final touches, fix script

src/samtools/samtools_stats/config.vsh.yaml

@@ -41,7 +41,7 @@ argument_groups:
         Exclude from statistics reads marked as duplicates.
     - name: --customized_index_file
       alternatives: -X 
-      type: file
+      type: boolean_true
       description: |
         Use a customized index file.
     - name: --required_flag

src/samtools/samtools_stats/script.sh

@@ -13,7 +13,6 @@ set -e
 $(which samtools) stats \
     ${par_coverage:+-c "$par_coverage"} \
     ${par_remove_dups:+-d} \
-    ${par_customized_index_file:+-X "$par_bai"} \
     ${par_required_flag:+-f "$par_required_flag"} \
     ${par_filtering_flag:+-F "$par_filtering_flag"} \
     ${par_GC_depth:+--GC-depth "$par_GC_depth"} \

src/samtools/samtools_stats/test.sh

@@ -17,11 +17,11 @@ echo ">>> Checking whether output is non-empty"
 [ ! -s "$test_dir/test.paired_end.sorted.txt" ] && echo "File 'test.paired_end.sorted.txt' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
-# compare using diff, but ingnoring the header line (starting with "#")
-diff <(grep -v "^#" "$test_dir/test.paired_end.sorted.txt") \
-    <(grep -v "^#" "$test_dir/ref.paired_end.sorted.txt") || \
+# compare using diff,  ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.paired_end.sorted.txt") || \
     (echo "Output file ref.paired_end.sorted.txt does not match expected output" && exit 1)
-    
+
 rm "$test_dir/test.paired_end.sorted.txt"
 
 ############################################################################################
@@ -40,9 +40,9 @@ echo ">>> Checking whether output is non-empty"
 [ ! -s "$test_dir/ref.d.paired_end.sorted.txt" ] && echo "File 'ref.d.paired_end.sorted.txt' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
-# compare using diff, but ingnoring the header line (starting with "#")
-diff <(grep -v "^#" "$test_dir/test.d.paired_end.sorted.txt") \
-    <(grep -v "^#" "$test_dir/ref.d.paired_end.sorted.txt") || \
+# compare using diff, ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.d.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.d.paired_end.sorted.txt") || \
     (echo "Output file ref.d.paired_end.sorted.txt does not match expected output" && exit 1)
 
 rm "$test_dir/test.d.paired_end.sorted.txt"
@@ -64,9 +64,9 @@ echo ">>> Checking whether output is non-empty"
 
 
 echo ">>> Checking whether output is correct"
-# compare using diff, but ingnoring the header line (starting with "#")
-diff <(grep -v "^#" "$test_dir/test.p.paired_end.sorted.txt") \
-    <(grep -v "^#" "$test_dir/ref.p.paired_end.sorted.txt") || \
+# compare using diff, ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.p.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.p.paired_end.sorted.txt") || \
     (echo "Output file ref.p.paired_end.sorted.txt does not match expected output" && exit 1)
 
 rm "$test_dir/test.p.paired_end.sorted.txt"