#include <multipath_alignment_emitter.hpp>
◆ MultipathAlignmentEmitter()
vg::MultipathAlignmentEmitter::MultipathAlignmentEmitter |
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ostream & |
out, |
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int |
num_threads, |
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const HandleGraph & |
graph, |
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const string |
out_format = "gamp" |
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) |
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Initialize with the intended output stream and the maximum number of threads that will be outputting. Optionally converts to single path alignments in either "gam" or "gaf" format.
◆ ~MultipathAlignmentEmitter()
vg::MultipathAlignmentEmitter::~MultipathAlignmentEmitter |
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◆ convert_multipath_alignment()
void vg::MultipathAlignmentEmitter::convert_multipath_alignment |
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const multipath_alignment_t & |
mp_aln, |
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Alignment & |
aln, |
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const string * |
prev_name = nullptr , |
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const string * |
next_name = nullptr |
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) |
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private |
◆ emit_pairs()
Emit paired read mappings as interleaved protobuf messages.
◆ emit_singles()
void vg::MultipathAlignmentEmitter::emit_singles |
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const string & |
name, |
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vector< multipath_alignment_t > && |
mp_alns |
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) |
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Emit read mappings as protobuf messages.
◆ set_read_group()
void vg::MultipathAlignmentEmitter::set_read_group |
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const string & |
read_group | ) |
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Choose a read group to apply to all emitted alignments.
◆ set_sample_name()
void vg::MultipathAlignmentEmitter::set_sample_name |
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const string & |
sample_name | ) |
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Choose a sample name to apply to all emitted alignments.
◆ aln_emitters
◆ graph
const HandleGraph& vg::MultipathAlignmentEmitter::graph |
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private |
the graph we're aligning against
◆ mp_aln_emitters
◆ multiplexer
shared multiplexer across streams
◆ out
ostream& vg::MultipathAlignmentEmitter::out |
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private |
the stream that everything is emitted into
◆ read_group
string vg::MultipathAlignmentEmitter::read_group |
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private |
read group applied to alignments
◆ sample_name
string vg::MultipathAlignmentEmitter::sample_name |
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private |
sample name applied to alignments
The documentation for this class was generated from the following files: