@Test(dataProvider = "excludeMatchingTests")
public void testExcludeMatching(
Set<String> values, Collection<String> filters, boolean exactMatch, Set<String> expected) {
Set<String> actual =
ListFileUtils.excludeMatching(
values, ListFileUtils.IDENTITY_STRING_CONVERTER, filters, exactMatch);
Assert.assertEquals(actual, expected);
}
@Test
public void testUnpackSet() throws Exception {
Set<String> expected = new HashSet<String>(Arrays.asList(publicTestDir + "exampleBAM.bam"));
Set<String> actual;
actual = ListFileUtils.unpackSet(Arrays.asList(publicTestDir + "exampleBAM.bam"));
Assert.assertEquals(actual, expected);
File tempListFile =
createTempListFile(
"testUnpackSet",
"#",
publicTestDir + "exampleBAM.bam",
"#" + publicTestDir + "foo.bam",
" # " + publicTestDir + "bar.bam");
actual = ListFileUtils.unpackSet(Arrays.asList(tempListFile.getAbsolutePath()));
Assert.assertEquals(actual, expected);
}
private void performBAMListFileUnpackingTest(
File tempListFile, List<SAMReaderID> expectedUnpackedFileList) throws Exception {
List<String> bamFiles = new ArrayList<String>();
bamFiles.add(tempListFile.getAbsolutePath());
List<SAMReaderID> unpackedBAMFileList =
ListFileUtils.unpackBAMFileList(bamFiles, new ParsingEngine(null));
Assert.assertEquals(
unpackedBAMFileList.size(),
expectedUnpackedFileList.size(),
"Unpacked BAM file list contains extraneous lines");
Assert.assertEquals(
unpackedBAMFileList,
expectedUnpackedFileList,
"Unpacked BAM file list does not contain correct BAM file names");
}