'.gitignore' now ignores 'output' directory

.gitignore

@@ -212,3 +212,4 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
+output

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Module",
+            "type": "python",
+            "request": "launch",
+            "module": "bmlsa.cli",
+            "args": [
+                "-I",
+                "id",
+                "-S",
+                "sequence",
+                "-B",
+                "BLASTp",
+                "${workspaceFolder}/tests/resources/SARS_CoV-2_genes.csv",
+                "${workspaceFolder}/tests/resources/NC_045512_coding.fasta",
+                "${workspaceFolder}/output"
+            ],
+            "justMyCode": true
+        }
+    ]
+}

Jenkinsfile

@@ -27,6 +27,7 @@ pipeline {
             steps {
                 sh "pip install dist/*.whl --force-reinstall"
                 sh "bmlsa -h"
+                sh "bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta /output/"
             }
         }
         stage("archive") {

src/bmlsa/cli.py

@@ -28,7 +28,7 @@ def run(args):
             '"--alignment-mode", or, at least "--behave-as". See help (-h) for '
             "more information."
         )
-        exit(1)
+        exit(3)
     queries = read_annotations_from_csv(
         args.annotations,
         args.id_header,
@@ -41,7 +41,7 @@ def run(args):
 
     if args.behave_as and args.behave_as not in DEFAULT_ALIGNMENT_PARAMETERS:
         logger.error('"--behave-as" received bad option.')
-        exit(1)
+        exit(3)
 
     scoring_parameter = (
         {
@@ -56,6 +56,7 @@ def run(args):
         else DEFAULT_ALIGNMENT_PARAMETERS[args.behave_as]
     )
 
+    os.makedirs(args.output, exist_ok=True)
     with open(args.sequence, "r") as sequence_fd:
         for sequence in SeqIO.parse(sequence_fd, "fasta"):
             aligned_annotations = align_many_to_one_ssw(

src/bmlsa/datatypes.py

@@ -14,7 +14,7 @@ class AlignedSequence:
         self._end = end
         self._id = id
         self._name = name
-        self._sequence = sequence
+        self._sequence = sequence.replace("\n", "").replace("\r", "")
         self._score = score
 
     @property