From 6e876684da7af69d1d5c826d84746285f30dfb07 Mon Sep 17 00:00:00 2001
From: rwdavies <robertwilliamdavies@gmail.com>
Date: Fri, 26 Jan 2024 20:03:56 +0000
Subject: [PATCH] Add test to give error when ref sample file size does not
 match hap file #93

---
 STITCH/R/reference.R                          | 21 ++++++++++++++-
 .../testthat/test-acceptance-reference.R      | 27 +++++++++++++++++++
 2 files changed, 47 insertions(+), 1 deletion(-)

diff --git a/STITCH/R/reference.R b/STITCH/R/reference.R
index 24ebd83..aa59173 100644
--- a/STITCH/R/reference.R
+++ b/STITCH/R/reference.R
@@ -43,6 +43,13 @@ get_and_initialize_from_reference <- function(
     plotHapSumDuringIterations
 ) {
 
+    ## quick validations of haps against sample file
+    ## some redunancy
+    validate_sample_file_vs_haplotype(
+        reference_sample_file,
+        reference_haplotype_file
+    )
+    
     print_message("Begin initializing paramters using reference haplotypes")
     ## get reference haplotypes matched to posfile
     ## NA's where there are no match
@@ -859,7 +866,19 @@ new_subset_of_single_reference_iteration <- function(
 
 
 
-
+validate_sample_file_vs_haplotype <- function(
+    reference_sample_file,
+    reference_haplotype_file
+) {
+    if (file.exists(reference_sample_file) & file.exists(reference_haplotype_file)) {
+        n1 <- nrow(read.table(reference_sample_file, header = TRUE))
+        n2 <- ncol(read.table(reference_haplotype_file, nrows = 1))
+        if (n1 != n2 / 2) {
+            stop(paste0("There are ", n1, " rows in the reference sample file and ", n2, " columns (i.e. ", n2 / 2, " samples) from the sample file. These files must match in a one to one fashion"))
+        }
+    }
+    NULL
+}
 
 
 
diff --git a/STITCH/tests/testthat/test-acceptance-reference.R b/STITCH/tests/testthat/test-acceptance-reference.R
index fdcb3a6..e07da70 100644
--- a/STITCH/tests/testthat/test-acceptance-reference.R
+++ b/STITCH/tests/testthat/test-acceptance-reference.R
@@ -109,6 +109,33 @@ test_that("STITCH can initialize with reference data", {
 })
 
 
+test_that("STITCH throws an error if reference panel information not sized properly", {
+
+    new_sample_file <- tempfile()
+    simple_write(
+        rbind(refpack$reference_samples, tail(refpack$reference_samples)),
+        new_sample_file
+    )
+
+    expect_error(
+        STITCH(
+            chr = data_package$chr,
+            bamlist = data_package$bamlist,
+            posfile = data_package$posfile,
+            genfile = data_package$genfile,
+            outputdir = tempdir(),
+            reference_haplotype_file = refpack$reference_haplotype_file,
+            reference_legend_file = refpack$reference_legend_file,
+            reference_sample_file = new_sample_file,
+            K = 2,
+            nGen = 100,
+            reference_populations = "GBR"
+        )
+    )
+
+})
+
+
 test_that("STITCH can initialize with reference data for S > 1", {
 
     for(output_format in c("bgvcf", "bgen")) {