Summary

Test suite

Test case 1

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.appendStringToFile(evoSuiteFile0, "shared_id");
  3: TabixReader tabixReader0 = new TabixReader("");
  4: char char0 = tabixReader0.getCommentChar();
  5: assertEquals('\u0000', char0);

Test case 2

  1: TabixReader.readLong((InputStream) null);

Test case 3

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.appendStringToFile(evoSuiteFile0, "shared_id");
  3: TabixReader tabixReader0 = new TabixReader("");
  4: VCFRecord vCFRecord0 = tabixReader0.getNextRecord("", (-966), 685);
  5: assertNull(vCFRecord0);

Test case 4

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: String[] stringArray0 = tabixReader0.getSeqNames();
  8: assertNotNull(stringArray0);

Test case 5

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: int int0 = tabixReader0.getEndColumn();
  8: assertEquals(0, int0);

Test case 6

  1: URL uRL0 = MockURL.getHttpExample();
  2: TabixReader tabixReader0 = new TabixReader("blast", uRL0);

Test case 7

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: byte[] byteArray0 = new byte[7];
  3: FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
  4: TabixReader tabixReader0 = new TabixReader("");
  5: tabixReader0.readLine();

Test case 8

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.appendStringToFile(evoSuiteFile0, "shared_id");
  3: TabixReader tabixReader0 = new TabixReader("");
  4: int int0 = tabixReader0.getSeqColumn();
  5: assertEquals(0, int0);

Test case 9

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.appendStringToFile(evoSuiteFile0, "shared_id");
  3: TabixReader tabixReader0 = new TabixReader("");
  4: int int0 = tabixReader0.getStartColumn();
  5: assertEquals(0, int0);

Test case 10

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: String string0 = tabixReader0.readLine();
  8: assertNull(string0);

Test case 11

  1: byte[] byteArray0 = new byte[5];
  2: byteArray0[0] = (byte)10;
  3: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  4: String string0 = TabixReader.readLine((InputStream) byteArraySeekableStream0);
  5: assertEquals(1L, byteArraySeekableStream0.position());
  6: assertEquals("", string0);

Test case 12

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: byte[] byteArray0 = new byte[7];
  3: FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
  4: TabixReader tabixReader0 = new TabixReader("");
  5: tabixReader0.query("");

Test case 13

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: byte[] byteArray0 = new byte[7];
  3: FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
  4: TabixReader tabixReader0 = new TabixReader("");
  5: tabixReader0.readIndex();
  6: assertEquals(0, tabixReader0.getSeqColumn());

Test case 14

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: String string0 = tabixReader0.getFileName();
  8: assertEquals("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", string0);

Test case 15

  1: MockFile mockFile0 = new MockFile("");
  2: Path path0 = mockFile0.toPath();
  3: SeekablePathStream seekablePathStream0 = new SeekablePathStream(path0);
  4: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(seekablePathStream0, 4);
  5: TabixReader.readInt(seekableBufferedStream0);

Test case 16

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: int[] intArray0 = tabixReader0.parseReg("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='");
  8: assertArrayEquals(new int[] {(-1), 0, Integer.MAX_VALUE}, intArray0);

Test case 17

  1: TabixReader tabixReader0 = new TabixReader("aD=");

Test case 18

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.createFolder(evoSuiteFile0);
  3: TabixReader tabixReader0 = new TabixReader("");

Test case 19

  1: TabixReader tabixReader0 = new TabixReader((String) null);

Test case 20

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);

Test case 21

  1: byte[] byteArray0 = new byte[14];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: TabixReader tabixReader0 = new TabixReader((String) null, byteArraySeekableStream0);

Test case 22

  1: byte[] byteArray0 = new byte[7];
  2: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/|C8!S.tbi");
  3: FileSystemHandling.createFolder(evoSuiteFile0);
  4: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  5: TabixReader tabixReader0 = new TabixReader("|C8!S", byteArraySeekableStream0);

Test case 23

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/blast.tbi");
  2: FileSystemHandling.createFolder(evoSuiteFile0);
  3: URL uRL0 = MockURL.getHttpExample();
  4: TabixReader tabixReader0 = new TabixReader("blast", uRL0);

Test case 24

  1: TabixReader tabixReader0 = new TabixReader((String) null, (URL) null);

Test case 25

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: byte[] byteArray0 = new byte[7];
  3: FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
  4: TabixReader tabixReader0 = new TabixReader("");
  5: tabixReader0.query((int) (byte) (-128), 6, (int) (byte) (-58));

Test case 26

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: tabixReader0.query("Usage: java -cp .:sam.jar TabixReader <in.gz> [region]");

Test case 27

  1: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
  2: FileSystemHandling.appendStringToFile(evoSuiteFile0, "shared_id");
  3: TabixReader tabixReader0 = new TabixReader("");
  4: tabixReader0.query("A6+,:,#KU^");

Test case 28

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: MockFile mockFile0 = new MockFile((File) null, "Usage: java -cp .:sam.jar TabixReader <in.gz> [region]");
  8: tabixReader0.readIndex((File) mockFile0);

Test case 29

  1: TabixReader.readInt((InputStream) null);

Test case 30

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='.tbi");
  4: FileSystemHandling.appendLineToFile(evoSuiteFile0, "20!t=k'va,z.q4x!");
  5: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  6: TabixReader tabixReader0 = new TabixReader("INSERT INTO feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not ) VALUES ( nextval('feature_cvterm_feature_cvterm_id_seq'), (SELECT feature_id FROM feature WHERE uniquename='", seekableBufferedStream0);
  7: byteArraySeekableStream0.close();
  8: tabixReader0.readLine();

Test case 31

  1: MockFile mockFile0 = new MockFile("");
  2: Path path0 = mockFile0.toPath();
  3: UnaryOperator<SeekableByteChannel> unaryOperator0 = UnaryOperator.identity();
  4: SeekablePathStream seekablePathStream0 = new SeekablePathStream(path0, unaryOperator0);
  5: DataInputStream dataInputStream0 = new DataInputStream(seekablePathStream0);
  6: SequenceInputStream sequenceInputStream0 = new SequenceInputStream(dataInputStream0, seekablePathStream0);
  7: TabixReader.readLine((InputStream) sequenceInputStream0);

Test case 32

  1: TabixReader.readLine((InputStream) null);

Test case 33

  1: URL uRL0 = MockURL.getHttpExample();
  2: SeekableHTTPStream seekableHTTPStream0 = new SeekableHTTPStream(uRL0);
  3: TabixReader.readLong(seekableHTTPStream0);

Test case 34

  1: byte[] byteArray0 = new byte[5];
  2: byteArray0[3] = (byte) (-127);
  3: ByteArrayInputStream byteArrayInputStream0 = new ByteArrayInputStream(byteArray0);
  4: TabixReader.readInt(byteArrayInputStream0);
  5: assertEquals(1, byteArrayInputStream0.available());

Test case 35

  1: byte[] byteArray0 = new byte[2];
  2: byteArray0[0] = (byte) (-36);
  3: SeekableMemoryStream seekableMemoryStream0 = new SeekableMemoryStream(byteArray0, "cbw% 2O2");
  4: int int0 = TabixReader.readInt(seekableMemoryStream0);
  5: assertEquals(220, int0);

Test case 36

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: int int0 = TabixReader.readInt(byteArraySeekableStream0);
  4: assertEquals(0, int0);

Test case 37

  1: byte[] byteArray0 = new byte[5];
  2: byteArray0[3] = (byte)10;
  3: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  4: String string0 = TabixReader.readLine((InputStream) byteArraySeekableStream0);
  5: assertEquals(4L, byteArraySeekableStream0.position());
  6: assertEquals("\u0000\u0000\u0000", string0);

Test case 38

  1: byte[] byteArray0 = new byte[7];
  2: byteArray0[0] = (byte)30;
  3: ByteArrayReader byteArrayReader0 = new ByteArrayReader(byteArray0);
  4: long long0 = TabixReader.readLong(byteArrayReader0);
  5: assertEquals(30L, long0);

Test case 39

  1: byte[] byteArray0 = new byte[0];
  2: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  3: SeekableBufferedStream seekableBufferedStream0 = new SeekableBufferedStream(byteArraySeekableStream0, 66);
  4: long long0 = TabixReader.readLong(seekableBufferedStream0);
  5: assertEquals(0L, long0);

Test case 40

  1: byte[] byteArray0 = new byte[14];
  2: byteArray0[1] = (byte) (-12);
  3: ByteArraySeekableStream byteArraySeekableStream0 = new ByteArraySeekableStream(byteArray0);
  4: TabixReader.readLine((InputStream) byteArraySeekableStream0);
  5: assertEquals(14L, byteArraySeekableStream0.position());
  6: assertTrue(byteArraySeekableStream0.eof());

Source Code

  1: No source found for uk.ac.sanger.artemis.components.variant.TabixReader

EvoSuite Parameters

  • TARGET_CLASS: uk.ac.sanger.artemis.components.variant.TabixReader
  • Size: 40
  • Length: 173
  • criterion: LINE;BRANCH;EXCEPTION;WEAKMUTATION;OUTPUT;METHOD;METHODNOEXCEPTION;CBRANCH
  • Coverage: 0.4456596327072362
  • BranchCoverage: 0.15544041450777202
  • MethodCoverage: 0.9
  • OutputCoverage: 0.43243243243243246


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