From b2f536f6af0473c5cdcc9db0a97effd02bc0145e Mon Sep 17 00:00:00 2001
From: deepchocolate <andreas@systerdyster.se>
Date: Wed, 21 Feb 2024 11:56:37 +0100
Subject: [PATCH] Added test of filtering individuals in LD estimation

---
 tests/test_LDpred2/run.sh        | 3 +++
 tests/test_LDpred2/scripts/ld.sh | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/tests/test_LDpred2/run.sh b/tests/test_LDpred2/run.sh
index c6a69342..da0a886a 100755
--- a/tests/test_LDpred2/run.sh
+++ b/tests/test_LDpred2/run.sh
@@ -54,6 +54,9 @@ export fileOutputSNPR=$DIR_DATA/public-data3.rds
 export fileKeepSNPS=/REF/hapmap3/w_hm3.justrs
 export fileOut=$DIR_TESTS/output/public-data.score
 
+# File with subset of individual IDs from the tutorial data
+export fileExtractIndividuals=$DIR_DATA/individual-ids.txt
+
 # BGEN files
 export fileBGEN=$DIR_DATA/example.bgen
 export fileBGENasRDS=$DIR_DATA/example.rds
diff --git a/tests/test_LDpred2/scripts/ld.sh b/tests/test_LDpred2/scripts/ld.sh
index 83ee47e3..4b749f9c 100644
--- a/tests/test_LDpred2/scripts/ld.sh
+++ b/tests/test_LDpred2/scripts/ld.sh
@@ -29,6 +29,8 @@ testSuccess $LDE --sumstats $fileSumstats25k rsid --thres-r2 0.2 --chr2use 21 22
 echo "Test restricting on SNPs provide by a SNP list file: $fileKeepSNPS"
 testSuccess $LDE --extract $fileKeepSNPS --file-ld-chr $dirOut/ld-chr@.rds --file-ld-map $dirOut/map.rds
 
+echo "Test extracting individuals using $fileExtractIndividuals"
+testSuccess $LDE --extract-individuals $fileExtractIndividuals --file-ld-chr $dirOut/ld-chr@.rds --file-ld-map $dirOut/map.rds
 echo "Test sampling individuals (N=400)"
 testSuccess $LDE --sample-individuals 400 --extract $fileKeepSNPS --file-ld-chr $dirOut/ld-chr@.rds --file-ld-map $dirOut/map.rds
 # Test this LDpred on this LD (restrict to chromosomes 20-22