Changeset 3672

Timestamp:

Jul 31, 2017, 10:12:05 AM (6 years ago)

Author:

Peter

Message:

for convenience add constructor that creates an iterator that iterates over whole chromosome (or from start until end of chr). Same thing can be accomplished by using constructor taking 4 arguments with 4th as bf::header().target_length(tid), where bf is first arg and tid is 2nd arg.

Location:

trunk

Files:

• test/bam_region_iterator.cc (modified) (1 diff)
• yat/omic/BamReadIterator.cc (modified) (1 diff)
• yat/omic/BamReadIterator.h (modified) (1 diff)

trunk/test/bam_region_iterator.cc

@@ -99 +99 @@
   }
 
+  {
+    BamReadIterator begin(bam_stream, 1);
+    BamReadIterator end;
+    if (begin == end) {
+      suite.add(false);
+      suite.err() << "error: BamReadIterator(2): begin == end\n";
+    }
+  }
+
 #endif
 }

trunk/yat/omic/BamReadIterator.cc

@@ -52 +52 @@
   {
     actor_ = boost::shared_ptr<Actor>(new IndexActor(bf, tid, start, end));
+    assert(actor_);
+    increment();
+  }
+
+
+  BamReadIterator::BamReadIterator(InBamFile& bf, int32_t tid, int32_t start)
+  {
+    actor_ =
+      boost::shared_ptr<Actor>(new IndexActor(bf, tid, start,
+                                              bf.header().target_length(tid)));
     assert(actor_);
     increment();

trunk/yat/omic/BamReadIterator.h

@@ -95 +95 @@
      */
     BamReadIterator(InBamFile& in, int32_t tid, int32_t start, int32_t end);
+
+    /**
+       Iterator that walks from tid:start to end of chromosome and
+       then it turns into an end-of-region iterator.
+
+       This function requires an index file is available, see
+       InBamFile::index().
+
+       All reads iterated over overlap with defined region, in other
+       words, iter->tid == \a tid; iter->end() > start
+
+       \param in file to iterate over
+       \param tid segment (chromosome) to iterate over
+       \param start left most position of specified region
+
+       \since New in yat 0.15
+     */
+    BamReadIterator(InBamFile& in, int32_t tid, int32_t start=0);
   private:
     friend class boost::iterator_core_access;