diff --git a/cli/src/cli/commands/run.ts b/cli/src/cli/commands/run.ts
index a3daca1ed..53c6314a2 100644
--- a/cli/src/cli/commands/run.ts
+++ b/cli/src/cli/commands/run.ts
@@ -167,9 +167,9 @@ export function runCommand(program: Command): Command {
       Options.defaultKgramsInWindow
     )
     .option(
-      "-e, --exclude-comments",
+      "-ic, --include-comments",
       Utils.indent(
-        "Exclude the comments during the tokenization process."
+        "Include the comments during the tokenization process."
       )
     )
     .action(async (locations, options) => run(locations, { ...options , ...program.opts() }));
@@ -212,7 +212,7 @@ export async function run(locations: string[], options: RunOptions): Promise<voi
       limitResults: options.limitResults,
       sortBy: options.sortBy,
       fragmentSortBy: options.fragmentSortBy,
-      excludeComments: options.excludeComments
+      includeComments: options.includeComments
     });
     const report = await dolos.analyzePaths(locations, options.ignore);
 
diff --git a/lib/src/lib/dolos.ts b/lib/src/lib/dolos.ts
index 24b1b150c..fe2e39af8 100644
--- a/lib/src/lib/dolos.ts
+++ b/lib/src/lib/dolos.ts
@@ -38,7 +38,7 @@ export class Dolos {
         this.language = this.languagePicker.detectLanguage(files);
         this.languageDetected = true;
       }
-      this.tokenizer = await this.language.createTokenizer({ excludeComments: this.options.excludeComments });
+      this.tokenizer = await this.language.createTokenizer({ includeComments: this.options.includeComments });
       this.index = new FingerprintIndex(this.options.kgramLength, this.options.kgramsInWindow, this.options.kgramData);
     }
     const warnings = [];
diff --git a/lib/src/lib/language.ts b/lib/src/lib/language.ts
index 0b2e0f8f6..a06088640 100644
--- a/lib/src/lib/language.ts
+++ b/lib/src/lib/language.ts
@@ -25,7 +25,7 @@ export abstract class Language {
     }
   }
 
-  public abstract createTokenizer(options: TokenizerOptions): Promise<Tokenizer>;
+  public abstract createTokenizer(options?: TokenizerOptions): Promise<Tokenizer>;
 }
 
 export class ProgrammingLanguage extends Language {
@@ -54,7 +54,7 @@ export class ProgrammingLanguage extends Language {
     return this.languageModule;
   }
 
-  async createTokenizer(options: TokenizerOptions): Promise<Tokenizer> {
+  async createTokenizer(options?: TokenizerOptions): Promise<Tokenizer> {
     const { CodeTokenizer } = await import ("./tokenizer/codeTokenizer.js");
     await this.loadLanguageModule();
     return new CodeTokenizer(this, options);
@@ -86,12 +86,12 @@ export class CustomTokenizerLanguage extends Language {
   constructor(
     readonly name: string,
     readonly extensions: string[],
-    readonly customTokenizer: ((self: Language, options: TokenizerOptions) => Promise<Tokenizer>)
+    readonly customTokenizer: ((self: Language, options?: TokenizerOptions) => Promise<Tokenizer>)
   ) {
     super(name, extensions);
   }
 
-  public async createTokenizer(options: TokenizerOptions): Promise<Tokenizer> {
+  public async createTokenizer(options?: TokenizerOptions): Promise<Tokenizer> {
     return await this.customTokenizer(this, options);
   }
 }
diff --git a/lib/src/lib/options.ts b/lib/src/lib/options.ts
index fdfa26cbb..c53dac250 100644
--- a/lib/src/lib/options.ts
+++ b/lib/src/lib/options.ts
@@ -11,7 +11,7 @@ export interface DolosOptions {
   sortBy: string | null;
   fragmentSortBy: string | null;
   kgramData: boolean;
-  excludeComments: boolean;
+  includeComments: boolean;
 }
 
 export type CustomOptions = Partial<DolosOptions>;
@@ -88,8 +88,8 @@ export class Options implements DolosOptions {
     return this.custom.kgramData == true;
   }
 
-  get excludeComments(): boolean {
-    return this.custom.excludeComments === true;
+  get includeComments(): boolean {
+    return this.custom.includeComments === true;
   }
 
   get limitResults(): number | null {
@@ -159,7 +159,7 @@ export class Options implements DolosOptions {
       sortBy: this.sortBy,
       fragmentSortBy: this.fragmentSortBy,
       kgramData: this.kgramData,
-      excludeComments: this.excludeComments,
+      includeComments: this.includeComments,
     };
   }
 
diff --git a/lib/src/lib/tokenizer/codeTokenizer.ts b/lib/src/lib/tokenizer/codeTokenizer.ts
index 79ebde3a8..d919969f8 100644
--- a/lib/src/lib/tokenizer/codeTokenizer.ts
+++ b/lib/src/lib/tokenizer/codeTokenizer.ts
@@ -14,7 +14,7 @@ export class CodeTokenizer extends Tokenizer {
    * @param language The language to use for this tokenizer.
    * @param options
    */
-  constructor(language: ProgrammingLanguage, options: TokenizerOptions) {
+  constructor(language: ProgrammingLanguage, options?: TokenizerOptions) {
     super(language, options);
     this.parser = new Parser();
     this.parser.setLanguage(language.getLanguageModule());
@@ -63,7 +63,7 @@ export class CodeTokenizer extends Tokenizer {
     );
 
     const isComment = node.type.includes("comment");
-    if (!this.options.excludeComments || !isComment) {
+    if (!isComment || this.options.includeComments) {
       tokens.push(this.newToken("(", location));
       tokens.push(this.newToken(node.type, location));
     }
@@ -78,7 +78,7 @@ export class CodeTokenizer extends Tokenizer {
       }
     }
 
-    if (!this.options.excludeComments || !isComment) {
+    if (!isComment || this.options.includeComments) {
       tokens.push(this.newToken(")", location));
     }
 
diff --git a/lib/src/lib/tokenizer/tokenizer.ts b/lib/src/lib/tokenizer/tokenizer.ts
index c0e1f7c58..c66967e74 100644
--- a/lib/src/lib/tokenizer/tokenizer.ts
+++ b/lib/src/lib/tokenizer/tokenizer.ts
@@ -6,16 +6,18 @@ export interface Token {
   location: Region;
 }
 
-export type TokenizerOptions = {
-  excludeComments: boolean;
-}
+export type TokenizerOptions = Partial<{
+  includeComments: boolean;
+}>
 
 export abstract class Tokenizer {
 
-  protected options: TokenizerOptions;
+  protected options: TokenizerOptions = {};
 
-  constructor(public readonly language: Language, options: TokenizerOptions) {
-    this.options = options;
+  constructor(public readonly language: Language, options?: TokenizerOptions) {
+    if (options !== undefined) {
+      this.options = options;
+    }
   }
 
 
diff --git a/lib/src/test/snapshots/tokenizer.test.ts.md b/lib/src/test/snapshots/tokenizer.test.ts.md
index 596461c56..f4b73991d 100644
--- a/lib/src/test/snapshots/tokenizer.test.ts.md
+++ b/lib/src/test/snapshots/tokenizer.test.ts.md
@@ -12,9 +12,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'program',
       '(',
-      'comment',
-      ')',
-      '(',
       'function_definition',
       '(',
       'word',
@@ -1081,9 +1078,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'list',
       '(',
       'command',
@@ -1793,9 +1787,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'compilation_unit',
       '(',
-      'comment',
-      ')',
-      '(',
       'using_directive',
       '(',
       'identifier',
@@ -6393,9 +6384,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'expression_statement',
       '(',
       'assignment_expression',
@@ -6771,9 +6759,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'expression_statement',
       '(',
       'call_expression',
@@ -9009,9 +8994,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'program',
       '(',
-      'line_comment',
-      ')',
-      '(',
       'class_declaration',
       '(',
       'modifiers',
@@ -10406,9 +10388,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'module',
       '(',
-      'comment',
-      ')',
-      '(',
       'function_definition',
       '(',
       'identifier',
@@ -11169,9 +11148,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'named_element',
       '(',
       'class_definition',
@@ -13352,9 +13328,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'named_element',
       '(',
       'component_clause',
@@ -13382,9 +13355,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'named_element',
       '(',
       'component_clause',
@@ -18716,9 +18686,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'braced_expression',
       '(',
-      'comment',
-      ')',
-      '(',
       'if_statement',
       '(',
       'binary_operator',
@@ -18959,9 +18926,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'call',
       '(',
       'identifier',
@@ -19040,9 +19004,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'binary_operator',
       '(',
       'identifier',
@@ -20827,9 +20788,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'ERROR',
       '(',
-      'comment',
-      ')',
-      '(',
       'keyword_drop',
       ')',
       '(',
@@ -20994,9 +20952,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'program',
       '(',
-      'comment',
-      ')',
-      '(',
       'interface_declaration',
       '(',
       'type_identifier',
@@ -22906,9 +22861,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'variable_declaration',
       '(',
       'variable_declarator',
@@ -23045,9 +22997,6 @@ Generated by [AVA](https://avajs.dev).
       '(',
       'source_file',
       '(',
-      'comment',
-      ')',
-      '(',
       'package_declaration',
       '(',
       'package_identifier',
@@ -23581,9 +23530,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'id_directive',
       '(',
       'text_macro_identifier',
@@ -23909,9 +23855,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'line_compiler_directive',
       '(',
       'unsigned_number',
@@ -24492,9 +24435,6 @@ Generated by [AVA](https://avajs.dev).
       'ERROR',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'ordered_port_connection',
       '(',
       'expression',
@@ -24564,9 +24504,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'ordered_port_connection',
       '(',
       'expression',
@@ -24740,9 +24677,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'parameter_port_declaration',
       '(',
       'parameter_declaration',
@@ -24811,9 +24745,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       ')',
-      '(',
-      'comment',
-      ')',
       ')',
       '(',
       'list_of_ports',
@@ -25069,9 +25000,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'statement_or_null',
       '(',
       'statement',
@@ -25116,9 +25044,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       ')',
-      '(',
-      'comment',
-      ')',
       ')',
       ')',
       ')',
@@ -25273,9 +25198,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'module_or_generate_item',
       '(',
       'continuous_assign',
@@ -25324,9 +25246,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'module_or_generate_item',
       '(',
       'continuous_assign',
@@ -25372,9 +25291,6 @@ Generated by [AVA](https://avajs.dev).
       ')',
       ')',
       '(',
-      'comment',
-      ')',
-      '(',
       'module_or_generate_item',
       '(',
       'continuous_assign',
diff --git a/lib/src/test/snapshots/tokenizer.test.ts.snap b/lib/src/test/snapshots/tokenizer.test.ts.snap
index 28bed1aeb..6988619d8 100644
Binary files a/lib/src/test/snapshots/tokenizer.test.ts.snap and b/lib/src/test/snapshots/tokenizer.test.ts.snap differ
diff --git a/lib/src/test/tokenizer.test.ts b/lib/src/test/tokenizer.test.ts
index 781ebf918..b4779b38b 100644
--- a/lib/src/test/tokenizer.test.ts
+++ b/lib/src/test/tokenizer.test.ts
@@ -27,26 +27,26 @@ const languageFiles = {
 } as {[key: string]: string};
 
 const tokenLength = {
-  "../samples/bash/caesar.sh": 1185,
+  "../samples/bash/caesar.sh": 1179,
   "../samples/c/caesar.c": 582,
-  "../samples/c-sharp/Caesar.cs": 606,
+  "../samples/c-sharp/Caesar.cs": 603,
   "../samples/char/caesar.txt": 3700,
-  "../samples/cpp/caesar.cpp": 801,
+  "../samples/cpp/caesar.cpp": 795,
   "../samples/elm/Caesar.elm": 753,
   "../samples/go/Caesar.go": 1032,
   "../samples/groovy/caesar.groovy": 282,
-  "../samples/java/Caesar.java": 522,
+  "../samples/java/Caesar.java": 519,
   "../samples/javascript/sample.js": 861,
-  "../samples/python/caesar.py": 309,
+  "../samples/python/caesar.py": 306,
   "../samples/php/caesar.php": 411,
-  "../samples/modelica/sample.mo": 7542,
-  "../samples/r/caesar.R": 594,
+  "../samples/modelica/sample.mo": 7533,
+  "../samples/r/caesar.R": 585,
   "../samples/rust/caesar.rs": 774,
   "../samples/scala/Caesar.scala": 366,
-  "../samples/sql/sample.sql": 543,
-  "../samples/tsx/sample.tsx": 1659,
-  "../samples/typescript/caesar.ts": 378,
-  "../samples/verilog/module.v": 2484
+  "../samples/sql/sample.sql": 540,
+  "../samples/tsx/sample.tsx": 1656,
+  "../samples/typescript/caesar.ts": 375,
+  "../samples/verilog/module.v": 2448
 } as {[key: string]: number};
 
 for (const [languageName, languageFile] of Object.entries(languageFiles)) {
@@ -68,7 +68,7 @@ for (const [languageName, languageFile] of Object.entries(languageFiles)) {
     const file = (await readPath(languageFile)).ok();
     const language = new LanguagePicker().detectLanguage([file]);
 
-    const tokenizer = await language.createTokenizer({ excludeComments: false });
+    const tokenizer = await language.createTokenizer();
     t.truthy(tokenizer);
 
     const { tokens } = tokenizer.tokenizeFile(file);
@@ -96,7 +96,7 @@ test("should be able to use external tree-sitter parsers (tree-sitter-json)", as
   const file = (await readPath("./package.json")).ok();
   const language = await (new LanguagePicker().findLanguage("json"));
 
-  const tokenizer = await language.createTokenizer({ excludeComments: false });
+  const tokenizer = await language.createTokenizer();
   t.truthy(tokenizer);
 
   const { tokens } = tokenizer.tokenizeFile(file);
@@ -107,7 +107,7 @@ test("should be able to parse larger files", async t => {
   const file = new File("long.js", "var test = 1;\n".repeat(10000));
   const language = await (new LanguagePicker().findLanguage("javascript"));
 
-  const tokenizer = await language.createTokenizer({ excludeComments: false });
+  const tokenizer = await language.createTokenizer();
   t.truthy(tokenizer);
 
   const { tokens } = tokenizer.tokenizeFile(file);
@@ -117,7 +117,7 @@ test("should be able to parse larger files", async t => {
 test("should be able to correctly tokenize a variable", async t => {
   const file = new File("long.js", "var test = 1;");
   const language = await (new LanguagePicker().findLanguage("javascript"));
-  const tokenizer = await language.createTokenizer({ excludeComments: false });
+  const tokenizer = await language.createTokenizer();
 
   const { tokens, mapping } = tokenizer.tokenizeFile(file);
   t.is(tokens.join(""), "(program(variable_declaration(variable_declarator(identifier)(number))))");
@@ -145,7 +145,7 @@ test("should be able to correctly tokenize a loop", async t => {
   const file = new File("long.js", "let i = 0;\nwhile (i < 10) {\n  i += 1;\n}");
   const language = await (new LanguagePicker().findLanguage("javascript"));
 
-  const tokenizer = await language.createTokenizer({ excludeComments: false });
+  const tokenizer = await language.createTokenizer();
   const { tokens, mapping } = tokenizer.tokenizeFile(file);
   t.is(tokens.join(""), "(program(lexical_declaration(variable_declarator(identifier)(number)))" +
       "(while_statement(parenthesized_expression(binary_expression(identifier)(number)))" +