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size_t | vg::io::unpaired_for_each_parallel (function< bool(Alignment &)> get_read_if_available, function< void(Alignment &)> lambda, uint64_t batch_size) |
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size_t | vg::io::paired_for_each_parallel_after_wait (function< bool(Alignment &, Alignment &)> get_pair_if_available, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size) |
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bool | vg::io::get_next_alignment_from_gaf (const HandleGraph &graph, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &g_buffer, Alignment &alignment) |
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bool | vg::io::get_next_interleaved_alignment_pair_from_gaf (const HandleGraph &graph, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &g_buffer, Alignment &mate1, Alignment &mate2) |
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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 (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda) |
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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 (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 (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 (const HandleGraph &graph, const Alignment &aln, bool cs_cigar, bool base_quals) |
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void | vg::io::gaf_to_alignment (const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln) |
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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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string | vg::io::string_quality_char_to_short (const string &quality) |
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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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void | vg::io::alignment_quality_short_to_char (Alignment &alignment) |
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