#include <hts_alignment_emitter.hpp>
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| SplicedHTSAlignmentEmitter (const string &filename, const string &format, const map< string, int64_t > &path_length, const PathPositionHandleGraph &graph, size_t max_threads) |
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| ~SplicedHTSAlignmentEmitter ()=default |
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| HTSAlignmentEmitter (const string &filename, const string &format, const map< string, int64_t > &path_length, size_t max_threads) |
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| ~HTSAlignmentEmitter () |
| Tear down an HTSAlignmentEmitter and destroy HTSlib structures. More...
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| HTSAlignmentEmitter (const HTSAlignmentEmitter &other)=delete |
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HTSAlignmentEmitter & | operator= (const HTSAlignmentEmitter &other)=delete |
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| HTSAlignmentEmitter (HTSAlignmentEmitter &&other)=delete |
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HTSAlignmentEmitter & | operator= (HTSAlignmentEmitter &&other)=delete |
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virtual void | emit_singles (vector< Alignment > &&aln_batch) |
| Emit a batch of Alignments. More...
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virtual void | emit_mapped_singles (vector< vector< Alignment >> &&alns_batch) |
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virtual void | emit_pairs (vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch) |
| Emit a batch of pairs of Alignments. More...
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virtual void | emit_mapped_pairs (vector< vector< Alignment >> &&alns1_batch, vector< vector< Alignment >> &&alns2_batch, vector< int64_t > &&tlen_limit_batch) |
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virtual void | emit_single (Alignment &&aln) |
| Emit a single Alignment. More...
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virtual void | emit_mapped_single (vector< Alignment > &&alns) |
| Emit a single Alignment with secondaries. All secondaries must have is_secondary set already. More...
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virtual void | emit_pair (Alignment &&aln1, Alignment &&aln2, int64_t tlen_limit=0) |
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virtual void | emit_mapped_pair (vector< Alignment > &&alns1, vector< Alignment > &&alns2, int64_t tlen_limit=0) |
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virtual | ~AlignmentEmitter ()=default |
| Allow destruction through base class pointer. More...
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size_t | min_splice_length = 20 |
| The minimum length of a deletion relative to the path that will be coded as a splice junction in the CIGAR. More...
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◆ SplicedHTSAlignmentEmitter()
vg::SplicedHTSAlignmentEmitter::SplicedHTSAlignmentEmitter |
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const string & |
filename, |
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const string & |
format, |
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const map< string, int64_t > & |
path_length, |
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const PathPositionHandleGraph & |
graph, |
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size_t |
max_threads |
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) |
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◆ ~SplicedHTSAlignmentEmitter()
vg::SplicedHTSAlignmentEmitter::~SplicedHTSAlignmentEmitter |
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default |
◆ convert_alignment()
void vg::SplicedHTSAlignmentEmitter::convert_alignment |
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const Alignment & |
aln, |
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vector< pair< int, char >> & |
cigar, |
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bool & |
pos_rev, |
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int64_t & |
pos, |
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string & |
path_name |
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privatevirtual |
◆ spliced_cigar_against_path()
vector< pair< int, char > > vg::SplicedHTSAlignmentEmitter::spliced_cigar_against_path |
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const Alignment & |
aln, |
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const string & |
path_name, |
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int64_t |
pos, |
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bool |
rev |
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private |
Convert a spliced alignment against a path to a cigar. The alignment must be colinear along a path and contain only mappings on the path, but it can have deletions relative to the path that follow edges in the graph.
◆ graph
Graph that alignments were aligned against.
◆ min_splice_length
size_t vg::SplicedHTSAlignmentEmitter::min_splice_length = 20 |
The minimum length of a deletion relative to the path that will be coded as a splice junction in the CIGAR.
The documentation for this class was generated from the following files: