#include <halRearrangement.h>
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enum | ID {
Insertion = 0,
Deletion,
Duplication,
Translocation,
Transposition,
Inversion,
Complex,
Invalid,
Gap,
Missing,
Nothing
} |
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class | counted_ptr< Rearrangement > |
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class | counted_ptr< const Rearrangement > |
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Interface for a rearrangement operation. Rearrangements are specifed by pairs of breakpoints in a top segment array. For now they are two-break (balance or not) rearrangements and translocations. Anything else will will be labled complex for now.
hal::Rearrangement::~Rearrangement |
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inlineprotectedpure virtual |
virtual std::pair<hal_index_t, hal_index_t> hal::Rearrangement::getDeletedRange |
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const |
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pure virtual |
Get the range in the parent that was deleted. Only valid to call this immediately after identifying a deletion with either of the above two functions. Otherwise, results are undefined
virtual std::pair<hal_index_t, hal_index_t> hal::Rearrangement::getDuplicatedRange |
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const |
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pure virtual |
Get the range in the parent that was duplicated. Only valid to call this immediately after identifying a duplication. Otherwise, results are undefined
virtual hal_size_t hal::Rearrangement::getGapLengthThreshold |
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const |
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pure virtual |
Return the maximum size of a simple indel such that it will be considered a gap (and factored out of breakpoint computations)
virtual ID hal::Rearrangement::getID |
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const |
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pure virtual |
Get the ID of the rearrangement
virtual std::pair<hal_index_t, hal_index_t> hal::Rearrangement::getInsertedRange |
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const |
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pure virtual |
Get the range in the parent that was inserted. Only valid to call this immediately after identifying a insertion. Otherwise, results are undefined
virtual TopSegmentIteratorConstPtr hal::Rearrangement::getLeftBreakpoint |
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const |
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pure virtual |
Left breakpoint is specified by the first base of the returned segment
virtual hal_size_t hal::Rearrangement::getLength |
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const |
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pure virtual |
Get the length of a rearrangement (ie number of bases that were inserted, deleted, moved, etc
virtual hal_size_t hal::Rearrangement::getNumContainedGapBases |
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const |
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pure virtual |
Get the total size (in bases) of gaps within the arrangement. Gaps are dependent on the gap threshold that can be specified below...
virtual hal_size_t hal::Rearrangement::getNumContainedGaps |
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const |
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pure virtual |
Get the number of gaps within the arrangement. Gaps are dependent on the gap threshold that can be specified below...
virtual TopSegmentIteratorConstPtr hal::Rearrangement::getRightBreakpoint |
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const |
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pure virtual |
Right breakpoint is specified by the last base of the returned segment
virtual bool hal::Rearrangement::identifyDeletionFromLeftBreakpoint |
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TopSegmentIteratorConstPtr |
topSegment | ) |
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pure virtual |
Test if segment at given index corresponds to a deletion (shortcut method used by column iterator)
virtual bool hal::Rearrangement::identifyFromLeftBreakpoint |
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TopSegmentIteratorConstPtr |
topSegment | ) |
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pure virtual |
Identify the rearrangement by scanning along the genome, skipping gaps until the matching breeakpoint is found. If no matching breakpint is found, the rearrangement cannot be identified and false is returned
virtual bool hal::Rearrangement::identifyInsertionFromLeftBreakpoint |
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TopSegmentIteratorConstPtr |
topSegment | ) |
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pure virtual |
Test if segment at given index corresponds to a breakpoint right before an insertion (shortcut method used by column iterator)
virtual bool hal::Rearrangement::identifyNext |
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pure virtual |
Start scanning from last identified breakpoint
virtual void hal::Rearrangement::setAtomic |
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bool |
atomic | ) |
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pure virtual |
Set atomic behaviour (so gaps and compatible segments are not used to merge larger segments. Will overcount rearrangements but useful sometimes (ie column iteraor). Will automatically set the gap threshold to 0.
virtual void hal::Rearrangement::setGapLengthThreshold |
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hal_size_t |
threshold | ) |
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pure virtual |
Specify the maximum size of a simple indel such that it will be considered a gap (and factored out of breakpoint computations)
The documentation for this class was generated from the following file: