BamTools
2.5.1
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Provides classes & methods related to sorting BamAlignments. More...
#include <Sort.h>
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 ®ion, const Compare &comp=Compare()) |
template<typename Compare > | |
static std::vector< BamAlignment > | GetSortedRegion (BamMultiReader &reader, const BamRegion ®ion, const Compare &comp=Compare()) |
Provides classes & methods related to sorting BamAlignments.
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inlinestatic |
Reads a region of alignments from position-sorted BAM files, then sorts by the provided compare function
[in] | reader | BamMultiReader opened on desired BAM files |
[in] | region | desired region-of-interest |
[in] | comp | comparison function object |
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inlinestatic |
Reads a region of alignments from a position-sorted BAM file, then sorts by the provided compare function
[in] | reader | BamReader opened on desired BAM file |
[in] | region | desired region-of-interest |
[in] | comp | comparison function object |
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inlinestatic |
Returns a sorted copy of the input alignments, using the provided compare function.
[in] | input | vector of alignments to be sorted |
[in] | comp | comparison function object |
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inlinestatic |
Sorts a std::vector of alignments (in-place), using the provided compare function.
[in,out] | data | vector of alignments to be sorted |
[in] | comp | comparison function object |