Changeset 3359

Timestamp:

Nov 23, 2014, 1:05:13 PM (8 years ago)

Author:

Peter

Message:

fix issues in OutBamFile::write. refs #794

Location:

trunk

Files:

• test/bam.cc (modified) (1 diff)
• yat/omic/BamFile.cc (modified) (1 diff)

trunk/test/bam.cc

@@ -83 +83 @@
   bam.cigar(cig);
   suite.out() << bam.cigar_str() << "\n";
-  suite.add(bam.cigar_str()=="");
+  if (!suite.add(bam.cigar_str()==""))
+    suite.err() << "error: expected cigar to be empty\n";
   os.write(bam);
 

trunk/yat/omic/BamFile.cc

@@ -200 +200 @@
   {
 #if YAT_HAVE_HTSLIB
-    if (bam_write1(sf_->fp.bgzf, read.bam_)<=0) {
-#else
-    if (samwrite(sf_, read.bam_)<=0) {
-#endif
-      throw OutBamFile::error(read);
-    }
+    assert(read.bam_);
+    if (is_open() && bam_write1(sf_->fp.bgzf, read.bam_)>0)
+      return;
+#else
+    if (samwrite(sf_, read.bam_)>0)
+      return;
+#endif
+    throw OutBamFile::error(read);
   }