Changeset 3175

Timestamp:

Mar 15, 2014, 9:15:51 AM (9 years ago)

Author:

Peter

Message:

new class BamPair?. refs #784

Location:

trunk

Files:

• test/bam_pair_analyse.cc (modified) (1 diff)
• yat/omic/BamPair.cc (added)
• yat/omic/BamPair.h (added)
• yat/omic/BamPairIterator.h (modified) (7 diffs)
• yat/omic/Makefile.am (modified) (2 diffs)
• yat/omic/algorithm.h (modified) (1 diff)

trunk/test/bam_pair_analyse.cc

@@ -73 +73 @@
   Counter counter;
   bam_pair_analyse(iter, end, counter);
-  suite.out() << counter.n_ << "\n";
-  suite.add(counter.n_==395);
+  if (!suite.add(counter.n_==395))
+    suite.err() << "n: " << counter.n_ << "; expected 395\n";
   is.close();
 }

trunk/yat/omic/BamPairIterator.h

@@ -25 +25 @@
 #include <iostream>
 
+#include "BamPair.h"
 #include "BamRead.h"
 
@@ -59 +60 @@
   class BamPairIterator
     : public boost::iterator_facade<
-    BamPairIterator<Base>, const std::pair<BamRead, BamRead>,
-    std::input_iterator_tag
+    BamPairIterator<Base>, const BamPair, std::input_iterator_tag
     >
   {
@@ -81 +81 @@
     Base iter_;
     Base end_;
-    std::pair<BamRead, BamRead> x_;
+    BamPair x_;
     boost::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
     typedef std::pair<int32_t, int32_t> Position;
@@ -87 +87 @@
     friend class boost::iterator_core_access;
 
-    const std::pair<BamRead, BamRead>& dereference(void) const;
+    const BamPair& dereference(void) const;
     bool equal(const BamPairIterator& other) const;
     void increment(void);
@@ -143 +143 @@
 
   template<typename Base>
-  const std::pair<BamRead, BamRead>&
+  const BamPair&
   BamPairIterator<Base>::dereference(void) const
   {
@@ -189 +189 @@
         for (; lower!=reads_->end() && lower->first == position; ++lower)
           if (same_query_name(lower->second, *iter_)) {
-            x_.first = lower->second;
-            x_.second = *iter_;
+            x_.first() = lower->second;
+            x_.second() = *iter_;
             return;
           }
@@ -199 +199 @@
           mate = siam_reads_->lower_bound(iter_->name());
         if (mate!=siam_reads_->end() && same_query_name(mate->second, *iter_)) {
-          x_.first = mate->second;
-          x_.second = *iter_;
+          x_.first() = mate->second;
+          x_.second() = *iter_;
           return;
         }

trunk/yat/omic/Makefile.am

@@ -21 +21 @@
 yat_libyat_la_SOURCES += yat/omic/BamFile.cc
 yat_libyat_la_SOURCES += yat/omic/BamHeader.cc
+yat_libyat_la_SOURCES += yat/omic/BamPair.cc
 yat_libyat_la_SOURCES += yat/omic/BamRead.cc
 yat_libyat_la_SOURCES += yat/omic/BamReadFilter.cc
@@ -36 +37 @@
 nobase_include_HEADERS += $(srcdir)/yat/omic/BamFile.h
 nobase_include_HEADERS += $(srcdir)/yat/omic/BamHeader.h
+nobase_include_HEADERS += $(srcdir)/yat/omic/BamPair.h
 nobase_include_HEADERS += $(srcdir)/yat/omic/BamPairIterator.h
 nobase_include_HEADERS += $(srcdir)/yat/omic/BamRead.h

trunk/yat/omic/algorithm.h

@@ -63 +63 @@
     BamPairIterator<Iterator> end(last, last);
     for (; iter!=end; ++iter)
-      visitor(iter->first, iter->second);
+      visitor(iter->first(), iter->second());
   }