more roundtrip tests

chrchang · Sep 28, 2023 · 6540ae6 · 6540ae6
1 parent d67c3ae
commit 6540ae6
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diff --git a/2.0/Tests/TEST_EXTRACT_CHR/run_tests.sh b/2.0/Tests/TEST_EXTRACT_CHR/run_tests.sh
@@ -22,3 +22,20 @@ do
     diff -q plink2x_c$c.bed plink2_c$c.bed
     diff -q plink2x_c$c.bim plink2_c$c.bim
 done
+
+# tmp_data is also suitable for ind-major-bed, ped, and tped round-trip tests.
+$1/plink2 $2 $3 --bfile tmp_data --export ind-major-bed --out plink2_roundtrip
+$1/plink2 $2 $3 --bfile plink2_roundtrip --make-bed --out plink2_test
+diff -q tmp_data.bed plink2_test.bed
+diff -q tmp_data.bim plink2_test.bim
+# .fam files aren't byte-for-byte identical due to spaces -> tabs.
+
+$1/plink2 $2 $3 --bfile tmp_data --export ped --out plink2_roundtrip
+$1/plink2 $2 $3 --pedmap plink2_roundtrip --make-bed --out plink2_test
+diff -q tmp_data.bed plink2_test.bed
+diff -q tmp_data.bim plink2_test.bim
+
+$1/plink2 $2 $3 --bfile tmp_data --export tped --out plink2_roundtrip
+$1/plink2 $2 $3 --tfile plink2_roundtrip --make-bed --out plink2_test
+diff -q tmp_data.bed plink2_test.bed
+diff -q tmp_data.bim plink2_test.bim
diff --git a/2.0/Tests/TEST_PHASED_VCF/run_tests.sh b/2.0/Tests/TEST_PHASED_VCF/run_tests.sh
@@ -14,6 +14,13 @@ $1/plink2 $2 $3 --vcf 1kg_phase3_chr21_start.vcf.gz --double-id --out plink2_dat
 $1/plink2 $2 $3 --pfile plink2_data --export bcf --out plink2_roundtrip
 $1/plink2 $2 $3 --bcf plink2_roundtrip.bcf --out plink2_roundtrip
 diff -q plink2_data.pgen plink2_roundtrip.pgen
+# Verify haps and hapslegend roundtrip.
+$1/plink2 $2 $3 --pfile plink2_data --export haps sample-v2 --out plink2_roundtrip
+$1/plink2 $2 $3 --haps plink2_roundtrip.haps --sample plink2_roundtrip.sample --real-ref-alleles --make-pgen --out plink2_roundtrip
+diff -q plink2_data.pgen plink2_roundtrip.pgen
+$1/plink2 $2 $3 --pfile plink2_data --export hapslegend sample-v2 --out plink2_roundtrip
+$1/plink2 $2 $3 --haps plink2_roundtrip.haps --legend plink2_roundtrip.legend 21 --sample plink2_roundtrip.sample --real-ref-alleles --make-pgen --out plink2_roundtrip
+diff -q plink2_data.pgen plink2_roundtrip.pgen
 
 $1/plink2 $2 $3 --pfile plink2_data --export vcf --out plink2_data