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| bool | vg::io::get_next_record_from_gaf (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &record) |
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| bool | vg::io::get_next_interleaved_record_pair_from_gaf (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &record1, gafkluge::GafRecord &record2) |
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| size_t | vg::io::gaf_unpaired_for_each (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda) |
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| size_t | vg::io::gaf_unpaired_for_each (const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda) |
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| size_t | vg::io::gaf_paired_interleaved_for_each (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda) |
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| size_t | vg::io::gaf_paired_interleaved_for_each (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda) |
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| size_t | vg::io::gaf_unpaired_for_each_parallel (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size) |
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| size_t | vg::io::gaf_unpaired_for_each_parallel (const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size) |
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| size_t | vg::io::gaf_paired_interleaved_for_each_parallel (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size) |
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| size_t | vg::io::gaf_paired_interleaved_for_each_parallel (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size) |
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| size_t | vg::io::gaf_paired_interleaved_for_each_parallel_after_wait (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size) |
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| size_t | vg::io::gaf_paired_interleaved_for_each_parallel_after_wait (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size) |
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| gafkluge::GafRecord | vg::io::alignment_to_gaf (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links) |
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| gafkluge::GafRecord | vg::io::alignment_to_gaf (const HandleGraph &graph, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links) |
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| void | vg::io::gaf_to_alignment (function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const gafkluge::GafRecord &gaf, Alignment &aln) |
| | Convert a GAF alignment into a vg Alignment. The alignment must be in node ID space. More...
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| void | vg::io::gaf_to_alignment (const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln) |
| | Convert a GAF alignment into a vg Alignment. The alignment must be in node ID space. More...
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| short | vg::io::quality_char_to_short (char c) |
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| char | vg::io::quality_short_to_char (short i) |
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| void | vg::io::alignment_quality_short_to_char (Alignment &alignment) |
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| string | vg::io::string_quality_short_to_char (const string &quality) |
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| void | vg::io::alignment_quality_char_to_short (Alignment &alignment) |
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| string | vg::io::string_quality_char_to_short (const string &quality) |
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