Initial test suite commit

[bamtools.git] / src / test / api / SamHeader / SamHeaderValidatorTest.h

diff --git a/src/test/api/SamHeader/SamHeaderValidatorTest.h b/src/test/api/SamHeader/SamHeaderValidatorTest.h
new file mode 100644 (file)
index 0000000..bec004a
--- /dev/null
+++ b/src/test/api/SamHeader/SamHeaderValidatorTest.h
@@ -0,0 +1,292 @@
+#ifndef SAMHEADER_VALIDATORTEST_H
+#define SAMHEADER_VALIDATORTEST_H
+
+#include "api/SamHeader.h"
+#include <gtest/gtest.h>
+#include <iostream>
+#include <string>
+
+TEST(SamHeader_ValidatorTest, EmptyHeader) {
+
+    BamTools::SamHeader header("");
+    std::string headerText = header.ToString();
+    ASSERT_TRUE(headerText.empty());
+    EXPECT_TRUE(header.IsValid());
+}
+
+TEST(SamHeader_ValidatorTest, Version) {
+
+    BamTools::SamHeader header("");
+
+    // empty - VALID HEADER
+    header.Version = "";
+    EXPECT_TRUE(header.IsValid());
+
+    // normal - VALID HEADER
+    header.Version = "1.1";
+    EXPECT_TRUE(header.IsValid());
+    header.Version = "11.1";
+    EXPECT_TRUE(header.IsValid());
+    header.Version = "1.11";
+
+    // no period - INVALID HEADER
+    header.Version = "11";
+    EXPECT_FALSE(header.IsValid());
+
+    // no major - INVALID HEADER
+    header.Version = ".1";
+    EXPECT_FALSE(header.IsValid());
+
+    // invalid major - INVALID HEADER
+    header.Version = "a.1";
+    EXPECT_FALSE(header.IsValid());
+
+    // no minor - INVALID HEADER
+    header.Version = "1.";
+    EXPECT_FALSE(header.IsValid());
+
+    // invalid minor - INVALID HEADER
+    header.Version = "1.a";
+    EXPECT_FALSE(header.IsValid());
+}
+
+TEST(SamHeader_ValidatorTest, GroupOrder) {
+
+    BamTools::SamHeader header("");
+
+    // empty - VALID HEADER
+    header.GroupOrder = "";
+    EXPECT_TRUE(header.IsValid());
+
+    // normal group order- VALID HEADER
+    header.GroupOrder = "none";
+    EXPECT_TRUE(header.IsValid());
+    header.GroupOrder = "query";
+    EXPECT_TRUE(header.IsValid());
+    header.GroupOrder = "reference";
+    EXPECT_TRUE(header.IsValid());
+
+    // invalid group order - INVALID HEADER
+    header.GroupOrder = "fake";
+    EXPECT_FALSE(header.IsValid());
+}
+
+TEST(SamHeader_ValidatorTest, SortOrder) {
+
+    BamTools::SamHeader header("");
+
+    // empty - VALID HEADER
+    header.SortOrder = "";
+    EXPECT_TRUE(header.IsValid());
+
+    // normal sort order- VALID HEADER
+    header.SortOrder = "coordinate";
+    EXPECT_TRUE(header.IsValid());
+    header.SortOrder = "queryname";
+    EXPECT_TRUE(header.IsValid());
+    header.SortOrder = "unsorted";
+    EXPECT_TRUE(header.IsValid());
+
+    // invalid sort order - INVALID HEADER
+    header.SortOrder = "fake";
+    EXPECT_FALSE(header.IsValid());
+}
+
+TEST(SamHeader_ValidatorTest, SequenceDictionary) {
+
+    BamTools::SamHeader header("");
+    BamTools::SamSequence sequence;
+
+    // --------------------------------
+    // empty - VALID HEADER
+
+    header.Sequences.Clear();
+    EXPECT_TRUE(header.IsValid());
+
+    // --------------------------------
+    // normal - VALID HEADER
+
+    sequence.Name   = "MT";
+    sequence.Length = "1000";
+    header.Sequences.Add(sequence);
+    EXPECT_TRUE(header.IsValid());
+
+    // normal ( length == MIN )
+    sequence.Name   = "MT";
+    sequence.Length = "1";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_TRUE(header.IsValid());
+
+    // normal ( length == MAX )
+    sequence.Name = "MT";
+    sequence.Length = "536870911";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_TRUE(header.IsValid());
+
+    // ---------------------------------
+    // missing required info - INVALID HEADER
+
+    // missing ID
+    sequence.Name = "";
+    sequence.Length = "1000";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // missing length
+    sequence.Name = "MT";
+    sequence.Length = "";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // -------------------------------------
+    // improper SN format - INVALID HEADER
+
+    // starts with *
+    sequence.Name = "*MT";
+    sequence.Length = "1000";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // starts with =
+    sequence.Name = "=MT";
+    sequence.Length = "1000";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // -----------------------------------------
+    // nonunique ID - INVALID HEADER
+
+    // this behavior is blocked by SamSequenceDictionary
+    // see SamSequenceDictionaryTest::AddDuplicateOk
+
+    // --------------------------------------------
+    // invalid length  - INVALID HEADER
+
+    // length = 0 (MIN == 1)
+    sequence.Name = "MT";
+    sequence.Length = "0";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // length = -1
+    sequence.Name = "MT";
+    sequence.Length = "-1";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+
+    // length = MAX + 1
+    sequence.Name ="MT";
+    sequence.Length = "536870912";
+    header.Sequences.Clear();
+    header.Sequences.Add(sequence);
+    EXPECT_FALSE(header.IsValid());
+}
+
+TEST(SamHeader_ValidatorTest, ReadGroupDictionary) {
+
+    BamTools::SamHeader header("");
+    BamTools::SamReadGroup readGroup;
+
+    // ---------------------------------
+    // empty - VALID HEADER
+
+    header.ReadGroups.Clear();
+    EXPECT_TRUE(header.IsValid());
+
+    // ---------------------------------
+    // normal - VALID HEADER
+
+    readGroup.ID = "Group123";
+    readGroup.PlatformUnit = "PU001";
+
+    // technology: none
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: capillary
+    readGroup.SequencingTechnology = "CAPILLARY";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: Helicos
+    readGroup.SequencingTechnology = "HELICOS";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: Illumina
+    readGroup.SequencingTechnology = "ILLUMINA";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: IonTorrent
+    readGroup.SequencingTechnology = "IONTORRENT";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: 454
+    readGroup.SequencingTechnology = "LS454";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: Pacific Bio
+    readGroup.SequencingTechnology = "PACBIO";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // technology: Solid
+    readGroup.SequencingTechnology = "SOLID";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_TRUE(header.IsValid());
+
+    // ---------------------------------
+    // missing ID - INVALID HEADER
+
+    readGroup.ID = "";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_FALSE(header.IsValid());
+
+    // -----------------------------------------
+    // nonunique ID - INVALID HEADER
+
+    // this behavior is blocked by SamReadGroupDictionary
+    // see SamReadGroupDictionaryTest::AddDuplicateOk
+
+    // ------------------------------------------
+    // nonunique platform unit - INVALID HEADER
+
+    BamTools::SamReadGroup dupPU("Group1");
+    BamTools::SamReadGroup dupPU2("Group2");
+    dupPU.PlatformUnit = "PU001";
+    dupPU2.PlatformUnit = "PU001";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(dupPU);
+    header.ReadGroups.Add(dupPU2);
+    EXPECT_FALSE(header.IsValid());
+
+    // ------------------------------------------------
+    // invalid sequencing technology - INVALID HEADER
+
+    readGroup.SequencingTechnology = "fake";
+    header.ReadGroups.Clear();
+    header.ReadGroups.Add(readGroup);
+    EXPECT_FALSE(header.IsValid());
+}
+
+#endif // SAMHEADER_VALIDATORTEST_H