Changeset 3160

Timestamp:

Jan 13, 2014, 8:08:30 AM (10 years ago)

Author:

Peter

Message:

closes #775

Location:

trunk

Files:

• test/bam.cc (modified) (3 diffs)
• yat/omic/BamFile.cc (modified) (2 diffs)
• yat/omic/BamFile.h (modified) (3 diffs)

trunk/test/bam.cc

@@ -1 +1 @@
 // $Id$
 //
-// Copyright (C) 2013 Peter Johansson
+// Copyright (C) 2013, 2014 Peter Johansson
 //
 // This program is free software; you can redistribute it and/or modify
@@ -192 +192 @@
 
 
+void test_open3(test::Suite& suite, const BamHeader& header)
+{
+  OutBamFile out("yaya.bam", header, 0);
+  out.close();
+  out.open("yaya.bam", header, 9);
+  out.close();
+  try {
+    out.open("yaya.bam", header, 10);
+    suite.add(false);
+    suite.err() << "open(\"yaya.bam\", header, 10): did not throw\n";
+  }
+  catch (std::invalid_argument& e) {
+    suite.err() << "expected exception: " << e.what() << "\n";
+  }
+  out.close();
+}
+
+
 void test1(test::Suite& suite)
 {
@@ -239 +257 @@
   test_sequence(suite, bam);
   test_name(suite, bam);
-}
-#endif
+  test_open3(suite, in.header());
+}
+#endif

trunk/yat/omic/BamFile.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2012, 2013 Peter Johansson
+  Copyright (C) 2012, 2013, 2014 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -132 +132 @@
 
 
+  OutBamFile::OutBamFile(const std::string& fn, const BamHeader& header,
+                         unsigned int c)
+  {
+    open(fn, header, c);
+  }
+
+
   void OutBamFile::open(const std::string& fn, const BamHeader& h)
   {
     open_base(fn, "wb", h.header_);
+  }
+
+
+  void OutBamFile::open(const std::string& fn, const BamHeader& h,
+                        unsigned int compression)
+  {
+    std::string mode("wb");
+    if (compression > 9) {
+      std::stringstream oss;
+      oss << "OutBamFile::open( " << fn << ", <header>, " << compression
+          << "): incorrect compression level\n";
+      throw std::invalid_argument(oss.str());
+    }
+    mode.push_back('0'+compression);
+    open_base(fn, mode, h.header_);
   }
 

trunk/yat/omic/BamFile.h

@@ -5 +5 @@
 
 /*
-  Copyright (C) 2012, 2013 Peter Johansson
+  Copyright (C) 2012, 2013, 2014 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -193 +193 @@
 
     /**
+       \brief Create an output bam file.
+
+       Equivalent to default constructor followed by a call to open(3).
+
+       \see open(const std::string&, const BamHeader&, unsigned int)
+
+       \since yat 0.12
+     */
+    OutBamFile(const std::string&, const BamHeader& header,
+               unsigned int compression);
+
+    /**
        \brief Open an output bam file.
 
@@ -202 +214 @@
      */
     void open(const std::string& fn, const BamHeader& hdr);
+
+    /**
+       \brief Open an output bam file.
+
+       Opens an output bam file and writes the header contained in \a
+       hdr. If \a fn is "-", \c stdout is used.
+
+       \param fn string specifying the filename
+       \param hdr header
+       \param compression a number [0,9] indicating level of
+       compression. 9 gives highest compression and 0 indicates no
+       compression (suitable for piping between applications)
+
+       \since yat 0.12
+     */
+    void open(const std::string& fn, const BamHeader& hdr,
+              unsigned int compression);
 
     /**