More tests

src/bcftools/bcftools_annotate/config.vsh.yaml

@@ -177,8 +177,7 @@ argument_groups:
       - name: --rename_annotations 
         type: file
         description: | 
-          rename annotations according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, 
-          each on a separate line. The old name must be prefixed with the annotation type: INFO, FORMAT, or FILTER.
+          Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT.
 
       - name: --rename_chromosomes
         type: file

src/bcftools/bcftools_annotate/script.sh

@@ -41,8 +41,8 @@ bcftools annotate \
     ${par_regions:+-r "$par_regions"} \
     ${par_regions_file:+-R "$par_regions_file"} \
     ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \
-    ${par_rename_annotations:+--rename-annotations "$par_rename_annotations"} \
-    ${par_rename_chromosomes:+--rename-chromosomes "$par_rename_chromosomes"} \
+    ${par_rename_annotations:+--rename-annots "$par_rename_annotations"} \
+    ${par_rename_chromosomes:+--rename-chrs "$par_rename_chromosomes"} \
     ${par_samples:+-s "$par_samples"} \
     ${par_single_overlaps:+--single-overlaps} \
     ${par_threads:+--threads "$par_threads"} \

src/bcftools/bcftools_annotate/test.sh

@@ -47,6 +47,10 @@ cat <<EOF > "$TMPDIR/annots.tsv"
 1	752722	752722	FooValue2	67890
 EOF
 
+cat <<EOF > "$TMPDIR/rename.tsv"
+INFO/.	Luigi
+EOF
+
 bgzip $TMPDIR/annots.tsv
 tabix -s1 -b2 -e3 $TMPDIR/annots.tsv.gz
 
@@ -55,14 +59,19 @@ cat <<EOF > "$TMPDIR/header.hdr"
 ##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">
 EOF
 
+cat <<EOF > "$TMPDIR/rename_chrm.tsv"
+1	chr1
+2	chr2
+EOF
+
 # Test 1: Remove ID annotations
 mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
 
 echo "> Run bcftools_annotate remove annotations"
 "$meta_executable" \
   --input "../example.vcf" \
   --output "annotated.vcf" \
-  --remove "ID"
+  --remove "ID" \
 
 # checks
 assert_file_exists "annotated.vcf"
@@ -108,10 +117,59 @@ echo "- test3 succeeded -"
 
 popd > /dev/null
 
-# echo
-# cat "annotated.vcf"
-# echo
-# exit 0
+# Test 4:
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+
+echo "> Run bcftools_annotate with --rename-annotations option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --rename_annotations "../rename.tsv"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate --rename-annots ../rename.tsv -o annotated.vcf"
+echo "- test4 succeeded -"
+
+popd > /dev/null
+
+# Test 5: Rename chromosomes
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
+
+echo "> Run bcftools_annotate with --rename-chromosomes option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --rename_chromosomes "../rename_chrm.tsv"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "chr1"
+echo "- test5 succeeded -"
+
+popd > /dev/null
+
+# Test 6: Sample option
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
+
+echo "> Run bcftools_annotate with -s option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --samples "SAMPLE1"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate -s SAMPLE1 -o annotated.vcf ../example.vcf"
+echo "- test6 succeeded -"
+
+popd > /dev/null
+
+
+
 
 echo "---- All tests succeeded! ----"
 exit 0