Changeset 3774

Timestamp:

Oct 26, 2018, 9:19:12 AM (5 years ago)

Author:

Peter

Message:

implement VcfIterator?. refs #905

Location:

trunk

Files:

• test/vcf_file.cc (modified) (2 diffs)
• yat/omic/Makefile.am (modified) (2 diffs)
• yat/omic/VcfFile.h (modified) (1 diff)
• yat/omic/VcfIterator.cc (added)
• yat/omic/VcfIterator.h (added)

trunk/test/vcf_file.cc

@@ -27 +27 @@
 #include "yat/omic/VcfFile.h"
 #include "yat/omic/VcfHeader.h"
+#include "yat/omic/VcfIterator.h"
 
+#include "yat/random/random.h"
+
+#include <algorithm>
+#include <iterator>
 #include <sstream>
+#include <vector>
 
 using namespace theplu::yat;
@@ -50 +56 @@
   omic::VCF entry;
   vcf.read(entry);
+  // create a vector VCFs from iterator range
+  omic::VcfIterator begin(vcf);
+  omic::VcfIterator end;
+  std::vector<omic::VCF> vec(begin, end);
+  if (vec.empty()) {
+    suite.add(false);
+    suite.err() << "error: vector is empty\n";
+  }
+
+  // randomise variants
+  random::random_shuffle(vec.begin(), vec.end());
+
+  // just illustrating how to output vcfs using ostream_iterator
+  std::stringstream os;
+  std::copy(vec.begin(), vec.end(),std::ostream_iterator<omic::VCF>(os, "\n"));
+  suite.out() << "output:\n" << os.str().substr(0, 100)
+              << "--->8 cut\n";
+  if (os.str().size() < 100) {
+    suite.add(false);
+    suite.err() << "error: too small output\n";
+  }
+
   vcf.close();
   return suite.return_value();

trunk/yat/omic/Makefile.am

@@ -40 +40 @@
 yat_libyat_la_SOURCES += yat/omic/VcfFile.cc
 yat_libyat_la_SOURCES += yat/omic/VcfHeader.cc
+yat_libyat_la_SOURCES += yat/omic/VcfIterator.cc
 
 nobase_include_HEADERS += $(srcdir)/yat/omic/algorithm.h
@@ -65 +66 @@
 nobase_include_HEADERS += $(srcdir)/yat/omic/VcfFile.h
 nobase_include_HEADERS += $(srcdir)/yat/omic/VcfHeader.h
+nobase_include_HEADERS += $(srcdir)/yat/omic/VcfIterator.h

trunk/yat/omic/VcfFile.h

@@ -120 +120 @@
     boost::scoped_ptr<std::ifstream> file_stream_;
     std::string name_;
+    friend class VcfIterator;
   };