|
| int | vg::hts_for_each (string &filename, function< void(Alignment &)> lambda) |
| |
| int | vg::hts_for_each_parallel (string &filename, function< void(Alignment &)> lambda) |
| |
| int | vg::hts_for_each (string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph) |
| |
| int | vg::hts_for_each_parallel (string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph) |
| |
| int | vg::fastq_for_each (string &filename, function< void(Alignment &)> lambda) |
| |
| bool | vg::get_next_alignment_from_fastq (gzFile fp, char *buffer, size_t len, Alignment &alignment) |
| |
| bool | vg::get_next_interleaved_alignment_pair_from_fastq (gzFile fp, char *buffer, size_t len, Alignment &mate1, Alignment &mate2) |
| |
| bool | vg::get_next_alignment_pair_from_fastqs (gzFile fp1, gzFile fp2, char *buffer, size_t len, Alignment &mate1, Alignment &mate2) |
| |
| size_t | vg::fastq_unpaired_for_each (const string &filename, function< void(Alignment &)> lambda) |
| |
| size_t | vg::fastq_paired_interleaved_for_each (const string &filename, function< void(Alignment &, Alignment &)> lambda) |
| |
| size_t | vg::fastq_paired_two_files_for_each (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda) |
| |
| size_t | vg::fastq_unpaired_for_each_parallel (const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size) |
| |
| size_t | vg::fastq_paired_interleaved_for_each_parallel (const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size) |
| |
| size_t | vg::fastq_paired_interleaved_for_each_parallel_after_wait (const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size) |
| |
| size_t | vg::fastq_paired_two_files_for_each_parallel (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size) |
| |
| size_t | vg::fastq_paired_two_files_for_each_parallel_after_wait (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size) |
| |
| bam_hdr_t * | vg::hts_file_header (string &filename, string &header) |
| |
| bam_hdr_t * | vg::hts_string_header (string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample) |
| |
| bam_hdr_t * | vg::hts_string_header (string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample) |
| |
| void | vg::write_alignment_to_file (const Alignment &aln, const string &filename) |
| |
| void | vg::mapping_cigar (const Mapping &mapping, vector< pair< int, char > > &cigar) |
| |
| string | vg::cigar_string (const vector< pair< int, char > > &cigar) |
| |
| string | vg::mapping_string (const string &source, const Mapping &mapping) |
| |
| void | vg::cigar_mapping (const bam1_t *b, Mapping &mapping) |
| |
| Alignment | vg::bam_to_alignment (const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle, const bam_hdr_t *bh, const PathPositionHandleGraph *graph) |
| |
| Alignment | vg::bam_to_alignment (const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle) |
| |
| void | vg::append_cigar_operation (const int length, const char operation, vector< pair< int, char >> &cigar) |
| |
| bam1_t * | vg::alignment_to_bam (bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max) |
| |
| bam1_t * | vg::alignment_to_bam (bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar) |
| |
| string | vg::alignment_to_sam (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max) |
| |
| string | vg::alignment_to_sam (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar) |
| |
| int32_t | vg::determine_flag (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, bool paired, const int32_t tlen_max) |
| | Returns the SAM bit-coded flag for alignment with. More...
|
| |
| vector< pair< int, char > > | vg::cigar_against_path (const Alignment &alignment, bool on_reverse_strand, int64_t &pos, size_t path_len, size_t softclip_suppress) |
| |
| void | vg::simplify_cigar (vector< pair< int, char >> &cigar) |
| |
| void | vg::mapping_against_path (Alignment &alignment, const bam1_t *b, const path_handle_t &path, const PathPositionHandleGraph *graph, bool on_reverse_strand) |
| |
| pair< int32_t, int32_t > | vg::compute_template_lengths (const int64_t &pos1, const vector< pair< int, char >> &cigar1, const int64_t &pos2, const vector< pair< int, char >> &cigar2) |
| |
| int32_t | vg::sam_flag (const Alignment &alignment, bool on_reverse_strand, bool paired) |
| |
| void | vg::parse_rg_sample_map (char *hts_header, map< string, string > &rg_sample) |
| | Populate a mapping from read group to sample name, given the text BAM header. More...
|
| |
| void | vg::parse_tid_path_handle_map (const bam_hdr_t *hts_header, const PathHandleGraph *graph, map< int, path_handle_t > &tid_path_handle) |
| |
| int | vg::alignment_to_length (const Alignment &a) |
| |
| int | vg::alignment_from_length (const Alignment &a) |
| |
| Alignment & | vg::extend_alignment (Alignment &a1, const Alignment &a2, bool debug) |
| |
| Alignment | vg::merge_alignments (const vector< Alignment > &alns) |
| |
| Alignment | vg::merge_alignments (const Alignment &a1, const Alignment &a2, bool debug) |
| |
| Alignment | vg::strip_from_start (const Alignment &aln, size_t drop) |
| |
| Alignment | vg::strip_from_end (const Alignment &aln, size_t drop) |
| |
| Alignment | vg::trim_alignment (const Alignment &aln, const Position &pos1, const Position &pos2) |
| |
| vector< Alignment > | vg::alignment_ends (const Alignment &aln, size_t len1, size_t len2) |
| |
| Alignment | vg::alignment_middle (const Alignment &aln, int len) |
| |
| const string | vg::hash_alignment (const Alignment &aln) |
| |
| Alignment | vg::reverse_complement_alignment (const Alignment &aln, const function< int64_t(id_t)> &node_length) |
| |
| void | vg::reverse_complement_alignment_in_place (Alignment *aln, const function< int64_t(id_t)> &node_length) |
| |
| vector< Alignment > | vg::reverse_complement_alignments (const vector< Alignment > &alns, const function< int64_t(int64_t)> &node_length) |
| |
| int | vg::non_match_start (const Alignment &alignment) |
| |
| int | vg::non_match_end (const Alignment &alignment) |
| |
| int | vg::softclip_start (const Alignment &alignment) |
| |
| int | vg::softclip_end (const Alignment &alignment) |
| |
| int | vg::softclip_trim (Alignment &alignment) |
| |
| int | vg::query_overlap (const Alignment &aln1, const Alignment &aln2) |
| |
| int | vg::edit_count (const Alignment &alignment) |
| |
| size_t | vg::to_length_after_pos (const Alignment &aln, const Position &pos) |
| |
| size_t | vg::from_length_after_pos (const Alignment &aln, const Position &pos) |
| |
| size_t | vg::to_length_before_pos (const Alignment &aln, const Position &pos) |
| |
| size_t | vg::from_length_before_pos (const Alignment &aln, const Position &pos) |
| |
| string | vg::signature (const Alignment &aln) |
| |
| pair< string, string > | vg::signature (const Alignment &aln1, const Alignment &aln2) |
| |
| string | vg::middle_signature (const Alignment &aln, int len) |
| |
| pair< string, string > | vg::middle_signature (const Alignment &aln1, const Alignment &aln2, int len) |
| |
| void | vg::translate_nodes (Alignment &a, const unordered_map< id_t, pair< id_t, bool > > &ids, const std::function< size_t(int64_t)> &node_length) |
| |
| void | vg::flip_nodes (Alignment &a, const set< int64_t > &ids, const std::function< size_t(int64_t)> &node_length) |
| |
| bool | vg::uses_Us (const Alignment &alignment) |
| |
| void | vg::convert_Us_to_Ts (Alignment &alignment) |
| | Replaces any U's in the sequence or the Path with T's. More...
|
| |
| void | vg::convert_Ts_to_Us (Alignment &alignment) |
| | Replaces any T's in the sequence or the Path with U's. More...
|
| |
| Alignment | vg::simplify (const Alignment &a, bool trim_internal_deletions) |
| |
| void | vg::normalize_alignment (Alignment &alignment) |
| | Merge adjacent edits of the same type and convert all N matches to mismatches. More...
|
| |
| map< id_t, int > | vg::alignment_quality_per_node (const Alignment &aln) |
| |
| void | vg::parse_bed_regions (istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback) |
| |
| void | vg::parse_gff_regions (istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback) |
| |
| void | vg::parse_bed_regions (istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments) |
| |
| void | vg::parse_gff_regions (istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments) |
| |
| Position | vg::alignment_start (const Alignment &aln) |
| |
| Position | vg::alignment_end (const Alignment &aln) |
| |
| map< string,vector< pair< size_t, bool > > > | vg::alignment_refpos_to_path_offsets (const Alignment &aln) |
| | return the path offsets as cached in the alignment More...
|
| |
| void | vg::alignment_set_distance_to_correct (Alignment &aln, const Alignment &base, const unordered_map< string, string > *translation) |
| |
| void | vg::alignment_set_distance_to_correct (Alignment &aln, const map< string, vector< pair< size_t, bool >>> &base_offsets, const unordered_map< string, string > *translation=nullptr) |
| |
| AlignmentValidity | vg::alignment_is_valid (const Alignment &aln, const HandleGraph *hgraph, bool check_sequence) |
| |
| Alignment | vg::target_alignment (const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse) |
| |
| Alignment | vg::target_alignment (const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping) |
| |
