vg::SplicedHTSAlignmentEmitter Member List

This is the complete list of members for vg::SplicedHTSAlignmentEmitter, including all inherited members.

atomic_header	vg::HTSWriter	protected
backing_files	vg::HTSWriter	protected
BGZF_FOOTER_LENGTH	vg::HTSWriter	protectedstatic
convert_alignment(const Alignment &aln, vector< pair< int, char >> &cigar, bool &pos_rev, int64_t &pos, string &path_name) const	vg::SplicedHTSAlignmentEmitter	privatevirtual
convert_paired(Alignment &aln1, Alignment &aln2, bam_hdr_t *header, int64_t tlen_limit, vector< bam1_t * > &dest)	vg::HTSAlignmentEmitter	private
convert_unpaired(Alignment &aln, bam_hdr_t *header, vector< bam1_t * > &dest)	vg::HTSAlignmentEmitter	private
emit_extra_message(const std::string &tag, std::string &&data)	vg::io::AlignmentEmitter	virtual
emit_mapped_pair(vector< Alignment > &&alns1, vector< Alignment > &&alns2, int64_t tlen_limit=0)	vg::io::AlignmentEmitter	virtual
emit_mapped_pairs(vector< vector< Alignment >> &&alns1_batch, vector< vector< Alignment >> &&alns2_batch, vector< int64_t > &&tlen_limit_batch)	vg::HTSAlignmentEmitter	virtual
emit_mapped_single(vector< Alignment > &&alns)	vg::io::AlignmentEmitter	virtual
emit_mapped_singles(vector< vector< Alignment >> &&alns_batch)	vg::HTSAlignmentEmitter	virtual
emit_pair(Alignment &&aln1, Alignment &&aln2, int64_t tlen_limit=0)	vg::io::AlignmentEmitter	virtual
emit_pairs(vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch)	vg::HTSAlignmentEmitter	virtual
emit_single(Alignment &&aln)	vg::io::AlignmentEmitter	virtual
emit_singles(vector< Alignment > &&aln_batch)	vg::HTSAlignmentEmitter	virtual
ensure_header(const string &read_group, const string &sample_name, size_t thread_number)	vg::HTSWriter	protected
format	vg::HTSWriter	protected
graph	vg::SplicedHTSAlignmentEmitter	private
header_mutex	vg::HTSWriter	protected
hts_mode	vg::HTSWriter	protected
HTSAlignmentEmitter(const string &filename, const string &format, const SequenceDictionary &sequence_dictionary, const unordered_map< string, size_t > &subpath_to_index, size_t max_threads)	vg::HTSAlignmentEmitter
HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete	vg::HTSAlignmentEmitter
HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete	vg::HTSAlignmentEmitter
HTSLIB_CRAM_THREADS	vg::HTSWriter	protectedstatic
HTSWriter(const string &filename, const string &format, const SequenceDictionary &sequence_dictionary, const unordered_map< string, size_t > &subpath_to_index, size_t max_threads)	vg::HTSWriter
HTSWriter(const HTSWriter &other)=delete	vg::HTSWriter
HTSWriter(HTSWriter &&other)=delete	vg::HTSWriter
initialize_sam_file(bam_hdr_t *header, size_t thread_number, bool keep_header=false)	vg::HTSWriter	protected
min_splice_length	vg::SplicedHTSAlignmentEmitter
multiplexer	vg::HTSWriter	protected
operator=(const HTSAlignmentEmitter &other)=delete	vg::HTSAlignmentEmitter
operator=(HTSAlignmentEmitter &&other)=delete	vg::HTSAlignmentEmitter
vg::HTSWriter::operator=(const HTSWriter &other)=delete	vg::HTSWriter
vg::HTSWriter::operator=(HTSWriter &&other)=delete	vg::HTSWriter
out_file	vg::HTSWriter	protected
output_is_bgzf	vg::HTSWriter	protected
sam_files	vg::HTSWriter	protected
sam_header	vg::HTSWriter	protected
save_records(bam_hdr_t *header, vector< bam1_t * > &records, size_t thread_number)	vg::HTSWriter	protected
sequence_dictionary	vg::HTSWriter	protected
SplicedHTSAlignmentEmitter(const string &filename, const string &format, const SequenceDictionary &sequence_dictionary, const unordered_map< string, size_t > &subpath_to_index, const PathPositionHandleGraph &graph, size_t max_threads)	vg::SplicedHTSAlignmentEmitter
subpath_to_index	vg::HTSWriter	protected
~AlignmentEmitter()=default	vg::io::AlignmentEmitter	virtual
~HTSAlignmentEmitter()=default	vg::HTSAlignmentEmitter
~HTSWriter()	vg::HTSWriter
~SplicedHTSAlignmentEmitter()=default	vg::SplicedHTSAlignmentEmitter