Changeset 3630 for trunk

Timestamp:

Mar 14, 2017, 8:05:31 AM (6 years ago)

Author:

Peter

Message:

Avoid compiler warnings when compiling against HTSLIB 1.4.

In struct bam1_t, 'm_data' has changed from 'int' to 'uint32_t', which
caused some "comparing signed and unsigned" warnings. Fix by
introducing private function: uint32_t BamRead::data_capacity(void)
const, and change signature on reserve.

Compiler complains if return value from sam_hdr_write is ignored. Fix
by pay attention to to it and trow if non-zero. Avoid repeating code
by introducing a third (private) open function taking the 'mode'.

Location:

trunk/yat/omic

Files:

• BamFile.cc (modified) (2 diffs)
• BamFile.h (modified) (1 diff)
• BamRead.cc (modified) (4 diffs)
• BamRead.h (modified) (2 diffs)

trunk/yat/omic/BamFile.cc

@@ -274 +274 @@
     if (!h.header_)
       throw utility::runtime_error("OutBamFile::open with null header");
-#if YAT_HAVE_HTSLIB
-    open_base(fn, "wb", NULL);
-    sam_hdr_write(sf_, h.header_);
-#else
-    open_base(fn, "wb", h.header_);
-#endif
+    open(fn, std::string("wb"), h);
   }
 
@@ -298 +293 @@
     else
       mode = "wu";
+#else
+    mode.push_back('0'+compression);
+#endif
+    open(fn, mode, h);
+  }
+
+
+  void OutBamFile::open(const std::string& fn, const std::string& mode,
+                        const BamHeader& h)
+  {
+#if YAT_HAVE_HTSLIB
     open_base(fn, mode, NULL);
-    sam_hdr_write(sf_, h.header_);
-#else
-    mode.push_back('0'+compression);
+    if (sam_hdr_write(sf_, h.header_)) {
+      std::ostringstream ss;
+      ss << "failed open '" << fn << "'";
+      throw utility::runtime_error(ss.str());
+    }
+#else
     open_base(fn, mode, h.header_);
 #endif

trunk/yat/omic/BamFile.h

@@ -318 +318 @@
 
   private:
+    void open(const std::string& fn, const std::string& mode,
+              const BamHeader& h);
+
   };
 

trunk/yat/omic/BamRead.cc

@@ -262 +262 @@
     data_size() += offset;
     core().n_cigar = c.size();
-    assert(data_size() <= bam_->m_data);
+    assert(static_cast<uint32_t>(data_size()) <= data_capacity());
   }
 
@@ -272 +272 @@
   bam1_core_t& BamRead::core(void)
   { return bam_->core; }
+
+
+  uint32_t BamRead::data_capacity(void) const
+  {
+    return bam_->m_data;
+  }
 
 
@@ -329 +335 @@
     memcpy(bam1_qname(bam_), n.c_str(), n.size()+1);
     data_size() += offset;
-    assert(data_size() <= bam_->m_data);
+    assert(static_cast<uint32_t>(data_size()) <= data_capacity());
   }
 
@@ -341 +347 @@
 
 
-  void BamRead::reserve(int n)
-  {
-    assert(bam_);
-    if (bam_->m_data >= n)
+  void BamRead::reserve(uint32_t n)
+  {
+    assert(bam_);
+    if (data_capacity() >= static_cast<uint32_t>(n))
       return;
     // at least double capacity
-    bam_->m_data = std::max(bam_->m_data<<1, n);
+    bam_->m_data = std::max(data_capacity()<<1, n);
     bam_->data = (uint8_t*)realloc(bam_->data, bam_->m_data);
     if (!bam_->data) {

trunk/yat/omic/BamRead.h

@@ -329 +329 @@
   private:
     // ensure capacity of data pointer is (at least) n
-    void reserve(int n);
+    void reserve(uint32_t n);
 
     bam1_t* bam_;
@@ -342 +342 @@
     int& data_size(void);
     const int& data_size(void) const;
+    uint32_t data_capacity(void) const;
   };