Changeset 3028

Timestamp:

Apr 21, 2013, 2:37:31 AM (10 years ago)

Author:

Peter

Message:

functions to access, append, and remove aux field. refs #746

Location:

trunk

Files:

• test/bam.cc (modified) (2 diffs)
• yat/omic/BamRead.cc (modified) (2 diffs)
• yat/omic/BamRead.h (modified) (1 diff)

trunk/test/bam.cc

@@ -51 +51 @@
 #ifdef HAVE_LIBBAM
 using namespace omic;
+
+void test_aux(test::Suite& suite, const BamRead& b)
+{
+  suite.out() << "test aux\n";
+  BamRead bam(b);
+
+  char c = 'h';
+  int size = bam.aux_size();
+  bam.aux_append("ZZ", 'A', 1, (uint8_t*)(&c));
+  suite.out() << "size: " << size << " " << bam.aux_size() << "\n";
+  suite.add(bam.aux_size() == size+4);
+  bam.aux("ZZ");
+  char c1 = bam_aux2A(bam.aux("ZZ"));
+  suite.out() << c << "==" << c1 << "\n";
+  suite.add(c==c1);
+  bam.aux_del("ZZ");
+  if (!suite.add(bam.aux_size() == size))
+    suite.err() << "error: incorrect size: " << bam.aux_size() << "\n";
+}
+
 
 void test_cigar(test::Suite& suite, const BamRead& b, const BamHeader& hdr)
@@ -144 +164 @@
   }
   test_cigar(suite, bam, in.header());
+  test_aux(suite, bam);
 }
 #endif

trunk/yat/omic/BamRead.cc

@@ -1 @@
-
 // $Id$
 
@@ -70 +69 @@
   const uint8_t* BamRead::aux(void) const
   {
+    assert(bam_);
     return bam1_aux(bam_);
+  }
+
+
+  const uint8_t* BamRead::aux(const char tag[2]) const
+  {
+    assert(bam_);
+    return bam_aux_get(bam_, tag);
+  }
+
+
+  void BamRead::aux_append(const char tag[2], char type,int len,uint8_t* data)
+  {
+    assert(bam_);
+    bam_aux_append(bam_, tag, type, len, data);
+  }
+
+
+  void BamRead::aux_del(const char tag[2])
+  {
+    assert(bam_);
+    bam_aux_del(bam_, bam_aux_get(bam_, tag));
+  }
+
+
+  int BamRead::aux_size(void) const
+  {
+    assert(bam_);
+    return bam_->l_aux;
   }
 

trunk/yat/omic/BamRead.h

@@ -118 +118 @@
 
     /**
+       \since New in yat 0.11
+     */
+    const uint8_t* aux(const char tag[2]) const;
+
+    /**
+       \since New in yat 0.11
+     */
+    void aux(const char tag[2], char type, int len, uint8_t* data);
+
+    /**
+       \since New in yat 0.11
+     */
+    void aux_append(const char tag[2], char type, int len, uint8_t* data);
+
+    /**
+       \since New in yat 0.11
+     */
+    void aux_del(const char tag[2]);
+
+    /**
+       \since New in yat 0.11
+     */
+    int aux_size(void) const;
+
+    /**
        \brief access core data struct