// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011 (DB)
+// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
// makes a virtual, unified header for all the bam files in the multireader
string BamMultiReaderPrivate::GetHeaderText(void) const {
+ // TODO: merge SamHeader objects instead of parsing string data (again)
+
// if only one reader is open
if ( m_readers.size() == 1 ) {
// reader could not open
else {
- cerr << "BamMultiReader WARNING: Could not open: "
+ cerr << "BamMultiReader WARNING: Could not open "
<< filename << ", ignoring file" << endl;
}
// attempt to set BamReader's region of interest
if ( !reader->SetRegion(region) ) {
- cerr << "BamMultiReader ERROR: could not jump " << reader->GetFilename() << " to "
+ cerr << "BamMultiReader WARNING: could not jump " << reader->GetFilename() << " to "
<< region.LeftRefID << ":" << region.LeftPosition << ".."
<< region.RightRefID << ":" << region.RightPosition << endl;
}