Extracted BamReaderPrivate & BamWriterPrivate from inner classes.

[bamtools.git] / src / toolkit / bamtools_sort.cpp

diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp
index 83584a6c8bd9b258bca86a6b4094b2761ceddc82..2f463ba610e389452a1be2181e8c7f390ee289a7 100644 (file)
--- a/src/toolkit/bamtools_sort.cpp
+++ b/src/toolkit/bamtools_sort.cpp
@@ -130,7 +130,7 @@ SortTool::SortTool(void)
     , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools sort", "sorts a BAM file", "[-in <filename>] [-out <filename>]");
+    Options::SetProgramInfo("bamtools sort", "sorts a BAM file", "[-in <filename>] [-out <filename>] [sortOptions]");
     
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
@@ -197,7 +197,10 @@ bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
     
     // open input BAM file
     BamReader inputReader;
-    inputReader.Open(m_settings->InputBamFilename);
+    if (!inputReader.Open(m_settings->InputBamFilename)) {
+        cerr << "Could not open " << m_settings->InputBamFilename << " for reading." << endl;
+        return false;
+    }
     
     // get basic data that will be shared by all temp/output files 
     m_headerText = inputReader.GetHeaderText();
@@ -322,4 +325,4 @@ bool SortTool::SortToolPrivate::WriteTempFile(const vector<BamAlignment>& buffer
     // close temp file & return success
     tempWriter.Close();
     return true;
-}
\ No newline at end of file
+}