Updated September 2019

With Angular CLI 6, angular-cli.json has been renamed to angular.json which contains the configuration. In angular.json, codeCoverage expects a boolean value, which sets whether code-coverage should be done with every test run or not. To exclude files from code coverage, there is a property codeCoverageExclude which accepts an array of files to be excluded from code coverage.

angular.json

"test": {
  "options": {
    "codeCoverageExclude": ["src/assets/vendor/**"],
    ...
  },
  ...
}

Updated answer

rc.0 has been released. You should be able to add the code snippet below to ignore files.

Original answer

Currently, you aren't able to do so in beta.32.3. A change is coming to allow this to happen. In the next release (probably rc.0), you will be able to do the following:

.angular-cli.json

"test": {
  "codeCoverage": {
    "exclude": [
      "src/app/quote/services/generated/**/*"
    ]
  },
  ...
}

Here is the way to do this:

1. Add client section to your karma.conf.js like this:

   plugins: [
       ...
   ],
   client: {
       codeCoverage: config.angularCli.codeCoverage
   },
   files: [
       ...
   ],
   

2. Change your test.ts to require files according to codeCoverage parameter:

   let context; 
   
   if (__karma__.config.codeCoverage) {
       context = require.context('./app/', true, /\.ts/);
   } else {
       context = require.context('./app/', true, /\.spec\.ts/);
   }
   
   context.keys().map(context);
   

UPDATE:

Since Angular CLI 1.5.0 additional steps are required:

3. Next to tsconfig.spec.json add tsconfig-cc.spec.json file with the following content:

   {
     "extends": "./tsconfig.spec.json",
     "include": [
       "**/*.ts"
     ]
   }
   

4. In your angular-cli.json add the following to apps array:

   {
     "root": "src/",
     "polyfills": "polyfills.ts",
     "test": "test.ts",
     "testTsconfig": "tsconfig-cc.spec.json"
   }
   

5. In your karma.conf.js add the following to angularCli section:

   app: config.angularCli.codeCoverage ? '1' : '0'  
   

   eventually it should look something like this:

   angularCli: {
       environment: 'dev',
       app: config.angularCli.codeCoverage ? '1' : '0'
   },
   

So what's happening here?

Apparently they have fixed Angular compiler plugin and it takes the file globs from tsconfig.spec.json now. As long as we include only **/*.spec.ts in tsconfig.spec.json these are the only files that will be included in coverage.

The obvious solution is making tsconfig.spec.json include all the files (in addition to require.context). However, this will slow down all the tests even when running without coverage (which we don't want to).

One of the solutions is using the ability of angular-cli to work with multiple apps.
By adding another entry into apps array, we're adding another configuration for "another" (which is actually the same one) app.
We strip out all the irrelevant information in this config, leaving just the test configuration, and put another tsconfig which includes all the ts files.
Finally, we're telling angular-cli karma plugin to run the tests with the configuration of the second app (index 1) in case it is running with code coverage and run with the configuration of the first app (index 0) if it is running without code coverage.

Important note: in this configuration I assume you have only one application in .angular-cli.json. In case you have more you have to adjust indexes accordingly.

First install the dependencies.

npm install karma karma-jasmine karma-chrome-launcher karma-jasmine-html-reporter karma-coverage-istanbul-reporter

Then run ng test.

ng test --code-coverage

Then run the server that shows you your report.

http-server -c-1 -o -p 9875 ./coverage

You should see something like this:

I wrote a blog post about this here.