BamTools::Algorithms::Sort Struct Reference

Provides classes & methods related to sorting BamAlignments. More...

#include <Sort.h>

List of all members.

Classes
struct	ByName
	Function object for comparing alignments by name. More...
struct	ByPosition
	Function object for comparing alignments by position. More...
struct	ByTag
	Function object for comparing alignments by tag value. More...
struct	Unsorted
	Placeholder function object. More...
Public Types
enum	Order { AscendingOrder = 0, DescendingOrder }
	Provides explicit values for specifying desired sort ordering. More...
Static Public Member Functions
template<typename Compare >
static void	SortAlignments (std::vector< BamAlignment > &data, const Compare &comp=Compare())
template<typename Compare >
static std::vector< BamAlignment >	SortAlignments (const std::vector< BamAlignment > &input, const Compare &comp=Compare())
template<typename Compare >
static std::vector< BamAlignment >	GetSortedRegion (BamReader &reader, const BamRegion &region, const Compare &comp=Compare())
template<typename Compare >
static std::vector< BamAlignment >	GetSortedRegion (BamMultiReader &reader, const BamRegion &region, const Compare &comp=Compare())

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Detailed Description

Provides classes & methods related to sorting BamAlignments.

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Member Enumeration Documentation

enum BamTools::Algorithms::Sort::Order

Provides explicit values for specifying desired sort ordering.

Enumerator:

AscendingOrder
DescendingOrder

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Member Function Documentation

template<typename Compare >

static std::vector<BamAlignment> BamTools::Algorithms::Sort::GetSortedRegion	(	BamMultiReader &	reader,
		const BamRegion &	region,
		const Compare &	comp = Compare()
	)			[inline, static]

Reads a region of alignments from position-sorted BAM files, then sorts by the provided compare function

            BamMultiReader reader;
            // open BAM files & index files

            BamRegion region;
            // define a region of interest (i.e. a exon or some other feature)

            // get all alignments covering that region, sorted by read group name
            std::vector<BamAlignments> a;
            a = Sort::GetSortedRegion(reader, region, Sort::ByTag<std::string>("RG"));

Parameters:

[in]	reader	BamMultiReader opened on desired BAM files
[in]	region	desired region-of-interest
[in]	comp	comparison function object

Returns:

sorted vector of the region's alignments

template<typename Compare >

static std::vector<BamAlignment> BamTools::Algorithms::Sort::GetSortedRegion	(	BamReader &	reader,
		const BamRegion &	region,
		const Compare &	comp = Compare()
	)			[inline, static]

Reads a region of alignments from a position-sorted BAM file, then sorts by the provided compare function

            BamReader reader;
            // open BAM file & index file

            BamRegion region;
            // define a region of interest (i.e. a exon or some other feature)

            // get all alignments covering that region, sorted by read group name
            std::vector<BamAlignments> a;
            a = Sort::GetSortedRegion(reader, region, Sort::ByTag<std::string>("RG"));

Parameters:

[in]	reader	BamReader opened on desired BAM file
[in]	region	desired region-of-interest
[in]	comp	comparison function object

Returns:

sorted vector of the region's alignments

template<typename Compare >

static std::vector<BamAlignment> BamTools::Algorithms::Sort::SortAlignments	(	const std::vector< BamAlignment > &	input,
		const Compare &	comp = Compare()
	)			[inline, static]

Returns a sorted copy of the input alignments, using the provided compare function.

            std::vector<BamAlignemnt> a;
            // populate data

            // get a copy of our original data, sorted by edit distance (descending order)
            std::vector<BamAligment> sortedData;
            sortedData = Sort::SortAlignments(a, Sort::ByTag<int>("NM", Sort::DescendingOrder));

Parameters:

[in]	input	vector of alignments to be sorted
[in]	comp	comparison function object

Returns:

sorted copy of the input data

template<typename Compare >

static void BamTools::Algorithms::Sort::SortAlignments	(	std::vector< BamAlignment > &	data,
		const Compare &	comp = Compare()
	)			[inline, static]

Sorts a std::vector of alignments (in-place), using the provided compare function.

            std::vector<BamAlignemnt> a;
            // populate data

            // sort our alignment list by edit distance
            Sort::SortAlignments(a, Sort::ByTag<int>("NM"));

Parameters:

[in,out]	data	vector of alignments to be sorted
[in]	comp	comparison function object

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The documentation for this struct was generated from the following file:

• Sort.h