,3630
+Chr8_3640,Chr8,3640
+Chr8_3650,Chr8,3650
+Chr8_3660,Chr8,3660
+Chr8_3670,Chr8,3670
+Chr8_3680,Chr8,3680
+Chr8_3690,Chr8,3690
+Chr8_3700,Chr8,3700
+Chr2_0200,Chr2,200
+Chr8_3710,Chr8,3710
+Chr8_3720,Chr8,3720
+Chr8_3730,Chr8,3730
+Chr8_3740,Chr8,3740
+Chr8_3750,Chr8,3750
+Chr8_3760,Chr8,3760
+Chr8_3770,Chr8,3770
+Chr8_3780,Chr8,3780
+Chr8_3790,Chr8,3790
+Chr8_3800,Chr8,3800
+Chr1_0040,Chr1,40
+Chr2_0210,Chr2,210
+Chr8_3810,Chr8,3810
+Chr8_3820,Chr8,3820
+Chr8_3830,Chr8,3830
+Chr8_3840,Chr8,3840
+Chr8_3850,Chr8,3850
+Chr8_3860,Chr8,3860
+Chr8_3870,Chr8,3870
+Chr8_3880,Chr8,3880
+Chr8_3890,Chr8,3890
+Chr8_3900,Chr8,3900
+Chr3_0220,Chr3,220
+Chr8_3910,Chr8,3910
+Chr8_3920,Chr8,3920
+Chr8_3930,Chr8,3930
+Chr8_3940,Chr8,3940
+Chr8_3950,Chr8,3950
+Chr8_3960,Chr8,3960
+Chr8_3970,Chr8,3970
+Chr8_3980,Chr8,3980
+Chr8_3990,Chr8,3990
+Chr8_4000,Chr8,4000
+Chr3_0230,Chr3,230
+Chr8_4010,Chr8,4010
+Chr8_4020,Chr8,4020
+Chr8_4030,Chr8,4030
+Chr8_4040,Chr8,4040
+Chr8_4050,Chr8,4050
+Chr8_4060,Chr8,4060
+Chr8_4070,Chr8,4070
+Chr8_4080,Chr8,4080
+Chr8_4090,Chr8,4090
+Chr8_4100,Chr8,4100
+Chr3_0240,Chr3,240
+Chr8_4110,Chr8,4110
+Chr8_4120,Chr8,4120
+Chr8_4130,Chr8,4130
+Chr8_4140,Chr8,4140
+Chr8_4150,Chr8,4150
+Chr8_4160,Chr8,4160
+Chr8_4170,Chr8,4170
+Chr8_4180,Chr8,4180
+Chr8_4190,Chr8,4190
+Chr8_4200,Chr8,4200
+Chr3_0250,Chr3,250
+Chr8_4210,Chr8,4210
+Chr8_4220,Chr8,4220
+Chr8_4230,Chr8,4230
+Chr8_4240,Chr8,4240
+Chr8_4250,Chr8,4250
+Chr8_4260,Chr8,4260
+Chr8_4270,Chr8,4270
+Chr8_4280,Chr8,4280
+Chr8_4290,Chr8,4290
+Chr8_4300,Chr8,4300
+Chr3_0260,Chr3,260
+Chr8_4310,Chr8,4310
+Chr8_4320,Chr8,4320
+Chr8_4330,Chr8,4330
+Chr8_4340,Chr8,4340
+Chr8_4350,Chr8,4350
+Chr8_4360,Chr8,4360
+Chr8_4370,Chr8,4370
+Chr8_4380,Chr8,4380
+Chr8_4390,Chr8,4390
+Chr8_4400,Chr8,4400
+Chr3_0270,Chr3,270
+Chr8_4410,Chr8,4410
+Chr8_4420,Chr8,4420
+Chr8_4430,Chr8,4430
+Chr8_4440,Chr8,4440
+Chr8_4450,Chr8,4450
+Chr8_4460,Chr8,4460
+Chr8_4470,Chr8,4470
+Chr8_4480,Chr8,4480
+Chr8_4490,Chr8,4490
+Chr8_4500,Chr8,4500
+Chr3_0280,Chr3,280
+Chr8_4510,Chr8,4510
+Chr8_4520,Chr8,4520
+Chr9_4530,Chr9,4530
+Chr9_4540,Chr9,4540
+Chr9_4550,Chr9,4550
+Chr9_4560,Chr9,4560
+Chr9_4570,Chr9,4570
+Chr9_4580,Chr9,4580
+Chr9_4590,Chr9,4590
+Chr9_4600,Chr9,4600
+Chr3_0290,Chr3,290
+Chr9_4610,Chr9,4610
+Chr9_4620,Chr9,4620
+Chr9_4630,Chr9,4630
+Chr9_4640,Chr9,4640
+Chr9_4650,Chr9,4650
+Chr9_4660,Chr9,4660
+Chr9_4670,Chr9,4670
+Chr9_4680,Chr9,4680
+Chr9_4690,Chr9,4690
+Chr9_4700,Chr9,4700
+Chr3_0300,Chr3,300
+Chr9_4710,Chr9,4710
+Chr9_4720,Chr9,4720
+Chr9_4730,Chr9,4730
+Chr9_4740,Chr9,4740
+Chr9_4750,Chr9,4750
+Chr9_4760,Chr9,4760
+Chr9_4770,Chr9,4770
+Chr9_4780,Chr9,4780
+Chr9_4790,Chr9,4790
+Chr9_4800,Chr9,4800
+Chr1_0050,Chr1,50
+Chr3_0310,Chr3,310
+Chr9_4810,Chr9,4810
+Chr3_0320,Chr3,320
+Chr3_0330,Chr3,330
+Chr3_0340,Chr3,340
+Chr3_0350,Chr3,350
+Chr3_0360,Chr3,360
+Chr3_0370,Chr3,370
+Chr3_0380,Chr3,380
+Chr3_0390,Chr3,390
+Chr3_0400,Chr3,400
+Chr1_0060,Chr1,60
+Chr3_0410,Chr3,410
+Chr3_0420,Chr3,420
+Chr3_0430,Chr3,430
+Chr3_0440,Chr3,440
+Chr3_0450,Chr3,450
+Chr3_0460,Chr3,460
+Chr3_0470,Chr3,470
+Chr3_0480,Chr3,480
+Chr3_0490,Chr3,490
+Chr3_0500,Chr3,500
+Chr1_0070,Chr1,70
+Chr3_0510,Chr3,510
+Chr3_0520,Chr3,520
+Chr3_0530,Chr3,530
+Chr3_0540,Chr3,540
+Chr3_0550,Chr3,550
+Chr3_0560,Chr3,560
+Chr3_0570,Chr3,570
+Chr3_0580,Chr3,580
+Chr3_0590,Chr3,590
+Chr3_0600,Chr3,600
+Chr1_0080,Chr1,80
+Chr3_0610,Chr3,610
+Chr4_0620,Chr4,620
+Chr4_0630,Chr4,630
+Chr4_0640,Chr4,640
+Chr4_0650,Chr4,650
+Chr4_0660,Chr4,660
+Chr4_0670,Chr4,670
+Chr4_0680,Chr4,680
+Chr4_0690,Chr4,690
+Chr4_0700,Chr4,700
+Chr1_0090,Chr1,90
+Chr4_0710,Chr4,710
+Chr4_0720,Chr4,720
+Chr4_0730,Chr4,730
+Chr4_0740,Chr4,740
+Chr4_0750,Chr4,750
+Chr4_0760,Chr4,760
+Chr4_0770,Chr4,770
+Chr4_0780,Chr4,780
+Chr4_0790,Chr4,790
+Chr4_0800,Chr4,800
diff --git a/man/fixMADC.Rd b/man/fixMADC.Rd
new file mode 100644
index 0000000..986ce7e
--- /dev/null
+++ b/man/fixMADC.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fixMADC.R
+\name{fixMADC}
+\alias{fixMADC}
+\title{Fix MADC File Allele IDs}
+\usage{
+fixMADC(madc.file, marker.file, n.summary.columns = NULL, output.file = NULL)
+}
+\arguments{
+\item{madc.file}{Path to the MADC file to be filtered}
+
+\item{marker.file}{Path to the three column marker ID file.
+\itemize{
+\item The first column is the existing list of unique CloneIDs (obtained from raw MADC CloneID),
+where each row is a unique CloneID.
+\item The second column is the chromosome that the marker is located (ie Chr01). No special characters (*#_-!.) are permitted in the
+chromosome name.
+\item The third column is the numeric position of the marker within the chromosome (ie 1234). No special characters (*#_-!.) are permitted.
+}}
+
+\item{n.summary.columns}{(optional) Number of summary columns to remove from MADC file not including the first three. Otherwise, the columns will be automatically detected and removed.}
+
+\item{output.file}{Path to save the fixed allele ID MADC file (if NULL, data will not be saved)}
+}
+\value{
+data.frame or saved csv file
+}
+\description{
+Process raw MADC files to format and update the allele IDs with user supplied Chr and Pos information
+}
+\details{
+This function can process raw MADC files to update the Allele IDs and Clone IDs to the Chr_Pos format with a user supplied file.
+The output MADC will be the standard fixed allele ID format to support use in madc2vcf and BIGapp functions.
+}
+\examples{
+#Example
+
+#Example MADC
+madc_file <- system.file("iris_DArT_MADC.csv", package="BIGr")
+marker_file <- system.file("iris_MADC_marker_file.csv", package="BIGr")
+
+#Fix the raw MADC file IDs to use the user provided Chr_Pos format
+fixedMADC_df <- fixMADC(madc.file = madc_file,
+                         marker.file = marker_file,
+                         n.summary.columns = NULL,
+                         output.file = NULL)
+
+
+
+}
diff --git a/tests/testthat/test-fixMADC.R b/tests/testthat/test-fixMADC.R
new file mode 100644
index 0000000..a51a53b
--- /dev/null
+++ b/tests/testthat/test-fixMADC.R
@@ -0,0 +1,616 @@
+library(testthat)
+library(dplyr)
+library(stringr)
+
+# ── Helpers: create temporary test fixtures ──────────────────────────────────
+
+#' Build a raw (unprocessed) MADC CSV with 7 filler rows of "*"
+create_raw_madc <- function(path, clone_ids, allele_ids, sample_names, counts_matrix,
+                            include_summary_cols = TRUE) {
+  n_rows <- length(clone_ids)
+  n_samples <- length(sample_names)
+
+  # Summary columns matching the full set the function auto-removes
+  summary_col_names <- c("ClusterConsensusSequence", "CallRate", "OneRatioRef",
+                         "OneRatioSnp", "FreqHomRef", "FreqHomSnp", "FreqHets",
+                         "PICRef", "PICSnp", "AvgPIC", "AvgCountRef",
+                         "AvgCountSnp", "RatioAvgCountRefAvgCountSnp")
+  extra_cols <- if (include_summary_cols) length(summary_col_names) else 0
+  total_cols <- 3 + extra_cols + n_samples  # AlleleID, CloneID, AlleleSequence + summary + samples
+
+  # 7 filler rows: col 1 = "*", other cols have placeholder metadata (like real DArT files)
+  filler <- matrix("*", nrow = 7, ncol = total_cols)
+
+  # Header row — real MADC: AlleleID (col1), CloneID (col2), AlleleSequence (col3)
+  summary_names <- if (include_summary_cols) summary_col_names else character(0)
+  header <- c("AlleleID", "CloneID", "AlleleSequence", summary_names, sample_names)
+
+  # Data rows
+  allele_seqs <- rep("ACTCTCAGGTGGAT", n_rows)
+  data_rows <- cbind(
+    AlleleID = allele_ids,
+    CloneID = clone_ids,
+    AlleleSequence = allele_seqs,
+    if (include_summary_cols) {
+      data.frame(
+        ClusterConsensusSequence = rep("ACTCTCAGGTGGAT", n_rows),
+        CallRate = 1.0, OneRatioRef = 1.0, OneRatioSnp = 1.0,
+        FreqHomRef = 0.5, FreqHomSnp = 0.3, FreqHets = 0.2,
+        PICRef = 0.4, PICSnp = 0.3, AvgPIC = 0.35,
+        AvgCountRef = 100, AvgCountSnp = 80,
+        RatioAvgCountRefAvgCountSnp = 1.25,
+        stringsAsFactors = FALSE
+      )
+    } else {
+      NULL
+    },
+    counts_matrix
+  )
+
+  # Write filler rows first (no header), then header + data
+  con <- file(path, open = "wt")
+  for (i in seq_len(nrow(filler))) {
+    writeLines(paste(filler[i, ], collapse = ","), con)
+  }
+  writeLines(paste(header, collapse = ","), con)
+  for (i in seq_len(nrow(data_rows))) {
+    writeLines(paste(data_rows[i, ], collapse = ","), con)
+  }
+  close(con)
+  invisible(path)
+}
+
+#' Build a preprocessed (no filler rows) MADC CSV
+create_preprocessed_madc <- function(path, clone_ids, allele_ids, sample_names, counts_matrix,
+                                     include_summary_cols = TRUE) {
+  n_rows <- length(clone_ids)
+
+  df <- data.frame(
+    AlleleID = allele_ids,
+    CloneID = clone_ids,
+    AlleleSequence = rep("ACTCTCAGGTGGAT", n_rows),
+    stringsAsFactors = FALSE
+  )
+  if (include_summary_cols) {
+    df$ClusterConsensusSequence <- rep("ACTCTCAGGTGGAT", n_rows)
+    df$CallRate <- 1.0
+    df$OneRatioRef <- 1.0
+    df$OneRatioSnp <- 1.0
+    df$FreqHomRef <- 0.5
+    df$FreqHomSnp <- 0.3
+    df$FreqHets <- 0.2
+    df$PICRef <- 0.4
+    df$PICSnp <- 0.3
+    df$AvgPIC <- 0.35
+    df$AvgCountRef <- 100
+    df$AvgCountSnp <- 80
+    df$RatioAvgCountRefAvgCountSnp <- 1.25
+  }
+  df <- cbind(df, counts_matrix)
+  colnames(df)[(ncol(df) - ncol(counts_matrix) + 1):ncol(df)] <- sample_names
+
+  write.csv(df, path, row.names = FALSE)
+  invisible(path)
+}
+
+#' Build a 3-column marker CSV
+create_marker_file <- function(path, clone_ids, chromosomes, positions) {
+  df <- data.frame(CloneID = clone_ids, Chr = chromosomes, Pos = positions,
+                   stringsAsFactors = FALSE)
+  write.csv(df, path, row.names = FALSE)
+  invisible(path)
+}
+
+
+# ── Shared fixtures ──────────────────────────────────────────────────────────
+
+sample_names  <- c("SampleA", "SampleB", "SampleC")
+clone_ids     <- c("marker1", "marker2", "marker3", "marker4")
+allele_ids    <- paste0(clone_ids, "|Ref")
+counts_matrix <- data.frame(
+  SampleA = c(10, 20, 30, 40),
+  SampleB = c(15, 25, 35, 45),
+  SampleC = c(12, 22, 32, 42)
+)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# ── 1. Basic happy-path with raw MADC (7 filler rows) ───────────────────────
+
+test_that("fixMADC correctly processes a raw MADC file and replaces IDs", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix,
+                  include_summary_cols = TRUE)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  # Should return a data.frame
+
+  expect_s3_class(result, "data.frame")
+
+
+  # CloneIDs should now be Chr_Pos format
+
+  expect_equal(unname(result$CloneID), c("Chr01_000000100", "Chr01_000000200", "Chr02_000000300", "Chr02_000000400"))
+
+  # AlleleID should have the new prefix with |Ref_0001 suffix
+  expect_true(all(grepl("\\|Ref_0001$", result$AlleleID)))
+  expect_equal(unname(result$AlleleID), c("Chr01_000000100|Ref_0001", "Chr01_000000200|Ref_0001", "Chr02_000000300|Ref_0001", "Chr02_000000400|Ref_0001"))
+
+  # Summary columns should be removed
+  summary_cols <- c("ClusterConsensusSequence", "CallRate", "OneRatioRef",
+                    "OneRatioSnp", "FreqHomRef", "FreqHomSnp", "FreqHets",
+                    "PICRef", "PICSnp", "AvgPIC", "AvgCountRef",
+                    "AvgCountSnp", "RatioAvgCountRefAvgCountSnp")
+  expect_false(any(summary_cols %in% colnames(result)))
+
+  # Sample columns should still be present
+  expect_true(all(sample_names %in% colnames(result)))
+})
+
+
+# ── 1b. Marker file in different order than MADC ─────────────────────────────
+
+test_that("fixMADC correctly maps IDs when marker file order differs from MADC", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix,
+                  include_summary_cols = TRUE)
+
+  # Marker file in reversed order relative to MADC
+  create_marker_file(marker_path,
+                     rev(clone_ids),
+                     c("Chr02", "Chr02", "Chr01", "Chr01"),
+                     c(400, 300, 200, 100))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  # marker1 -> Chr01_100, marker2 -> Chr01_200, marker3 -> Chr02_300, marker4 -> Chr02_400
+  # (same mapping regardless of marker file row order)
+  expect_equal(unname(result$CloneID), c("Chr01_000000100", "Chr01_000000200", "Chr02_000000300", "Chr02_000000400"))
+  expect_equal(unname(result$AlleleID), c("Chr01_000000100|Ref_0001", "Chr01_000000200|Ref_0001", "Chr02_000000300|Ref_0001", "Chr02_000000400|Ref_0001"))
+})
+
+
+# ── 1c. Duplicate CloneIDs with different AlleleID suffixes ──────────────────
+
+test_that("fixMADC correctly handles multiple rows per CloneID (Ref/Alt pairs)", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  # Two markers, each with a Ref and Alt row = 4 rows total
+  dup_clone_ids  <- c("marker1", "marker1", "marker2", "marker2")
+  dup_allele_ids <- c("marker1|Ref", "marker1|Alt", "marker2|Ref", "marker2|Alt")
+  dup_counts     <- data.frame(
+    SampleA = c(10, 5, 20, 8),
+    SampleB = c(15, 3, 25, 6),
+    SampleC = c(12, 4, 22, 7)
+  )
+
+  create_raw_madc(madc_path, dup_clone_ids, dup_allele_ids, sample_names, dup_counts,
+                  include_summary_cols = TRUE)
+  create_marker_file(marker_path,
+                     c("marker1", "marker2"),
+                     c("Chr01", "Chr02"),
+                     c(100, 200))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  # All 4 rows should be present
+
+  expect_equal(nrow(result), 4)
+
+  # CloneIDs should both be updated (duplicates are expected)
+  expect_equal(unname(result$CloneID), c("Chr01_000000100", "Chr01_000000100", "Chr02_000000200", "Chr02_000000200"))
+
+  # AlleleIDs should have updated suffixes: Ref -> Ref_0001, Alt -> Alt_0002
+  expect_equal(unname(result$AlleleID),
+               c("Chr01_000000100|Ref_0001", "Chr01_000000100|Alt_0002", "Chr02_000000200|Ref_0001", "Chr02_000000200|Alt_0002"))
+
+  # Sample data should be intact
+  expect_equal(result$SampleA, c(10, 5, 20, 8))
+})
+
+
+# ── 2. Preprocessed MADC (no filler rows) triggers error ────────────────────
+
+test_that("fixMADC errors when MADC appears preprocessed (no filler rows)", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_preprocessed_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "already use fixed allele IDs"
+  )
+
+})
+
+
+# ── 3. Manual n.summary.columns removal ─────────────────────────────────────
+
+test_that("n.summary.columns removes the correct number of extra columns", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix,
+                  include_summary_cols = TRUE)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  # 13 summary columns start at col 4, so columns 4:16
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path,
+                    n.summary.columns = 13)
+
+  expect_s3_class(result, "data.frame")
+  expect_false("CallRate" %in% colnames(result))
+  expect_false("ClusterConsensusSequence" %in% colnames(result))
+  expect_true(all(sample_names %in% colnames(result)))
+})
+
+
+# ── 4. Marker file validation — duplicate CloneIDs ──────────────────────────
+
+test_that("fixMADC errors on duplicate marker IDs in column 1", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  # Duplicate first marker
+  create_marker_file(marker_path,
+                     c("marker1", "marker1", "marker2", "marker3"),
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "duplicate marker IDs"
+  )
+})
+
+
+# ── 5. Marker file validation — duplicate Chr_Pos ───────────────────────────
+
+test_that("fixMADC errors on duplicate Chr_Pos combinations", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 100, 300, 400))  # Chr01_100 appears twice
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "duplicate Chr and Pos"
+  )
+})
+
+
+# ── 6. Marker file validation — special chars in chromosome ─────────────────
+
+test_that("fixMADC errors on special characters in chromosome column", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids[1:2], allele_ids[1:2], sample_names,
+                  counts_matrix[1:2, ])
+  create_marker_file(marker_path,
+                     clone_ids[1:2],
+                     c("Chr_01", "Chr02"),  # underscore in chr name
+                     c(100, 200))
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "Special characters.*chromosome"
+  )
+})
+
+
+# ── 7. Marker file validation — special chars in position ───────────────────
+
+test_that("fixMADC errors on special characters in position column", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids[1:2], allele_ids[1:2], sample_names,
+                  counts_matrix[1:2, ])
+  create_marker_file(marker_path,
+                     clone_ids[1:2],
+                     c("Chr01", "Chr02"),
+                     c("1.5", "200"))  # decimal in position
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "Special characters.*position|position.*must be numeric"
+  )
+})
+
+
+# ── 8. Marker file validation — non-numeric position ────────────────────────
+
+test_that("fixMADC errors when position column is not numeric", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids[1:2], allele_ids[1:2], sample_names,
+                  counts_matrix[1:2, ])
+  create_marker_file(marker_path,
+                     clone_ids[1:2],
+                     c("Chr01", "Chr02"),
+                     c("abc", "def"))
+
+  expect_error(
+    fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "must be numeric"
+  )
+})
+
+
+# ── 9. Missing CloneIDs in marker file triggers warning + removal ───────────
+
+test_that("fixMADC warns and removes CloneIDs not in marker file", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  # Marker file only has 3 of the 4 markers
+  create_marker_file(marker_path,
+                     clone_ids[1:3],
+                     c("Chr01", "Chr01", "Chr02"),
+                     c(100, 200, 300))
+
+  expect_warning(
+    result <- fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "not found in the marker file"
+  )
+
+  # Only 3 rows should remain
+  expect_equal(nrow(result), 3)
+  expect_false("marker4" %in% result$CloneID)
+})
+
+
+# ── 10. Output file is written when output.file is provided ─────────────────
+
+test_that("fixMADC writes CSV when output.file is specified", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+  output_path <- tempfile()  # function appends ".csv"
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  fixMADC(madc.file = madc_path,
+          marker.file = marker_path,
+          output.file = output_path)
+
+  written_file <- paste0(output_path, "_fixedID.csv")
+  expect_true(file.exists(written_file))
+
+  saved <- read.csv(written_file)
+  expect_equal(saved$CloneID, c("Chr01_000000100", "Chr01_000000200", "Chr02_000000300", "Chr02_000000400"))
+})
+
+
+# ── 11. AlleleID with Alt suffix is handled ─────────────────────────────────
+
+test_that("fixMADC correctly handles |Alt suffixes in AlleleID", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  alt_allele_ids <- paste0(clone_ids, "|Alt")
+
+  create_raw_madc(madc_path, clone_ids, alt_allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  expect_true(all(grepl("\\|Alt_0002$", result$AlleleID)))
+  expect_equal(unname(result$AlleleID[1]), "Chr01_000000100|Alt_0002")
+})
+
+
+# ── 11b. AlleleID with |RefMatch and |AltMatch suffixes ─────────────────────
+
+test_that("fixMADC correctly handles |RefMatch and |AltMatch suffixes", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  match_allele_ids <- c("marker1|RefMatch", "marker2|AltMatch",
+                        "marker3|RefMatch", "marker4|AltMatch")
+
+  create_raw_madc(madc_path, clone_ids, match_allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  expect_equal(unname(result$AlleleID),
+               c("Chr01_000000100|RefMatch_0001", "Chr01_000000200|AltMatch_0001",
+                 "Chr02_000000300|RefMatch_0001", "Chr02_000000400|AltMatch_0001"))
+})
+
+
+# ── 11c. Duplicate RefMatch/AltMatch suffixes are numbered ──────────────────
+
+test_that("fixMADC appends _0001, _0002 etc. to duplicate RefMatch/AltMatch within a CloneID", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  # One marker with Ref, Alt, 2x RefMatch, 3x AltMatch = 7 rows
+  dup_clone_ids  <- rep("marker1", 7)
+  dup_allele_ids <- c("marker1|Ref", "marker1|Alt",
+                      "marker1|RefMatch", "marker1|RefMatch",
+                      "marker1|AltMatch", "marker1|AltMatch", "marker1|AltMatch")
+  dup_counts <- data.frame(
+    SampleA = c(10, 5, 8, 12, 3, 6, 2),
+    SampleB = c(15, 3, 9, 11, 4, 7, 1),
+    SampleC = c(12, 4, 7, 13, 2, 5, 3)
+  )
+
+  create_raw_madc(madc_path, dup_clone_ids, dup_allele_ids, sample_names, dup_counts)
+  create_marker_file(marker_path,
+                     c("marker1"),
+                     c("Chr01"),
+                     c(100))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  expect_equal(nrow(result), 7)
+
+  # Ref always gets _0001, Alt always gets _0002
+  expect_equal(unname(result$AlleleID[1]), "Chr01_000000100|Ref_0001")
+  expect_equal(unname(result$AlleleID[2]), "Chr01_000000100|Alt_0002")
+
+  # Duplicate RefMatch rows should be numbered _0001, _0002
+  expect_equal(unname(result$AlleleID[3]), "Chr01_000000100|RefMatch_0001")
+  expect_equal(unname(result$AlleleID[4]), "Chr01_000000100|RefMatch_0002")
+
+  # Duplicate AltMatch rows should be numbered _0001, _0002, _0003
+  expect_equal(unname(result$AlleleID[5]), "Chr01_000000100|AltMatch_0001")
+  expect_equal(unname(result$AlleleID[6]), "Chr01_000000100|AltMatch_0002")
+  expect_equal(unname(result$AlleleID[7]), "Chr01_000000100|AltMatch_0003")
+})
+
+
+# ── 11d. All suffix types are numbered even when unique per CloneID ───────────
+
+test_that("fixMADC numbers all suffix types including single RefMatch/AltMatch per CloneID", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  # Two markers, each with Ref, Alt, one RefMatch, one AltMatch
+  mixed_clone_ids  <- c("marker1", "marker1", "marker1", "marker1",
+                        "marker2", "marker2", "marker2", "marker2")
+  mixed_allele_ids <- c("marker1|Ref", "marker1|Alt", "marker1|RefMatch", "marker1|AltMatch",
+                        "marker2|Ref", "marker2|Alt", "marker2|RefMatch", "marker2|AltMatch")
+  mixed_counts <- data.frame(
+    SampleA = c(10, 5, 8, 3, 20, 8, 12, 6),
+    SampleB = c(15, 3, 9, 4, 25, 6, 11, 7),
+    SampleC = c(12, 4, 7, 2, 22, 7, 13, 5)
+  )
+
+  create_raw_madc(madc_path, mixed_clone_ids, mixed_allele_ids, sample_names, mixed_counts)
+  create_marker_file(marker_path,
+                     c("marker1", "marker2"),
+                     c("Chr01", "Chr02"),
+                     c(100, 200))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  # All suffixes are always numbered: Ref_0001, Alt_0002, RefMatch_0001, AltMatch_0001
+  expect_equal(unname(result$AlleleID),
+               c("Chr01_000000100|Ref_0001", "Chr01_000000100|Alt_0002", "Chr01_000000100|RefMatch_0001", "Chr01_000000100|AltMatch_0001",
+                 "Chr02_000000200|Ref_0001", "Chr02_000000200|Alt_0002", "Chr02_000000200|RefMatch_0001", "Chr02_000000200|AltMatch_0001"))
+})
+
+
+# ── 12. Whitespace in marker file is trimmed ────────────────────────────────
+
+test_that("fixMADC trims whitespace in marker file columns", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids[1:2], allele_ids[1:2], sample_names,
+                  counts_matrix[1:2, ])
+
+  # Write marker file with extra whitespace
+  df <- data.frame(
+    CloneID = c("  marker1  ", " marker2"),
+    Chr = c("Chr01 ", " Chr02"),
+    Pos = c(" 100", "200 "),
+    stringsAsFactors = FALSE
+  )
+  write.csv(df, marker_path, row.names = FALSE)
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path)
+
+  expect_equal(unname(result$CloneID), c("Chr01_000000100", "Chr02_000000200"))
+})
+
+
+# ── 13. Returns NULL (invisibly) when writing to file ────────────────────────
+
+test_that("fixMADC returns NULL when output.file is provided", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+  output_path <- tempfile()
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path, clone_ids,
+                     c("Chr01", "Chr01", "Chr02", "Chr02"),
+                     c(100, 200, 300, 400))
+
+  result <- fixMADC(madc.file = madc_path,
+                    marker.file = marker_path,
+                    output.file = output_path)
+
+  expect_null(result)
+})
+
+
+# ── 14. Empty marker file (no matching IDs) removes all rows ────────────────
+
+test_that("fixMADC warns and returns empty df when no CloneIDs match", {
+  madc_path   <- tempfile(fileext = ".csv")
+  marker_path <- tempfile(fileext = ".csv")
+
+  create_raw_madc(madc_path, clone_ids, allele_ids, sample_names, counts_matrix)
+  create_marker_file(marker_path,
+                     c("noMatch1", "noMatch2"),
+                     c("Chr01", "Chr02"),
+                     c(100, 200))
+
+  expect_warning(
+    result <- fixMADC(madc.file = madc_path, marker.file = marker_path),
+    "not found in the marker file"
+  )
+
+  expect_equal(nrow(result), 0)
+})