Fixes #245

gamgee/individual_field_value.h

@@ -5,6 +5,7 @@
 #include "utils/hts_memory.h"
 #include "utils/utils.h"
 #include "utils/variant_field_type.h"
+#include "missing.h"
 
 #include "htslib/vcf.h"
 
@@ -157,6 +158,17 @@ class IndividualFieldValue {
   VALUE_TYPE front() const { return operator[](0); }                    ///< @brief convenience function to access the first element
   VALUE_TYPE back() const { return operator[](m_format_ptr->n - 1); }   ///< @brief convenience function to access the last element
 
+  /**
+   * @brief returns true if all of the values are missing
+   */
+  bool missing() const {
+    for (const auto value : *this)
+      // use qualifier to avoid recursion
+      if (!gamgee::missing(value))
+        return false;
+    return true;
+  }
+
  private:
   std::shared_ptr<bcf1_t> m_body;
   const bcf_fmt_t* m_format_ptr;

test/variant_reader_test.cpp

@@ -638,8 +638,13 @@ BOOST_AUTO_TEST_CASE( single_variant_reader_missing_data )
   for (const auto& record : SingleVariantReader{"testdata/test_variants_missing_data.vcf"}){ // include all 11 samples
     BOOST_CHECK_EQUAL(record.n_samples(), 11u); 
     const auto gt_for_all_samples = record.genotypes();
+    const auto ad_for_all_samples = record.integer_individual_field("AD");
+    const auto gq_for_all_samples = record.integer_individual_field("GQ");
+    const auto pl_for_all_samples = record.integer_individual_field("PL");
+
     for (const auto& gt_for_single_sample: gt_for_all_samples) {
       BOOST_CHECK(missing(gt_for_single_sample));
+      BOOST_CHECK(gt_for_single_sample.missing());
       BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2u);
       BOOST_CHECK(missing(gt_for_single_sample.allele_string(0)));
       BOOST_CHECK(missing(gt_for_single_sample.allele_string(1)));
@@ -648,6 +653,18 @@ BOOST_AUTO_TEST_CASE( single_variant_reader_missing_data )
       BOOST_CHECK(missing(gt_for_single_sample[0]));
       BOOST_CHECK(missing(gt_for_single_sample[1]));
     }
+    for (const auto& ad_for_single_sample: ad_for_all_samples) {
+      BOOST_CHECK(missing(ad_for_single_sample));
+      BOOST_CHECK(ad_for_single_sample.missing());
+    }
+    for (const auto& gq_for_single_sample: gq_for_all_samples) {
+      BOOST_CHECK(missing(gq_for_single_sample));
+      BOOST_CHECK(gq_for_single_sample.missing());
+    }
+    for (const auto& pl_for_single_sample: pl_for_all_samples) {
+      BOOST_CHECK(missing(pl_for_single_sample));
+      BOOST_CHECK(pl_for_single_sample.missing());
+    }
   }
 }