update beagle tests so zcat doesn't break on mac

gymrek-lab · Nov 22, 2023 · 263717c · 263717c
1 parent 90ff40a
commit 263717c
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/scripts/trtools_prep_beagle_vcf.sh b/scripts/trtools_prep_beagle_vcf.sh
@@ -70,14 +70,14 @@ while read -r line ; do
 	# this assumes the output meta line ordering of Beagle 5.4 VCFs
 	if (( line_num == 3 )) ; then
 		for meta_line in '##source' '##command' ; do
-			zcat "$ref_panel" | awk '/^'"$meta_line"'/ {print $0} /^#CHROM/ {exit}' | sed -e 's/##/##preimuptation_/' >> "$temp_file"
+			zcat < "$ref_panel" | awk '/^'"$meta_line"'/ {print $0} /^#CHROM/ {exit}' | sed -e 's/##/##preimuptation_/' >> "$temp_file"
 		done
 		for meta_line in '##contig' '##ALT' '##INFO=<ID=END' ; do
-			zcat "$ref_panel" | awk '/^'"$meta_line"'/ {print $0} /^#CHROM/ {exit}' >> "$temp_file"
+			zcat < "$ref_panel" | awk '/^'"$meta_line"'/ {print $0} /^#CHROM/ {exit}' >> "$temp_file"
 		done
 	fi
 	line_num=$(( line_num+1 ))
-done < <(zcat "$imputed")
+done < <(zcat < "$imputed")
 
 
 echo "bgzipping and tabix indexing"

diff --git a/test/cmdline_tests.sh b/test/cmdline_tests.sh
@@ -225,14 +225,14 @@ if ! [[ -f "$prep_beagle_out".tbi ]] ; then
     exit 1
 fi
 
-if (( 1172 != $(zcat "$prep_beagle_out" | grep -vc '#') )) ; then
+if (( 1172 != $(zcat < "$prep_beagle_out" | grep -vc '#') )) ; then
     echo "prep_beagle_vcf outputted a file that didn't have the expected number of lines (1172)"
     exit 1
 fi
 
-if (( 1172 != $(zcat "$prep_beagle_out" | grep -v '#' | grep -c 'START') )) ||
-    (( 1172 != $(zcat "$prep_beagle_out" | grep -v '#' | grep -c 'END') )) ||
-    (( 1172 != $(zcat "$prep_beagle_out" | grep -v '#' | grep -c 'PERIOD') ))
+if (( 1172 != $(zcat < "$prep_beagle_out" | grep -v '#' | grep -c 'START') )) ||
+    (( 1172 != $(zcat < "$prep_beagle_out" | grep -v '#' | grep -c 'END') )) ||
+    (( 1172 != $(zcat < "$prep_beagle_out" | grep -v '#' | grep -c 'PERIOD') ))
 then
     echo "prep_beagle_vcf outputted a file that didn't have the expected number of INFO annotations"
     exit 1