MultiReader (&MultiMerger) now using Algorithms::Sort objects

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

diff --git a/src/toolkit/bamtools_count.cpp b/src/toolkit/bamtools_count.cpp
index c17b25776df476a1317cef2218b8693202a27b47..d438eab9595502e6051e71d70cca5c84404662bd 100644 (file)
--- a/src/toolkit/bamtools_count.cpp
+++ b/src/toolkit/bamtools_count.cpp
@@ -10,6 +10,7 @@
 
 #include "bamtools_count.h"
 
+#include <api/BamAlgorithms.h>
 #include <api/BamMultiReader.h>
 #include <utils/bamtools_options.h>
 #include <utils/bamtools_utilities.h>
@@ -62,6 +63,26 @@ struct CountTool::CountToolPrivate {
         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
@@ -81,8 +102,74 @@ bool CountTool::CountToolPrivate::Run(void) {
 
     // 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
@@ -96,18 +183,29 @@ bool CountTool::CountToolPrivate::Run(void) {
             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