Merge pull request #357 from broadinstitute/dr_rev_htslib_nov6

Update gamgee to work with revved version of htslib
broadinstitute · Nov 6, 2014 · e55dbd8 · e55dbd8
2 parents 25e3d9f + 3ec5db2
commit e55dbd8
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/gamgee/utils/variant_utils.cpp b/gamgee/utils/variant_utils.cpp
@@ -24,6 +24,8 @@ void subset_variant_samples(bcf_hdr_t* hdr_ptr, const std::vector<std::string>&
     sample_list.erase(sample_list.size() - 1);
     bcf_hdr_set_samples(hdr_ptr, sample_list.c_str(), false);
   }
+
+  // NOTE: must NOT call bcf_hdr_sync() here, since htslib calls it for us in bcf_hdr_set_samples()
 }
 
 void merge_variant_headers(const std::shared_ptr<bcf_hdr_t>& dest_hdr_ptr, const std::shared_ptr<bcf_hdr_t>& src_hdr_ptr) {
@@ -39,6 +41,7 @@ void merge_variant_headers(const std::shared_ptr<bcf_hdr_t>& dest_hdr_ptr, const
 
   // vcf.h    "After all samples have been added, NULL must be passed to update internal header structures."
   bcf_hdr_add_sample(dest_hdr_ptr.get(), nullptr);
+  bcf_hdr_sync(dest_hdr_ptr.get());
 }
 
 }
diff --git a/gamgee/variant.h b/gamgee/variant.h
@@ -176,8 +176,8 @@ class Variant {
 
   bcf_fmt_t*  find_individual_field(const std::string& tag) const { return bcf_get_fmt(m_header.m_header.get(), m_body.get(), tag.c_str());  }
   bcf_info_t* find_shared_field(const std::string& tag)     const { return bcf_get_info(m_header.m_header.get(), m_body.get(), tag.c_str()); }
-  bcf_fmt_t*  find_individual_field(const uint32_t index) const { return bcf_get_fmt_idx(m_body.get(), index);                    }
-  bcf_info_t* find_shared_field(const uint32_t index)     const { return bcf_get_info_idx(m_body.get(), index);                   }
+  bcf_fmt_t*  find_individual_field(const uint32_t index) const { return bcf_get_fmt_id(m_body.get(), index); }
+  bcf_info_t* find_shared_field(const uint32_t index)     const { return bcf_get_info_id(m_body.get(), index); }
   bool check_field(const int32_t type_field, const int32_t type_value, const int32_t index) const;
   inline AlleleType allele_type_from_difference(const int diff) const;
 

diff --git a/gamgee/variant_header_builder.h b/gamgee/variant_header_builder.h
@@ -58,14 +58,20 @@ class VariantHeaderBuilder {
    * @brief create a new VariantHeader by copying the contents of this builder into a new object.  Allows for reuse.
    */
   VariantHeader build() const {
+    // Need to sync the header before returning it so that changes will be reflected in the final product
+    bcf_hdr_sync(m_header.get());
     return VariantHeader{utils::make_shared_variant_header(utils::variant_header_deep_copy(m_header.get()))};
   }
 
   /**
    * @brief create a new VariantHeader by moving the contents of this builder into a new object.
    * More efficient but does not allow for reuse.
    */
-  VariantHeader one_time_build() const { return VariantHeader{move(m_header)}; }
+  VariantHeader one_time_build() const {
+    // Need to sync the header before returning it so that changes will be reflected in the final product
+    bcf_hdr_sync(m_header.get());
+    return VariantHeader{move(m_header)};
+  }
 
  private:
   std::shared_ptr<bcf_hdr_t> m_header;