#include <srpe.hpp>
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void | call_svs_paired_end (vg::VG *graph, ifstream &gamstream, vector< BREAKPOINT > &bps, string refpath="") |
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void | call_svs_split_read (vg::VG *graph, ifstream &gamstream, vector< BREAKPOINT > &bps, string refpath="") |
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void | call_svs (string graphfile, string gamfile, string refpath) |
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double | discordance_score (vector< Alignment > alns, VG *subgraph) |
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void | aln_to_bseq (Alignment &a, fml_seq1_t *read) |
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void | assemble (vector< Alignment > alns, vector< fml_utg_t > &unitigs) |
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void | assemble (string refpath, int64_t start_pos, int64_t end_pos, vector< fml_utg_t > &unitigs) |
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void | assemble (int64_t node_id, int64_t offset, int window_size) |
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◆ aln_to_bseq()
void vg::SRPE::aln_to_bseq |
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Alignment & |
a, |
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fml_seq1_t * |
read |
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) |
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◆ assemble() [1/3]
void vg::SRPE::assemble |
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int64_t |
node_id, |
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int64_t |
offset, |
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int |
window_size |
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) |
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◆ assemble() [2/3]
void vg::SRPE::assemble |
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string |
refpath, |
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int64_t |
start_pos, |
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int64_t |
end_pos, |
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vector< fml_utg_t > & |
unitigs |
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) |
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◆ assemble() [3/3]
void vg::SRPE::assemble |
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vector< Alignment > |
alns, |
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vector< fml_utg_t > & |
unitigs |
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) |
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function assemble inputs: a vector of Alignments to be assembled (based on their sequences) outputs:
◆ call_svs()
void vg::SRPE::call_svs |
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string |
graphfile, |
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string |
gamfile, |
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string |
refpath |
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) |
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◆ call_svs_paired_end()
void vg::SRPE::call_svs_paired_end |
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vg::VG * |
graph, |
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ifstream & |
gamstream, |
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vector< BREAKPOINT > & |
bps, |
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string |
refpath = "" |
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) |
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◆ call_svs_split_read()
void vg::SRPE::call_svs_split_read |
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vg::VG * |
graph, |
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ifstream & |
gamstream, |
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vector< BREAKPOINT > & |
bps, |
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string |
refpath = "" |
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) |
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◆ discordance_score()
double vg::SRPE::discordance_score |
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vector< Alignment > |
alns, |
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VG * |
subgraph |
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) |
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◆ aln_to_mate
map<string, string> vg::SRPE::aln_to_mate |
◆ depth
◆ ff
◆ graph
◆ intervals
vector<pair<int, int> > vg::SRPE::intervals |
◆ max_reads
int vg::SRPE::max_reads = 125 |
◆ name_to_aln
◆ overlapping_refs
bool vg::SRPE::overlapping_refs = false |
◆ pindexes
◆ ref_names
vector<string> vg::SRPE::ref_names |
The documentation for this class was generated from the following files: