--- /dev/null
+// ***************************************************************************
+// BamAlgorithms.h (c) 2009 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 29 September 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides generic algorithms that are intended to work with BamTools data
+// structures. Where possible, these are intended to be STL-compatible.
+// ***************************************************************************
+
+#ifndef BAMALGORITHMS_H
+#define BAMALGORITHMS_H
+
+#include <api/api_global.h>
+#include <api/BamAlignment.h>
+#include <api/BamReader.h>
+#include <api/BamMultiReader.h>
+#include <algorithm>
+#include <functional>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+namespace Algorithms {
+
+// -------------------------------------------------------
+// Built-in function objects for comparing BamAlignments
+
+typedef std::binary_function<BamAlignment, BamAlignment, bool> BamAlignmentComparer;
+
+// Algorithms::SortByName<Compare>
+// compare alignments by name (default comparison is std::less<std::string> )
+template<template <typename> class Compare = std::less>
+struct API_EXPORT SortByName : public BamAlignmentComparer {
+ bool operator()(const BamTools::BamAlignment& lhs,
+ const BamTools::BamAlignment& rhs)
+ {
+ Compare<std::string> comp;
+ return comp(lhs.Name, rhs.Name);
+ }
+};
+
+// Algorithms::SortByPosition<Compare>
+// compare alignments by position (default comparison is std::less<int>)
+template<template <typename> class Compare = std::less>
+struct API_EXPORT SortByPosition : public BamAlignmentComparer {
+ bool operator()(const BamTools::BamAlignment& lhs,
+ const BamTools::BamAlignment& rhs)
+ {
+ // force unmapped aligmnents to end
+ if ( lhs.RefID == -1 ) return false;
+ if ( rhs.RefID == -1 ) return true;
+
+ // otherwise compare first on RefID, then position
+ Compare<int32_t> comp;
+ if ( lhs.RefID == rhs.RefID )
+ return comp(lhs.Position, rhs.Position);
+ return comp(lhs.RefID, rhs.RefID);
+ }
+};
+
+// Algorithms::SortByTag<Compare>("XY")
+// compare alignments by tag value (default comparison is std::less<T>)
+// where T is the expected tag type (e.g. RG -> string, NM -> int, etc.)
+template<typename T, template <typename> class Compare = std::less>
+struct API_EXPORT SortByTag : public BamAlignmentComparer {
+
+ // ctor - needed to provide the tag name ("RG", "NM", "Aq", etc)
+ explicit SortByTag(const std::string& tag) : m_tag(tag) { }
+
+ bool operator()(const BamTools::BamAlignment& lhs,
+ const BamTools::BamAlignment& rhs)
+ {
+ // force alignments without tag to end
+ T lhsTagValue;
+ T rhsTagValue;
+ if ( !lhs.GetTag(m_tag, lhsTagValue) ) return false;
+ if ( !rhs.GetTag(m_tag, rhsTagValue) ) return true;
+
+ // otherwise compare tag values
+ Compare<T> comp;
+ return comp(lhsTagValue, rhsTagValue);
+ }
+
+ private:
+ std::string m_tag;
+};
+
+// Algorithms::Unsorted
+// placeholder comparison object, ignores the alignments' data
+// N.B. - returning false typically retains initial insertion order
+struct API_EXPORT Unsorted : public BamAlignmentComparer {
+ bool operator()(const BamTools::BamAlignment& /*lhs*/,
+ const BamTools::BamAlignment& /*rhs*/)
+ {
+ return false;
+ }
+};
+
+API_EXPORT template<typename Compare>
+std::vector<BamAlignment> SortReaderRegion(BamReader& reader,
+ const BamRegion& region,
+ const Compare& comp = Compare())
+{
+ // return empty container if unable to find region
+ if ( !reader.IsOpen() ) return std::vector<BamAlignment>();
+ if ( !reader.SetRegion(region) ) return std::vector<BamAlignment>();
+
+ // iterate through region, grabbing alignments
+ BamAlignment al;
+ std::vector<BamAlignment> results;
+ while ( reader.GetNextAlignment(al) )
+ results.push_back(al);
+
+ // sort & return alignments
+ std::sort(results.begin(), results.end(), comp);
+ return results;
+}
+
+API_EXPORT template<typename Compare>
+std::vector<BamAlignment> SortReaderRegion(BamMultiReader& reader,
+ const BamRegion& region,
+ const Compare& comp = Compare())
+{
+ // return empty container if unable to find region
+ if ( !reader.HasOpenReaders() ) return std::vector<BamAlignment>();
+ if ( !reader.SetRegion(region) ) return std::vector<BamAlignment>();
+
+ // iterate through region, grabbing alignments
+ BamAlignment al;
+ std::vector<BamAlignment> results;
+ while ( reader.GetNextAlignment(al) )
+ results.push_back(al);
+
+ // sort & return alignments
+ std::sort(results.begin(), results.end(), comp);
+ return results;
+}
+
+} // namespace Algorithms
+} // namespace BamTools
+
+#endif // BAM_ALGORITHMS_H
#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);
+ }
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Unsorted Alignments" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::stable_sort(alignments.begin(), alignments.end(), Algorithms::Unsorted());
+ printAlignments(alignments);
+ cerr << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by name)" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Algorithms::SortByName<>());
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by tag Aq)" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Algorithms::SortByTag<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(), Algorithms::SortByTag<int, std::greater>("Aq"));
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+
+
+
+// // ########################################
+// // original
+// // ########################################
+//
+// while ( reader.GetNextAlignmentCore(al) )
+// ++alignmentCount;
+//
+// //#########################################
}
// otherwise attempt to use region as constraint
// if index data available for all BAM files, we can use SetRegion
if ( reader.IsIndexLoaded() ) {
- // 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;
+
+ alignments = Algorithms::SortReaderRegion(reader, region, Algorithms::SortByName<>() );
+ printAlignments(alignments);
+
+ cerr << "################################" << endl;
+
+ alignments = Algorithms::SortReaderRegion(reader, region, Algorithms::SortByTag<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
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