// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 29 September 2011 (DB)
+// Last modified: 10 October 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>
+#include "api/algorithms/Sort.h"
-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
+/*! \namespace BamTools::Algorithms
+ \brief Provides convenient classes & methods for working with BAM data
+*/
#endif // BAM_ALGORITHMS_H