Expunge the copy-then-move idiom

closes #256 and make @droazen happy.
broadinstitute · Sep 24, 2014 · 91b6e14 · 91b6e14
1 parent 5bb653a
commit 91b6e14
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Showing 7 changed files with 11 additions and 11 deletions.
diff --git a/gamgee/indexed_sam_reader.h b/gamgee/indexed_sam_reader.h
@@ -42,11 +42,11 @@ class IndexedSamReader {
      * @param filename the name of the bam/cram file
      * @param interval_list Samtools style intervals to look for records
      */
-    IndexedSamReader(const std::string& filename, std::vector<std::string> interval_list) :
+    IndexedSamReader(const std::string& filename, const std::vector<std::string>& interval_list) :
       m_sam_file_ptr {utils::make_shared_hts_file(sam_open(filename.c_str(), "r"))}, // TODO: Not checking for errors.
       m_sam_index_ptr {utils::make_shared_hts_index(sam_index_load(m_sam_file_ptr.get(), filename.c_str()))}, // TODO: Not checking for errors.
       m_sam_header_ptr { utils::make_shared_sam_header(sam_hdr_read(m_sam_file_ptr.get())) }, // TODO: Not checking for errors.
-      m_interval_list {std::move(interval_list)} {
+      m_interval_list {interval_list} {
     }
 
     /**

diff --git a/gamgee/indexed_variant_iterator.cpp b/gamgee/indexed_variant_iterator.cpp
@@ -23,10 +23,10 @@ IndexedVariantIterator::IndexedVariantIterator() :
 IndexedVariantIterator::IndexedVariantIterator(const std::shared_ptr<htsFile>& file_ptr,
                                                const std::shared_ptr<hts_idx_t>& index_ptr,
                                                const std::shared_ptr<bcf_hdr_t>& header_ptr,
-                                               const std::vector<std::string> interval_list) :
+                                               const std::vector<std::string>& interval_list) :
   VariantIterator { file_ptr, header_ptr },
   m_variant_index_ptr { index_ptr },
-  m_interval_list { interval_list.empty() ? all_intervals : move(interval_list) },
+  m_interval_list { interval_list.empty() ? all_intervals : interval_list },
   m_interval_iter { m_interval_list.begin() },
   m_index_iter_ptr { utils::make_unique_hts_itr(bcf_itr_querys(m_variant_index_ptr.get(), m_variant_header_ptr.get(), m_interval_iter->c_str())) }
 {

diff --git a/gamgee/indexed_variant_iterator.h b/gamgee/indexed_variant_iterator.h
@@ -34,7 +34,7 @@ class IndexedVariantIterator : public VariantIterator {
   IndexedVariantIterator(const std::shared_ptr<htsFile>& file_ptr,
                          const std::shared_ptr<hts_idx_t>& index_ptr,
                          const std::shared_ptr<bcf_hdr_t>& header_ptr,
-                         const std::vector<std::string> interval_list = all_intervals);
+                         const std::vector<std::string>& interval_list = all_intervals);
 
   /**
    * @brief an IndexedVariantIterator cannot be copied safely, as it is iterating over a stream.

diff --git a/gamgee/indexed_variant_reader.h b/gamgee/indexed_variant_reader.h
@@ -37,11 +37,11 @@ class IndexedVariantReader {
    * @param interval_list a vector of intervals represented by strings.  Empty vector for all intervals.
    *
    */
-  IndexedVariantReader(const std::string& filename, const std::vector<std::string> interval_list) :
+  IndexedVariantReader(const std::string& filename, const std::vector<std::string>& interval_list) :
     m_variant_file_ptr { utils::make_shared_hts_file(bcf_open(filename.c_str(), "r")) },
     m_variant_index_ptr { utils::make_shared_hts_index(bcf_index_load(filename.c_str())) },
     m_variant_header_ptr { utils::make_shared_variant_header(bcf_hdr_read(m_variant_file_ptr.get())) },
-    m_interval_list { std::move(interval_list) }
+    m_interval_list { interval_list }
   {}
 
   /**

diff --git a/gamgee/interval.h b/gamgee/interval.h
@@ -46,8 +46,8 @@ class Interval {
    * @param stop        stop location (inclusive)
    * @param output_type desired output format (only used if Interval is sent to output stream)
    */
-  explicit Interval(std::string chr, const uint32_t start, const uint32_t stop, const IntervalType output_type = IntervalType::GATK) :
-    m_chr{std::move(chr)},
+  explicit Interval(const std::string& chr, const uint32_t start, const uint32_t stop, const IntervalType output_type = IntervalType::GATK) :
+    m_chr{chr},
     m_start{start},
     m_stop{stop},
     m_output_type{output_type} 

diff --git a/gamgee/multiple_variant_iterator.cpp b/gamgee/multiple_variant_iterator.cpp
@@ -7,7 +7,7 @@ MultipleVariantIterator::MultipleVariantIterator() :
   m_variant_vector {}
 {}
 
-MultipleVariantIterator::MultipleVariantIterator(const std::vector<std::shared_ptr<htsFile>> variant_files, const std::shared_ptr<bcf_hdr_t> variant_header) :
+MultipleVariantIterator::MultipleVariantIterator(const std::vector<std::shared_ptr<htsFile>>& variant_files, const std::shared_ptr<bcf_hdr_t>& variant_header) :
   m_queue {},
   m_variant_vector {}
 {

diff --git a/gamgee/multiple_variant_iterator.h b/gamgee/multiple_variant_iterator.h
@@ -28,7 +28,7 @@ class MultipleVariantIterator {
    * @param variant_files  vector of vcf/bcf files opened via the bcf_open() macro from htslib
    * @param variant_header the combined vcf/bcf file header
    */
-  MultipleVariantIterator(const std::vector<std::shared_ptr<htsFile>> variant_files, const std::shared_ptr<bcf_hdr_t> variant_header);
+  MultipleVariantIterator(const std::vector<std::shared_ptr<htsFile>>& variant_files, const std::shared_ptr<bcf_hdr_t>& variant_header);
 
   /**
    * @brief a MultipleVariantIterator move constructor guarantees all objects will have the same state.