Changeset 3408 for trunk/yat/omic/BamHeader.cc

Timestamp:

Apr 16, 2015, 2:22:24 AM (8 years ago)

Author:

Peter

Message:

Implement functions to get/set free text in BamHeader?. As setting the
header text modifies underlying data, copy and assignment are now
implemented as hard copy (rather than the implicit pointer copy as
before). It also means that the bam_hdr_t* is no longer owned by
InBamFile?, but is now owned by BamHeader? and destroyed in its
destructor.

refs #817

File:

• trunk/yat/omic/BamHeader.cc (modified) (5 diffs)

trunk/yat/omic/BamHeader.cc

@@ -27 +27 @@
 
 #include <cassert>
+#include <cstdlib>
+#include <cstring>
 #include <string>
 #include <sstream>
+#include <utility>
 
 namespace theplu {
@@ -37 +40 @@
     : header_(NULL)
   {
+  }
+
+
+  BamHeader::~BamHeader(void)
+  {
+#if YAT_HAVE_HTSLIB
+    bam_hdr_destroy(header_);
+#else
+    bam_header_destroy(header_);
+#endif
+  }
+
+
+  BamHeader::BamHeader(const BamHeader& other)
+  {
+#ifndef YAT_HAVE_HTSLIB
+    using namespace detail; // for bam_hdr_dup in YAT_HAVE_LIBBAM mode
+#endif
+    header_ = bam_hdr_dup(other.header_);
   }
 
@@ -70 +92 @@
 
 
+  void BamHeader::swap(BamHeader& other)
+  {
+    std::swap(header_, other.header_);
+  }
+
+
   uint32_t BamHeader::target_length(size_t tid) const
   {
@@ -81 +109 @@
     assert(tid < static_cast<size_t>(n_targets()));
     return header_->target_name[tid];
+  }
+
+
+  std::string BamHeader::text(void) const
+  {
+    assert(header_);
+    return std::string(header_->text, header_->l_text);
+  }
+
+  void BamHeader::text(const std::string& txt)
+  {
+#ifdef YAT_HAVE_HTSLIB
+    // destroy the old
+    bam_hdr_destroy(header_);
+    // and create header pointer
+    header_ = sam_hdr_parse(txt.size(), txt.c_str());
+#endif
+    header_->l_text = txt.size();
+    header_->text = (char*)realloc(header_->text, txt.size()+1);
+    memcpy(header_->text, txt.c_str(), txt.size()+1);
+#ifndef YAT_HAVE_HTSLIB
+    sam_header_parse(header_);
+#endif
   }
 
@@ -118 +169 @@
   }
 
+
+  void swap(BamHeader& lhs, BamHeader& rhs)
+  {
+    lhs.swap(rhs);
+  }
+
+
+  BamHeader& BamHeader::operator=(const BamHeader& rhs)
+  {
+    BamHeader tmp(rhs);
+    swap(tmp);
+    return *this;
+  }
+
+#ifndef YAT_HAVE_HTSLIB
+  namespace detail {
+    bam_header_t * bam_hdr_dup(const bam_header_t* other)
+    {
+      // taken from htslib 1.2.1 and adjusted to fit old struct bam_header_t
+      if (!other)
+        return NULL;
+      bam_header_t* h = bam_header_init();
+      if (!h)
+        return NULL;
+      // copy stuff
+      h->n_targets = other->n_targets;
+      h->l_text = other->l_text;
+      h->n_text = other->n_text;
+      h->dict = NULL;
+      h->hash = NULL;
+      h->rg2lib = NULL;
+
+      h->text = (char*)calloc(h->l_text + 1, 1);
+      memcpy(h->text, other->text, h->l_text);
+      h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
+      h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
+      for (int i = 0; i < h->n_targets; ++i) {
+        h->target_len[i] = other->target_len[i];
+        h->target_name[i] = strdup(other->target_name[i]);
+      }
+      return h;
+    }
+  }
+#endif
+
 }}}