#include "bamtools_count.h"
+#include <api/BamAlgorithms.h>
#include <api/BamMultiReader.h>
#include <utils/bamtools_options.h>
#include <utils/bamtools_utilities.h>
CountTool::CountSettings* m_settings;
};
+static
+void printAlignments(const vector<BamAlignment>& alignments) {
+
+ vector<BamAlignment>::const_iterator alIter = alignments.begin();
+ vector<BamAlignment>::const_iterator alEnd = alignments.end();
+ for ( ; alIter != alEnd; ++alIter ) {
+ const BamAlignment& a = (*alIter);
+
+ cerr << a.Name
+ << "\t" << a.RefID << ":" << a.Position;
+
+ int aqValue;
+ bool hasTag = a.GetTag("Aq", aqValue);
+ cerr << "\tAq=";
+ if ( hasTag ) cerr << aqValue;
+ else cerr << "?";
+ cerr << endl;
+ }
+}
+
bool CountTool::CountToolPrivate::Run(void) {
// if no '-in' args supplied, default to stdin
// if no region specified, count entire file
if ( !m_settings->HasRegion ) {
- while ( reader.GetNextAlignmentCore(al) )
+
+
+ vector<BamAlignment> alignments;
+ while ( reader.GetNextAlignment(al) ) {
++alignmentCount;
+
+ if ( alignments.size() < 100 )
+ alignments.push_back(al);
+ }
+
+ using namespace BamTools::Algorithms;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Unsorted Alignments" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::stable_sort(alignments.begin(), alignments.end(), Sort::Unsorted());
+ printAlignments(alignments);
+ cerr << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by name)" << endl
+ << "------------------------------" << endl
+ << endl;
+// std::sort(alignments.begin(), alignments.end(), Sort::ByName());
+ Algorithms::SortAlignments(alignments, Sort::ByName());
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by tag Aq)" << endl
+ << "------------------------------" << endl
+ << endl;
+// std::sort(alignments.begin(), alignments.end(), Sort::ByTag<int>("Aq"));
+ Algorithms::SortAlignments(alignments, Sort::ByTag<int>("Aq"));
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by tag Aq) desc" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Sort::ByTag<int>("Aq", Sort::DescendingOrder));
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+
+
+
+// // ########################################
+// // original
+// // ########################################
+//
+// while ( reader.GetNextAlignmentCore(al) )
+// ++alignmentCount;
+//
+// //#########################################
}
// otherwise attempt to use region as constraint
reader.LocateIndexes();
// if index data available for all BAM files, we can use SetRegion
- if ( reader.IsIndexLoaded() ) {
+ if ( reader.HasIndexes() ) {
- // attempt to set region on reader
- if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
- cerr << "bamtools count ERROR: set region failed. Check that REGION describes a valid range" << endl;
- reader.Close();
- return false;
- }
+ vector<BamAlignment> alignments;
+ using namespace BamTools::Algorithms;
+
+ alignments = GetSortedRegion(reader, region, Sort::ByName() );
+ printAlignments(alignments);
+
+ cerr << "################################" << endl;
+
+ alignments = GetSortedRegion(reader, region, Sort::ByTag<int>("Aq"));
+ printAlignments(alignments);
+
+// // attempt to set region on reader
+// if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+// cerr << "bamtools count ERROR: set region failed. Check that REGION describes a valid range" << endl;
+// reader.Close();
+// return false;
+// }
- // everything checks out, just iterate through specified region, counting alignments
- while ( reader.GetNextAlignmentCore(al) )
- ++alignmentCount;
+// // everything checks out, just iterate through specified region, counting alignments
+// while ( reader.GetNextAlignmentCore(al) )
+// ++alignmentCount;
}
// no index data available, we have to iterate through until we