Fixed signed-unsigned comparison errors in tests

test/indexed_sam_reader_test.cpp

@@ -16,7 +16,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_intervals )
 
     for (const auto& sam : IndexedSingleSamReader{filename, interval_list}) {
       BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-      BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+      BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
       ++read_counter;
     }
     BOOST_CHECK_EQUAL(read_counter, 15u);
@@ -27,10 +27,10 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_intervals )
       auto interval_read_counter = 0u;
       for (const auto& sam : IndexedSingleSamReader{filename, vector<string>{interval}}) {
         BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-        BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+        BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
         ++interval_read_counter;
       }
-      BOOST_CHECK_EQUAL(interval_read_counter, interval_read_counts[interval_number]);
+      BOOST_CHECK_EQUAL(interval_read_counter, static_cast<uint32_t>(interval_read_counts[interval_number]));
       ++interval_number;
     }
   }
@@ -43,7 +43,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_entire_file )
     auto read_counter = 0u;
     for (const auto& sam : IndexedSingleSamReader{filename, entire_file}) {
       BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-      BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+      BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
       ++read_counter;
     }
     BOOST_CHECK_EQUAL(read_counter, 33u);
@@ -57,7 +57,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_unmapped )
     auto read_counter = 0u;
     for (const auto& sam : IndexedSingleSamReader{filename, unmapped_reads}) {
       BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-      BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+      BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
       ++read_counter;
     }
     BOOST_CHECK_EQUAL(read_counter, 0u);
@@ -71,7 +71,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_empty )
     auto read_counter = 0u;
     for (const auto& sam : IndexedSingleSamReader{filename, empty_list}) {
       BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-      BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+      BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
       ++read_counter;
     }
     BOOST_CHECK_EQUAL(read_counter, 0u);

test/sam_builder_test.cpp

@@ -305,9 +305,9 @@ BOOST_AUTO_TEST_CASE( set_multiple_data_fields_from_scratch ) {
   BOOST_CHECK_EQUAL(constructed_read.cigar().to_string(), "1M1I1M");
   BOOST_CHECK_EQUAL(constructed_read.bases().to_string(), "ACT");
   BOOST_CHECK_EQUAL(constructed_read.base_quals().to_string(), "1 2 3");
-  BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1);
-  BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142);
-  BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199);
+  BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1u);
+  BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142u);
+  BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199u);
 }
 
 BOOST_AUTO_TEST_CASE( reconstruct_complete_read ) {
@@ -365,19 +365,19 @@ BOOST_AUTO_TEST_CASE( build_multiple_reads ) {
   BOOST_CHECK_EQUAL(constructed_read.cigar().to_string(), "1M1I1M");
   BOOST_CHECK_EQUAL(constructed_read.bases().to_string(), "ACT");
   BOOST_CHECK_EQUAL(constructed_read.base_quals().to_string(), "1 2 3");
-  BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1);
-  BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142);
-  BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199);
+  BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1u);
+  BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142u);
+  BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199u);
 
   auto second_read = builder.set_chromosome(2).set_cigar("2M1I").set_bases("GGA").build();
 
   BOOST_CHECK_EQUAL(second_read.name(), "foo");
   BOOST_CHECK_EQUAL(second_read.cigar().to_string(), "2M1I");
   BOOST_CHECK_EQUAL(second_read.bases().to_string(), "GGA");
   BOOST_CHECK_EQUAL(second_read.base_quals().to_string(), "1 2 3");
-  BOOST_CHECK_EQUAL(second_read.chromosome(), 2);
-  BOOST_CHECK_EQUAL(second_read.alignment_start(), 142);
-  BOOST_CHECK_EQUAL(second_read.mate_alignment_start(), 199);
+  BOOST_CHECK_EQUAL(second_read.chromosome(), 2u);
+  BOOST_CHECK_EQUAL(second_read.alignment_start(), 142u);
+  BOOST_CHECK_EQUAL(second_read.mate_alignment_start(), 199u);
 }
 BOOST_AUTO_TEST_CASE( set_illegal_base_quals ) {
   auto header = SingleSamReader{"testdata/test_simple.bam"}.header();

test/sam_header_test.cpp

@@ -10,10 +10,10 @@ BOOST_AUTO_TEST_CASE( sam_header ) {
   auto reader = SingleSamReader{"testdata/test_simple.bam"};
   auto header = reader.header();
   BOOST_CHECK_EQUAL("chr1", header.sequence_name(0));
-  BOOST_CHECK_EQUAL(100000, header.sequence_length("chr1"));
-  BOOST_CHECK_EQUAL(100000, header.sequence_length(0));
-  BOOST_CHECK_EQUAL(0, header.sequence_length("foo"));
-  BOOST_CHECK_EQUAL(1, header.n_sequences());
+  BOOST_CHECK_EQUAL(100000u, header.sequence_length("chr1"));
+  BOOST_CHECK_EQUAL(100000u, header.sequence_length(0));
+  BOOST_CHECK_EQUAL(0u, header.sequence_length("foo"));
+  BOOST_CHECK_EQUAL(1u, header.n_sequences());
 }
 
 /** @todo Need a way to modify the header in between these copies/moves to make sure these are working properly! */

test/sam_reader_test.cpp

@@ -13,7 +13,7 @@ BOOST_AUTO_TEST_CASE( single_readers )
     auto read_counter = 0u;
     for (const auto& sam : SingleSamReader{filename}) {
       BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125");
-      BOOST_CHECK_EQUAL(sam.chromosome(), 0);
+      BOOST_CHECK_EQUAL(sam.chromosome(), 0u);
       ++read_counter;
     }
     BOOST_CHECK_EQUAL(read_counter, 33u);

test/sam_test.cpp

@@ -34,9 +34,9 @@ void check_first_read(Sam& record) {
   BOOST_CHECK_EQUAL(record.mate_alignment_start(), aln);
   const auto actual_cigar = record.cigar();
   BOOST_CHECK_EQUAL(actual_cigar.to_string(), expected_cigar);
-  BOOST_CHECK_EQUAL(actual_cigar.size(), expected_cigar_size);
+  BOOST_CHECK_EQUAL(actual_cigar.size(), static_cast<uint32_t>(expected_cigar_size));
   BOOST_CHECK_EQUAL(static_cast<int>(Cigar::cigar_op(actual_cigar[0])), static_cast<int>(expected_cigar_element_operator));
-  BOOST_CHECK_EQUAL(Cigar::cigar_oplen(actual_cigar[0]), expected_cigar_element_length);
+  BOOST_CHECK_EQUAL(Cigar::cigar_oplen(actual_cigar[0]), static_cast<uint32_t>(expected_cigar_element_length));
   BOOST_CHECK_EQUAL(record.bases().to_string(), expected_bases);
   const auto actual_quals = record.base_quals();
   BOOST_CHECK_EQUAL(actual_quals.size(), expected_quals.size());
@@ -425,6 +425,6 @@ BOOST_AUTO_TEST_CASE( sam_off_by_one_uber_test ) {
   const auto header = SingleSamReader{"testdata/test_simple.bam"}.header();
   auto builder = SamBuilder{header};
   const auto record = builder.set_name("TEST").set_bases("A").set_cigar("1M").set_base_quals({20}).set_alignment_start(1).build();
-  BOOST_CHECK_EQUAL(record.alignment_start(), 1);
-  BOOST_CHECK_EQUAL(record.alignment_stop(), 1);
+  BOOST_CHECK_EQUAL(record.alignment_start(), 1u);
+  BOOST_CHECK_EQUAL(record.alignment_stop(), 1u);
 }

test/select_if_test.cpp

@@ -33,8 +33,8 @@ BOOST_AUTO_TEST_CASE( select_if_individual_fields ) {
       const auto hom_ref = [](const IndividualFieldValue<int32_t>& x) { return x[0] == 0; };
       const auto comput_gq_select = Variant::select_if(g_quals.begin(), g_quals.end(), high_gq);
       const auto comput_pl_select = Variant::select_if(p_likes.begin(), p_likes.end(), hom_ref);
-      BOOST_CHECK_EQUAL(comput_gq_select.size(), 3);
-      BOOST_CHECK_EQUAL(comput_pl_select.size(), 3);
+      BOOST_CHECK_EQUAL(comput_gq_select.size(), 3u);
+      BOOST_CHECK_EQUAL(comput_pl_select.size(), 3u);
       const auto actual_gq_select = actual_gq_selects[record_idx];
       const auto actual_pl_select = actual_pl_selects[record_idx];
       BOOST_CHECK(comput_pl_select == actual_pl_select);
@@ -45,8 +45,8 @@ BOOST_AUTO_TEST_CASE( select_if_individual_fields ) {
 }
 
 BOOST_AUTO_TEST_CASE( select_if_shared_field ) {
-  const auto truth_an_counts = std::vector<int>{1,1,1,1,1};
-  const auto truth_af_counts = std::vector<int>{0,0,0,0,1};
+  const auto truth_an_counts = std::vector<uint32_t>{1,1,1,1,1};
+  const auto truth_af_counts = std::vector<uint32_t>{0,0,0,0,1};
   auto truth_index = 0u;
   for (const auto& record : SingleVariantReader{"testdata/test_variants.vcf"}) {
     const auto an = record.integer_shared_field("AN");

test/variant_header_test.cpp

@@ -19,9 +19,9 @@ BOOST_AUTO_TEST_CASE( variant_header_builder_simple_building ) {
   const auto chromosomes = vector<string>{"chr1", "chr2", "chr3", "chr4"};
   const auto filters     = vector<string>{"LOW_QUAL", "PASS", "VQSR_FAILED"};
   const auto shareds       = vector<string>{"DP", "MQ", "RankSum"};
-  const auto shareds_indices = vector<uint32_t>{3,4,5};  // looks arbitrary but these are the indices of the shared fields because the filters get 0, 1 and 2.
+  const auto shareds_indices = vector<int32_t>{3,4,5};  // looks arbitrary but these are the indices of the shared fields because the filters get 0, 1 and 2.
   const auto individuals     = vector<string>{"GQ", "PL", "DP"};
-  const auto individuals_indices = vector<uint32_t>{6,7,3}; // the last index gets the same number as the info index. Weird, but that's how htslib deals with this.
+  const auto individuals_indices = vector<int32_t>{6,7,3}; // the last index gets the same number as the info index. Weird, but that's how htslib deals with this.
   auto builder = VariantHeaderBuilder{};
   builder.add_source("Gamgee api test");
   builder.advanced_add_arbitrary_line("##unused=<XX=AA,Description=\"Unused generic\">");