Changeset 3357

Timestamp:

Nov 23, 2014, 2:54:44 AM (8 years ago)

Author:

Peter

Message:

refs #794. implement open and close functions

Location:

trunk/yat/omic

Files:

• BamFile.cc (modified) (4 diffs)
• BamFile.h (modified) (5 diffs)

trunk/yat/omic/BamFile.cc

@@ -88 +88 @@
   {
 #if YAT_HAVE_HTSLIB
-    assert(0 && "FIXME");
+    open_base(fn, "rb", NULL);
+    header_.header_ = sam_hdr_read(sf_);
 #else
     open_base(fn, "rb", NULL);
@@ -165 +166 @@
   {
 #if YAT_HAVE_HTSLIB
-    assert(0 && "FIXME");
+    open_base(fn, "wb", NULL);
+    sam_hdr_write(sf_, h.header_);
 #else
     open_base(fn, "wb", h.header_);
@@ -183 +185 @@
     }
 #if YAT_HAVE_HTSLIB
-    assert(0 && "FIXME");
+    if (compression)
+      mode.push_back('0'+compression);
+    else
+      mode = "wu";
+    open_base(fn, mode, NULL);
+    sam_hdr_write(sf_, h.header_);
 #else
     mode.push_back('0'+compression);
@@ -194 +201 @@
   {
 #if YAT_HAVE_HTSLIB
-    if (bam_write1(sf_->fp.bgzf, read.bam_)) {
+    if (bam_write1(sf_->fp.bgzf, read.bam_)<=0) {
 #else
     if (samwrite(sf_, read.bam_)<=0) {

trunk/yat/omic/BamFile.h

@@ -79 +79 @@
 
        \see samopen
-     */
-#ifndef YAT_HAVE_HTSLIB
+
+       \note \a aux is ignored when compiling against htslib
+     */
     void open_base(const std::string& fn, const std::string& mode,
                    const void* aux);
-#endif
 
 #ifndef YAT_HAVE_HTSLIB
@@ -308 +308 @@
   {
 #if YAT_HAVE_HTSLIB
-    // FIXME, check that sam_close returns 0 (for success)
-    sam_close(sf_);
+    if (sf_==NULL)
+      return;
+    if (sam_close(sf_))
+      throw utility::IO_error("BamFile::close() failed");
 #else
     samclose(sf_);
@@ -324 +326 @@
 
 
-#ifndef YAT_HAVE_HTSLIB
   template<class Derived>
   void BamFile<Derived>::open_base(const std::string& fn,
@@ -332 +333 @@
     filename_ = fn;
     YAT_ASSERT(!sf_);
+#if YAT_HAVE_HTSLIB
+    YAT_ASSERT(aux==NULL); // aux is ignored in htslib mode
+    sf_ = sam_open(fn.c_str(), mode.c_str());
+#else
     sf_ = samopen(fn.c_str(), mode.c_str(), aux);
+#endif
     if (!sf_) {
       std::ostringstream ss;
@@ -339 +345 @@
     }
   }
-#endif
 
 }}}