vg
tools for working with variation graphs
vg::HTSAlignmentEmitter Member List

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

atomic_headervg::HTSAlignmentEmitterprivate
backing_filesvg::HTSAlignmentEmitterprivate
BGZF_FOOTER_LENGTHvg::HTSAlignmentEmitterprivatestatic
convert_alignment(const Alignment &aln, vector< pair< int, char >> &cigar, bool &pos_rev, int64_t &pos, string &path_name) constvg::HTSAlignmentEmitterprivatevirtual
convert_paired(Alignment &aln1, Alignment &aln2, bam_hdr_t *header, int64_t tlen_limit, vector< bam1_t * > &dest)vg::HTSAlignmentEmitterprivate
convert_unpaired(Alignment &aln, bam_hdr_t *header, vector< bam1_t * > &dest)vg::HTSAlignmentEmitterprivate
emit_mapped_pair(vector< Alignment > &&alns1, vector< Alignment > &&alns2, int64_t tlen_limit=0)vg::io::AlignmentEmittervirtual
emit_mapped_pairs(vector< vector< Alignment >> &&alns1_batch, vector< vector< Alignment >> &&alns2_batch, vector< int64_t > &&tlen_limit_batch)vg::HTSAlignmentEmittervirtual
emit_mapped_single(vector< Alignment > &&alns)vg::io::AlignmentEmittervirtual
emit_mapped_singles(vector< vector< Alignment >> &&alns_batch)vg::HTSAlignmentEmittervirtual
emit_pair(Alignment &&aln1, Alignment &&aln2, int64_t tlen_limit=0)vg::io::AlignmentEmittervirtual
emit_pairs(vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch)vg::HTSAlignmentEmittervirtual
emit_single(Alignment &&aln)vg::io::AlignmentEmittervirtual
emit_singles(vector< Alignment > &&aln_batch)vg::HTSAlignmentEmittervirtual
ensure_header(const Alignment &sniff, size_t thread_number)vg::HTSAlignmentEmitterprivate
formatvg::HTSAlignmentEmitterprivate
header_mutexvg::HTSAlignmentEmitterprivate
hts_modevg::HTSAlignmentEmitterprivate
HTSAlignmentEmitter(const string &filename, const string &format, const map< string, int64_t > &path_length, size_t max_threads)vg::HTSAlignmentEmitter
HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=deletevg::HTSAlignmentEmitter
HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=deletevg::HTSAlignmentEmitter
initialize_sam_file(bam_hdr_t *header, size_t thread_number, bool keep_header=false)vg::HTSAlignmentEmitterprivate
multiplexervg::HTSAlignmentEmitterprivate
operator=(const HTSAlignmentEmitter &other)=deletevg::HTSAlignmentEmitter
operator=(HTSAlignmentEmitter &&other)=deletevg::HTSAlignmentEmitter
out_filevg::HTSAlignmentEmitterprivate
output_is_bgzfvg::HTSAlignmentEmitterprivate
path_lengthvg::HTSAlignmentEmitterprivate
sam_filesvg::HTSAlignmentEmitterprivate
sam_headervg::HTSAlignmentEmitterprivate
save_records(bam_hdr_t *header, vector< bam1_t * > &records, size_t thread_number)vg::HTSAlignmentEmitterprivate
~AlignmentEmitter()=defaultvg::io::AlignmentEmittervirtual
~HTSAlignmentEmitter()vg::HTSAlignmentEmitter