vdj_pipe
pipeline for processing DNA sequence data
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Main namespace of vdj_pipe library. More...
Classes | |
class | Ambiguous_window_filter |
class | Apply_many |
Apply enclosed processing step multiple times to sequence reads of specified kind: forward, reverse, or merged. More... | |
class | Apply_one |
Apply enclosed processing step once to a sequence read of specified kind: forward, reverse, or merged. More... | |
class | Average_quality_filter |
class | Average_quality_window_filter |
struct | base_exception |
class | Best_match_pair |
struct | Blank |
class | Blank_step |
class | Character_filter |
class | Command_line_options |
class | Composition_stats |
struct | Config_paired_emid_reads |
struct | Config_paired_reads |
struct | Config_single_reads |
class | External_mid_infile |
Look for external MIDs in separate files. More... | |
class | External_mid_inline |
Look for external MIDs in FASTA/Q description lines. More... | |
class | File |
class | File_input |
File target is supposed to exist at construction time. More... | |
class | File_istream |
class | File_ostream |
class | File_ostream_queue |
stack of recently used output file streams More... | |
class | File_ostream_variant |
Select output file based on variables in value map. More... | |
class | File_output |
File target is created if needed at construction time. More... | |
class | Find_shared |
struct | Finish_visitor |
class | Get_match_length |
Set a fraction of sequence length to match. More... | |
class | Group_count |
class | Group_unique |
class | Histogram_1d |
simple unsigned integer-based histogram More... | |
class | Histogram_step |
class | Homopolymer_filter |
class | Id_iterator |
struct | Identity |
why is it not in STL? More... | |
class | Input_manager |
struct | Is_ambiguous |
class | Length_filter |
struct | Lib_info |
library info More... | |
class | Match_fraction_length |
Set a fraction of sequence length to match. More... | |
struct | Match_full_length |
Require full sequence to match. More... | |
class | Match_ignore_ends |
Set a minimal sequence length to match allowing for some mismatch at ends. More... | |
class | Match_min_length |
Set a minimal sequence length to match. More... | |
class | Match_step |
class | Merge_paired |
struct | Merge_result |
class | Min_quality_filter |
class | Min_quality_window_filter |
struct | Null_buff |
class | Output_manager |
class | Parser_fasta |
class | Parser_fastq |
Parser for FASTQ files. More... | |
class | Parser_qual |
class | Pipe_environment |
class | Pipe_paired_emid_read |
process paired reads with external MIDs More... | |
class | Pipe_paired_read |
process paired reads with external MIDs More... | |
class | Pipe_single_read |
class | Pipeline |
class | Pipeline_input |
struct | Qual_record |
class | Qual_stats |
class | Quality |
struct | Queable_ofstream |
struct | Read_ginfo |
Read ID and group ID. More... | |
class | Read_ginfo_store |
Read ID and group ID. More... | |
class | Read_info |
class | Read_info_store |
Store sequence-related information. More... | |
struct | Run_visitor |
class | Seq_entry |
class | Seq_file |
class | Seq_file_entry |
class | Seq_file_map |
class | Seq_fls |
store short sequence in an integer More... | |
class | Seq_map_aligned |
class | Seq_map_full |
class | Seq_map_short |
struct | Seq_match |
struct | Seq_meta |
struct | Seq_pos |
struct | Seq_qual_record |
struct | Seq_record |
class | Seq_store |
Store sequence and related information. More... | |
struct | Sequence_bstats |
struct | Sequence_gstats |
class | Step_registry |
class | Step_variant_store |
class | Summary_visitor |
class | Summary_visitor2 |
struct | Type_index |
class | Unambiguous_interval_iter |
class | Value_ids_emid |
Provides access to standard eMID values. More... | |
class | Value_ids_paired |
Provides access to standard values for paired read pipeline. More... | |
class | Value_ids_single |
Provides access to standard values for single read pipeline. More... | |
class | Value_map |
Store values mapped against name strings and value IDs. More... | |
struct | Value_names |
class | Variable_path |
class | Vm_access_paired |
Access to value map for paired read pipeline and processing steps. More... | |
class | Vm_access_paired_emid |
Access to value map for paired eMID read pipeline and processing steps. More... | |
class | Vm_access_single |
struct | Wrap |
class | Write_seq |
class | Write_value |
Typedefs | |
typedef boost::filesystem::path | path_t |
typedef boost::variant< Blank, bool, long, double, std::string, sequence_interval, Qual_record::quality > | value_variant |
typedef boost::numeric::interval< int, boost::numeric::interval_lib::policies< boost::numeric::interval_lib::rounded_math< int >, detail::Interval_checking_policy< int > > > | sequence_interval |
typedef Seq_pos< Read_id > | sub_seq |
typedef Seq_pos< Seq_id > | super_seq |
typedef boost::multi_array< int, 2 > | scoring_matrix_t |
typedef boost::make_recursive_variant_over< step::paired_read_vector >::type | step_variant_paired |
typedef boost::make_recursive_variant_over< step::paired_emid_read_vector >::type | step_variant_paired_emid |
typedef boost::make_recursive_variant_over< step::single_read_vector >::type | step_variant_single |
typedef boost::make_recursive_variant_over< step::all_steps_vector >::type | step_variant_all |
Enumerations | |
enum | Nucleotide { Adenine = 0, Cytosine = 1, Guanine = 2, Thymine = 3, Any = 4, Uracil = 5, Purine = 6, Pyrimidine = 7, Ketone = 8, Amine = 9, Strong = 10, Weak = 11, not_A = 12, not_C = 13, not_G = 14, not_T = 15 } |
Functions | |
VDJ_PIPE_KEYWORD_STRUCT (Character_filter::kwds,(chars)) | |
VDJ_PIPE_KEYWORD_STRUCT (Length_filter::kwds,(min)(max)(trim)) | |
VDJ_PIPE_KEYWORD_STRUCT (Homopolymer_filter::kwds,(max_length)) | |
VDJ_PIPE_KEYWORD_STRUCT (Min_quality_filter::kwds,(min_quality)) | |
VDJ_PIPE_KEYWORD_STRUCT (Average_quality_filter::kwds,(min_quality)) | |
VDJ_PIPE_KEYWORD_STRUCT (Min_quality_window_filter::kwds,(min_quality)(min_length)) | |
VDJ_PIPE_KEYWORD_STRUCT (Average_quality_window_filter::kwds,(min_quality)(min_length)(window_length)) | |
VDJ_PIPE_KEYWORD_STRUCT (Ambiguous_window_filter::kwds,(min_length)(max_ambiguous)) | |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(min_score)(merge_score)(merge_sigar)(trimmed)) | |
VDJ_PIPE_KEYWORD_STRUCT (Find_shared::kwds,(min_length)(ignore_ends)(fraction_match)(consensus_trim)(min_duplicates)(trimmed)(reverse)(unset_value)(out_summary)(out_group_unique)(out_group_duplicates)(out_unique)(out_duplicates)(out_redundancy_histogram)) | |
std::string | to_string (detail::Queable_ofstream_types::val_vector const v) |
compression::Compression | guess_compression_magic (std::string const &path) |
compression::Compression | guess_compression_ext (bfs::path const &p) |
compression::Compression | guess_compression_ext (std::string const &path) |
format::Format | guess_format (std::string const &path, const compression::Compression c) |
std::pair< compression::Compression, format::Format > | guess_compression_format (std::string const &path) |
std::string | ensure_path_writable (std::string const &path) |
create file if does not exist along with parent directories if needed More... | |
std::string | ensure_path_writable (std::string const &path, std::string const &header) |
if file does not exist, create and write header; create parent directories if needed More... | |
bool | is_path_readable (std::string const &path) |
std::string | ensure_path_readable (std::string const &path) |
std::size_t | hash_value (File const &f) |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(trimmed)(reverse)(elements)(combinations)) | |
std::ostream & | stamp (std::ostream &os, std::string const &pref="## ", std::string const &delim="; ", std::string const &suff="\n") |
std::string | stamp (std::string const &pref="## ", std::string const &delim="; ", std::string const &suff="\n") |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(out_prefix)(out_path_composition)(out_path_gc_hist)) | |
VDJ_PIPE_KEYWORD_STRUCT (help_kwds,(general)(steps)) | |
std::ostream & | print_step_category (std::ostream &os, std::string const &cat) |
void | path_decompose (std::string const &path, std::vector< std::string > &tv, std::vector< std::string > &nv) |
separate path into non-name and name areas More... | |
std::string | path_assemble (std::vector< std::string > const &templ, detail::Queable_ofstream_types::val_ref_vector const &vals) |
assemble path from template and values More... | |
compression::Compression | extension_to_compression (std::string const &ext) |
guess file compression from low case extension string More... | |
compression::Compression | compression_magic (std::istream &is) |
guess file compression from magic number More... | |
format::Format | extension_to_format (std::string const &ext) |
guess file format from low case extension string More... | |
void | input_csv_to_tree (std::istream &is, bpt::ptree &pt) |
Convert input data descriptions in CSV format into property tree. More... | |
void | process_options (bpt::ptree const &pt) |
void | process_single_reads (bpt::ptree const &pt) |
void | process_paired_reads (bpt::ptree const &pt) |
void | process_paired_emid_reads (bpt::ptree const &pt) |
step_variant_paired_emid | create_step_paired_emid (Vm_access_paired_emid const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
void | merge (std::string const &s1, Seq_qual_record::quality const &qv1, std::string const &s2,Seq_qual_record::quality const &qv2,const unsigned min_score, Merge_result &mr) |
void | combine_option_trees (bpt::ptree &pt1, bpt::ptree const &pt2) |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(name)(out_path)) | |
step_variant_single | create_step_single (Vm_access_single const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(out_path)(names)(unset_value)) | |
std::string | sanitize (const char c) |
std::string | sanitize (std::string const &str) |
std::string | sanitize (const boost::string_ref str, const std::size_t max_len) |
value_variant | parse_variant (std::string const &s) |
step_variant_paired | create_step_paired (Vm_access_paired const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
void | store_values (Seq_file_entry const &sfe, Value_map &vm) |
VDJ_PIPE_KEYWORD_STRUCT (kwds,(out_path)(trimmed)(reverse_complemented)(skip_empty)(unset_value)) | |
std::size_t | hash_value (Blank const &) |
template<class ChT , class Tr > | |
std::basic_ostream< ChT, Tr > & | operator<< (std::basic_ostream< ChT, Tr > &os, Blank const &) |
std::string const & | variable_type_str (const int which) |
bool | is_blank (value_variant const &vv) |
std::string const & | variable_type_str (value_variant const &vv) |
sequence_interval | sequence_interval_invalid () |
template<class MinLength > | |
void | remove_subsequences (Seq_store &ss, gdst::Gdst &st, MinLength const &min_len) |
identify unique sequences in sequence store, insert them into suffix tree, and remove non-unique ones More... | |
template<class Ch , class Tr > | |
std::basic_ostream< Ch, Tr > & | print_split (std::basic_ostream< Ch, Tr > &os, const boost::string_ref str, const Ch delim, const unsigned length) |
print string splitting it into parts of equal length More... | |
template<class Ch , class Tr > | |
std::basic_ostream< Ch, Tr > & | print_fasta (std::basic_ostream< Ch, Tr > &os, std::string const &name, Seq_record::sequence const &sequence, const unsigned length=80) |
print FASTA record More... | |
template<class Ch , class Tr > | |
std::basic_ostream< Ch, Tr > & | print_fasta (std::basic_ostream< Ch, Tr > &os, const std::string &name, const boost::string_ref sequence, const unsigned length=80) |
print FASTA record More... | |
template<class Ch , class Tr > | |
std::basic_ostream< Ch, Tr > & | print_qual (std::basic_ostream< Ch, Tr > &os, std::string const &name, Qual_record::quality const &qual, const unsigned length=80) |
print QUAL record More... | |
template<class Ch , class Tr > | |
std::basic_ostream< Ch, Tr > & | print_fastq (std::basic_ostream< Ch, Tr > &os, std::string const &name, Seq_record::sequence const &sequence, Qual_record::quality const &qual, const int offset=33) |
print FASTQ record More... | |
template<class Seq > | |
int | identity (Seq const &s1, const boost::string_ref s2, scoring_matrix_t const &sm, const std::size_t=0) |
template<unsigned N, typename S > | |
int | identity (const Seq_fls< N, S > seq1, const Seq_fls< N, S > seq2, scoring_matrix_t const &sm, const unsigned len=N) |
template<class ChT , class Tr > | |
std::basic_ostream< ChT, Tr > & | operator<< (std::basic_ostream< ChT, Tr > &os, Qual_record::quality const &qual) |
bool | operator== (Seq_entry const &se1, Seq_entry const &se2) |
bool | operator== (const boost::string_ref se1, Seq_entry const &se2) |
bool | operator== (Seq_entry const &se1, const boost::string_ref se2) |
std::size_t | hash_value (Seq_entry const &se) |
std::pair< std::size_t, std::size_t > | longest_average_interval (Qual_record::quality const &q, const std::size_t min_q, const std::size_t win) |
std::pair< std::size_t, std::size_t > | longest_min_interval (Qual_record::quality const &q, const Qual_record::quality::value_type min_q) |
std::pair< std::size_t, std::size_t > | longest_unambiguous_interval (Seq_record::sequence const &seq, const std::size_t max) |
template<class Id > | |
bool | operator== (Seq_pos< Id > const &rp1, Seq_pos< Id > const &rp2) |
template<class Id > | |
bool | operator< (Seq_pos< Id > const &rp1, Seq_pos< Id > const &rp2) |
template<class Id > | |
bool | operator< (Seq_pos< Id > const &rp1, const Id rp2) |
template<class Id > | |
bool | operator< (const Id rp1, Seq_pos< Id > const &rp2) |
Nucleotide | nucleotide_index (const char c) |
bool | is_ambiguous (const char c) |
Nucleotide | complement (const Nucleotide n) |
char | complement (const char c) |
char | to_capital (const Nucleotide n) |
char | to_small (const Nucleotide n) |
template<int Match, int Mismatch, int Approximate, int Uncertain> | |
scoring_matrix_t const & | scoring_matrix () |
int | identity (const Nucleotide n1, const Nucleotide n2, scoring_matrix_t const &sm=scoring_matrix< 2,-2, 1, 0 >()) |
template<class Range > | |
std::string | complement (Range const &r) |
std::string | transform (const boost::string_ref seq, sequence_interval const &si, const bool reverse) |
Reverse-complement (optionally) a portion of a sequence. More... | |
template<class Ostr > | |
Ostr & | operator<< (Ostr &ostr, const Read_info si) |
VDJ_PIPE_DECL void | process_options (boost::property_tree::ptree const &pt) |
VDJ_PIPE_DECL void | process_single_reads (boost::property_tree::ptree const &pt) |
VDJ_PIPE_DECL void | process_paired_reads (boost::property_tree::ptree const &pt) |
VDJ_PIPE_DECL void | process_paired_emid_reads (boost::property_tree::ptree const &pt) |
VDJ_PIPE_OBJECT_ID (Val_id) | |
VDJ_PIPE_OBJECT_ID (Mid_id) | |
VDJ_PIPE_OBJECT_ID (Path_id) | |
VDJ_PIPE_OBJECT_ID (Read_id) | |
VDJ_PIPE_OBJECT_ID (Seq_id) | |
VDJ_PIPE_OBJECT_ID (Mapped_id) | |
template<class Id > | |
boost::iterator_range< Id_iterator< Id > > | id_range (const Id id1, const Id id2) |
template<typename T > | |
void | unused_variable (T const &) |
template<> | |
Config_paired_reads::processing_step | create_step< Config_paired_reads > (Config_paired_reads::value_map_access const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
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Config_single_reads::processing_step | create_step< Config_single_reads > (Config_single_reads::value_map_access const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
template<> | |
Config_paired_emid_reads::processing_step | create_step< Config_paired_emid_reads > (Config_paired_emid_reads::value_map_access const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
template<class Config > | |
Config::processing_step | create_step (typename Config::value_map_access const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe) |
Variables | |
static bool | stamp_flag_ = true |
static Null_buff | null_buff |
Main namespace of vdj_pipe library.
typedef boost::filesystem::path vdj_pipe::path_t |
typedef boost::multi_array<int,2> vdj_pipe::scoring_matrix_t |
typedef boost::numeric::interval< int, boost::numeric::interval_lib::policies< boost::numeric::interval_lib::rounded_math<int>, detail::Interval_checking_policy<int> > > vdj_pipe::sequence_interval |
typedef boost::make_recursive_variant_over<step::all_steps_vector>::type vdj_pipe::step_variant_all |
typedef boost::make_recursive_variant_over<step::paired_read_vector>::type vdj_pipe::step_variant_paired |
typedef boost::make_recursive_variant_over<step::paired_emid_read_vector>::type vdj_pipe::step_variant_paired_emid |
typedef boost::make_recursive_variant_over<step::single_read_vector>::type vdj_pipe::step_variant_single |
typedef Seq_pos<Read_id> vdj_pipe::sub_seq |
typedef Seq_pos<Seq_id> vdj_pipe::super_seq |
typedef boost::variant< Blank, bool, long, double, std::string, sequence_interval, Qual_record::quality > vdj_pipe::value_variant |
enum vdj_pipe::Nucleotide |
void vdj_pipe::combine_option_trees | ( | bpt::ptree & | pt1, |
bpt::ptree const & | pt2 | ||
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VDJ_PIPE_DECL compression::Compression vdj_pipe::compression_magic | ( | std::istream & | is | ) |
guess file compression from magic number
Example ".gz" ".bz2"
Config::processing_step vdj_pipe::create_step | ( | typename Config::value_map_access const & | vma, |
boost::property_tree::ptree const & | pt, | ||
Pipe_environment & | pe | ||
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VDJ_PIPE_DECL step_variant_paired vdj_pipe::create_step_paired | ( | Vm_access_paired const & | vma, |
boost::property_tree::ptree const & | pt, | ||
Pipe_environment & | pe | ||
) |
VDJ_PIPE_DECL step_variant_paired_emid vdj_pipe::create_step_paired_emid | ( | Vm_access_paired_emid const & | vma, |
boost::property_tree::ptree const & | pt, | ||
Pipe_environment & | pe | ||
) |
VDJ_PIPE_DECL step_variant_single vdj_pipe::create_step_single | ( | Vm_access_single const & | vma, |
boost::property_tree::ptree const & | pt, | ||
Pipe_environment & | pe | ||
) |
VDJ_PIPE_DECL std::string vdj_pipe::ensure_path_readable | ( | std::string const & | path | ) |
if | path not readable |
VDJ_PIPE_DECL std::string vdj_pipe::ensure_path_writable | ( | std::string const & | path | ) |
create file if does not exist along with parent directories if needed
VDJ_PIPE_DECL std::string vdj_pipe::ensure_path_writable | ( | std::string const & | path, |
std::string const & | header | ||
) |
if file does not exist, create and write header; create parent directories if needed
VDJ_PIPE_DECL compression::Compression vdj_pipe::extension_to_compression | ( | std::string const & | ext | ) |
guess file compression from low case extension string
Example ".gz" ".bz2"
VDJ_PIPE_DECL format::Format vdj_pipe::extension_to_format | ( | std::string const & | ext | ) |
guess file format from low case extension string
Example ".fq" ".fasta"
compression::Compression vdj_pipe::guess_compression_ext | ( | bfs::path const & | p | ) |
VDJ_PIPE_DECL compression::Compression vdj_pipe::guess_compression_ext | ( | std::string const & | path | ) |
VDJ_PIPE_DECL std::pair< compression::Compression, format::Format > vdj_pipe::guess_compression_format | ( | std::string const & | path | ) |
VDJ_PIPE_DECL compression::Compression vdj_pipe::guess_compression_magic | ( | std::string const & | path | ) |
VDJ_PIPE_DECL format::Format vdj_pipe::guess_format | ( | std::string const & | path, |
const compression::Compression | c | ||
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VDJ_PIPE_DECL std::size_t vdj_pipe::hash_value | ( | File const & | f | ) |
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compute identity score
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compute identity score
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void vdj_pipe::input_csv_to_tree | ( | std::istream & | is, |
bpt::ptree & | pt | ||
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Convert input data descriptions in CSV format into property tree.
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VDJ_PIPE_DECL bool vdj_pipe::is_path_readable | ( | std::string const & | path | ) |
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win
is at least min_q
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min_q
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max
ambiguous nucleotides VDJ_PIPE_DECL void vdj_pipe::merge | ( | std::string const & | s1, |
Seq_qual_record::quality const & | qv1, | ||
std::string const & | s2, | ||
Seq_qual_record::quality const & | qv2, | ||
const unsigned | min_score, | ||
Merge_result & | mr | ||
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VDJ_PIPE_DECL value_variant vdj_pipe::parse_variant | ( | std::string const & | s | ) |
VDJ_PIPE_DECL std::string vdj_pipe::path_assemble | ( | std::vector< std::string > const & | templ, |
detail::Queable_ofstream_types::val_ref_vector const & | vals | ||
) |
assemble path from template and values
Example: out_dir/{name1}-dir/{name2}file.fna
VDJ_PIPE_DECL void vdj_pipe::path_decompose | ( | std::string const & | path, |
std::vector< std::string > & | tv, | ||
std::vector< std::string > & | nv | ||
) |
separate path into non-name and name areas
Example: out_dir/{name1}-dir/{name2}file.fna
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print FASTA record
os | output stream |
name | FASTA description string |
sequence | FASTA sequence string |
length | sequence line length |
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print FASTA record
os | output stream |
name | FASTA description string |
sequence | FASTA sequence string |
length | sequence line length |
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print FASTQ record
os | output stream |
name | FASTA description string |
sequence | FASTA sequence string |
qual | quality scores |
offset | quality score to char conversion offset |
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print QUAL record
os | output stream |
name | FASTA description string |
qual | quality scores |
length | quality line length |
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print string splitting it into parts of equal length
os | output stream |
str | input string |
delim | characters to insert between the parts of the string |
length | string part length |
std::ostream& vdj_pipe::print_step_category | ( | std::ostream & | os, |
std::string const & | cat | ||
) |
VDJ_PIPE_DECL void vdj_pipe::process_options | ( | boost::property_tree::ptree const & | pt | ) |
void vdj_pipe::process_options | ( | bpt::ptree const & | pt | ) |
VDJ_PIPE_DECL void vdj_pipe::process_paired_emid_reads | ( | boost::property_tree::ptree const & | pt | ) |
void vdj_pipe::process_paired_emid_reads | ( | bpt::ptree const & | pt | ) |
VDJ_PIPE_DECL void vdj_pipe::process_paired_reads | ( | boost::property_tree::ptree const & | pt | ) |
void vdj_pipe::process_paired_reads | ( | bpt::ptree const & | pt | ) |
VDJ_PIPE_DECL void vdj_pipe::process_single_reads | ( | boost::property_tree::ptree const & | pt | ) |
void vdj_pipe::process_single_reads | ( | bpt::ptree const & | pt | ) |
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identify unique sequences in sequence store, insert them into suffix tree, and remove non-unique ones
VDJ_PIPE_DECL std::string vdj_pipe::sanitize | ( | const char | c | ) |
VDJ_PIPE_DECL std::string vdj_pipe::sanitize | ( | std::string const & | str | ) |
VDJ_PIPE_DECL std::string vdj_pipe::sanitize | ( | const boost::string_ref | str, |
const std::size_t | max_len | ||
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VDJ_PIPE_DECL std::ostream & vdj_pipe::stamp | ( | std::ostream & | os, |
std::string const & | pref, | ||
std::string const & | delim, | ||
std::string const & | suff | ||
) |
VDJ_PIPE_DECL std::string vdj_pipe::stamp | ( | std::string const & | pref, |
std::string const & | delim, | ||
std::string const & | suff | ||
) |
VDJ_PIPE_DECL void vdj_pipe::store_values | ( | Seq_file_entry const & | sfe, |
Value_map & | vm | ||
) |
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inline |
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inline |
std::string vdj_pipe::to_string | ( | detail::Queable_ofstream_types::val_vector const | v | ) |
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inline |
Reverse-complement (optionally) a portion of a sequence.
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inline |
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inline |
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inline |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(min_score)(merge_score)(merge_sigar)(trimmed) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(out_path)(trimmed)(reverse_complemented)(skip_empty)(unset_value) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(out_prefix)(out_path_composition)(out_path_gc_hist) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(out_path)(names)(unset_value) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(trimmed)(reverse)(elements)(combinations) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | kwds | , |
(name)(out_path) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | help_kwds | , |
(general)(steps) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Character_filter::kwds | , |
(chars) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Find_shared::kwds | , |
(min_length)(ignore_ends)(fraction_match)(consensus_trim)(min_duplicates)(trimmed)(reverse)(unset_value)(out_summary)(out_group_unique)(out_group_duplicates)(out_unique)(out_duplicates)(out_redundancy_histogram) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Length_filter::kwds | , |
(min)(max)(trim) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Homopolymer_filter::kwds | , |
(max_length) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Min_quality_filter::kwds | , |
(min_quality) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Average_quality_filter::kwds | , |
(min_quality) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Min_quality_window_filter::kwds | , |
(min_quality)(min_length) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Average_quality_window_filter::kwds | , |
(min_quality)(min_length)(window_length) | |||
) |
vdj_pipe::VDJ_PIPE_KEYWORD_STRUCT | ( | Ambiguous_window_filter::kwds | , |
(min_length)(max_ambiguous) | |||
) |
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Val_id | ) |
Mapped value ID
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Mid_id | ) |
Molecular identifier ID
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Path_id | ) |
Filesystem path ID
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Read_id | ) |
Sequencing read ID
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Seq_id | ) |
Sequence ID
vdj_pipe::VDJ_PIPE_OBJECT_ID | ( | Mapped_id | ) |
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static |
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static |