SYMBOL INDEX (291 symbols across 52 files) FILE: src/alignment.cc type chromap (line 5) | namespace chromap { function GetLongestMatchLength (line 7) | int GetLongestMatchLength(const char *pattern, const char *text, function AdjustGapBeginning (line 24) | int AdjustGapBeginning(const Strand mapping_strand, const char *ref, function GenerateNMAndMDTag (line 85) | void GenerateNMAndMDTag(const char *pattern, const char *text, function BandedAlignPatternToText (line 141) | int BandedAlignPatternToText(int error_threshold, const char *pattern, function BandedAlignPatternToTextWithDropOff (line 197) | int BandedAlignPatternToTextWithDropOff(int error_threshold, function BandedAlignPatternToTextWithDropOffFrom3End (line 285) | int BandedAlignPatternToTextWithDropOffFrom3End(int error_threshold, function BandedAlign4PatternsToText (line 378) | void BandedAlign4PatternsToText(int error_threshold, const char **patt... function BandedAlign8PatternsToText (line 503) | void BandedAlign8PatternsToText(int error_threshold, const char **patt... function BandedTraceback (line 656) | void BandedTraceback(int error_threshold, int min_num_errors, function BandedTracebackToEnd (line 720) | void BandedTracebackToEnd(int error_threshold, int min_num_errors, FILE: src/alignment.h function namespace (line 9) | namespace chromap { FILE: src/barcode_translator.h function namespace (line 17) | namespace chromap { FILE: src/bed_mapping.h function namespace (line 8) | namespace chromap { function class (line 64) | class MappingWithoutBarcode : public Mapping { function class (line 116) | class PairedEndMappingWithBarcode : public Mapping { function Tn5Shift (line 165) | void Tn5Shift() { function class (line 180) | class PairedEndMappingWithoutBarcode : public Mapping { FILE: src/candidate.h function namespace (line 6) | namespace chromap { FILE: src/candidate_position_generating_config.h function namespace (line 6) | namespace chromap { FILE: src/candidate_processor.cc type chromap (line 10) | namespace chromap { FILE: src/candidate_processor.h function namespace (line 18) | namespace chromap { FILE: src/chromap.cc type chromap (line 15) | namespace chromap { FILE: src/chromap.h function namespace (line 39) | namespace chromap { function compute_cardinality (line 65) | inline size_t compute_cardinality() { function class (line 81) | class Chromap { type _mm_history (line 293) | struct _mm_history type _mm_history (line 736) | struct _mm_history type _mm_history (line 737) | struct _mm_history FILE: src/chromap_driver.cc type chromap (line 13) | namespace chromap { function AddIndexingOptions (line 16) | void AddIndexingOptions(cxxopts::Options &options) { function AddMappingOptions (line 25) | void AddMappingOptions(cxxopts::Options &options) { function AddInputOptions (line 85) | void AddInputOptions(cxxopts::Options &options) { function AddOutputOptions (line 103) | void AddOutputOptions(cxxopts::Options &options) { function AddDevelopmentOptions (line 132) | void AddDevelopmentOptions(cxxopts::Options &options) { function AddPeakOptions (line 161) | void AddPeakOptions(cxxopts::Options &options) { function GetMatchedFilePaths (line 174) | std::vector GetMatchedFilePaths(const std::string &patter... function GetMatchedFilePaths (line 199) | std::vector GetMatchedFilePaths( function main (line 770) | int main(int argc, char *argv[]) { FILE: src/chromap_driver.h function namespace (line 4) | namespace chromap { FILE: src/cxxopts.hpp type cxxopts (line 63) | namespace cxxopts function String (line 87) | inline class UnicodeStringIterator (line 94) | class UnicodeStringIterator : public method UnicodeStringIterator (line 99) | UnicodeStringIterator(const icu::UnicodeString* string, int32_t pos) method value_type (line 105) | value_type method UnicodeStringIterator (line 123) | UnicodeStringIterator& method UnicodeStringIterator (line 130) | UnicodeStringIterator function String (line 141) | inline function String (line 148) | inline function String (line 161) | String& function stringLength (line 173) | inline function toUTF8String (line 180) | inline function empty (line 190) | inline function T (line 223) | T function stringLength (line 229) | inline function String (line 236) | inline function String (line 243) | inline function String (line 251) | String& function toUTF8String (line 258) | std::string function empty (line 264) | inline class Value (line 295) | class Value : public std::enable_shared_from_this class OptionException (line 341) | class OptionException : public std::exception method OptionException (line 344) | explicit OptionException(std::string message) method CXXOPTS_NODISCARD (line 349) | CXXOPTS_NODISCARD class OptionSpecException (line 360) | class OptionSpecException : public OptionException method OptionSpecException (line 364) | explicit OptionSpecException(const std::string& message) class OptionParseException (line 370) | class OptionParseException : public OptionException method OptionParseException (line 373) | explicit OptionParseException(const std::string& message) class option_exists_error (line 379) | class option_exists_error : public OptionSpecException method option_exists_error (line 382) | explicit option_exists_error(const std::string& option) class invalid_option_format_error (line 388) | class invalid_option_format_error : public OptionSpecException method invalid_option_format_error (line 391) | explicit invalid_option_format_error(const std::string& format) class option_syntax_exception (line 397) | class option_syntax_exception : public OptionParseException { method option_syntax_exception (line 399) | explicit option_syntax_exception(const std::string& text) class option_not_exists_exception (line 406) | class option_not_exists_exception : public OptionParseException method option_not_exists_exception (line 409) | explicit option_not_exists_exception(const std::string& option) class missing_argument_exception (line 415) | class missing_argument_exception : public OptionParseException method missing_argument_exception (line 418) | explicit missing_argument_exception(const std::string& option) class option_requires_argument_exception (line 426) | class option_requires_argument_exception : public OptionParseException method option_requires_argument_exception (line 429) | explicit option_requires_argument_exception(const std::string& option) class option_not_has_argument_exception (line 437) | class option_not_has_argument_exception : public OptionParseException method option_not_has_argument_exception (line 440) | option_not_has_argument_exception class option_not_present_exception (line 454) | class option_not_present_exception : public OptionParseException method option_not_present_exception (line 457) | explicit option_not_present_exception(const std::string& option) class option_has_no_value_exception (line 463) | class option_has_no_value_exception : public OptionException method option_has_no_value_exception (line 466) | explicit option_has_no_value_exception(const std::string& option) class argument_incorrect_type (line 475) | class argument_incorrect_type : public OptionParseException method argument_incorrect_type (line 478) | explicit argument_incorrect_type class option_required_exception (line 489) | class option_required_exception : public OptionParseException method option_required_exception (line 492) | explicit option_required_exception(const std::string& option) function throw_or_mimic (line 501) | void throw_or_mimic(const std::string& text) type values (line 519) | namespace values type detail (line 531) | namespace detail type SignedCheck (line 534) | struct SignedCheck type SignedCheck (line 537) | struct SignedCheck type SignedCheck (line 561) | struct SignedCheck function check_signed_range (line 569) | void function checked_negate (line 577) | void function checked_negate (line 587) | void function integer_parser (line 594) | void function stringstream_parser (line 664) | void stringstream_parser(const std::string& text, T& value) function parse_value (line 673) | inline function parse_value (line 680) | inline function parse_value (line 687) | inline function parse_value (line 694) | inline function parse_value (line 701) | inline function parse_value (line 708) | inline function parse_value (line 715) | inline function parse_value (line 722) | inline function parse_value (line 729) | inline function parse_value (line 752) | inline function parse_value (line 763) | void function parse_value (line 769) | void function parse_value (line 783) | void function parse_value (line 792) | inline type type_is_container (line 804) | struct type_is_container type type_is_container> (line 810) | struct type_is_container> class abstract_value (line 816) | class abstract_value : public Value method abstract_value (line 821) | abstract_value() method abstract_value (line 827) | explicit abstract_value(T* t) method abstract_value (line 834) | abstract_value& operator=(const abstract_value&) = default; method abstract_value (line 836) | abstract_value(const abstract_value& rhs) method parse (line 854) | void method is_container (line 860) | bool method parse (line 866) | void method has_default (line 872) | bool method has_implicit (line 878) | bool method default_value (line 884) | std::shared_ptr method implicit_value (line 892) | std::shared_ptr method no_implicit_value (line 900) | std::shared_ptr method get_default_value (line 907) | std::string method get_implicit_value (line 913) | std::string method is_boolean (line 919) | bool method T (line 925) | const T& class standard_value (line 947) | class standard_value : public abstract_value method override (line 954) | const override class standard_value (line 961) | class standard_value : public abstract_value method standard_value (line 966) | standard_value() method standard_value (line 971) | explicit standard_value(bool* b) method clone (line 977) | std::shared_ptr method set_default_and_implicit (line 985) | void function value (line 997) | std::shared_ptr function value (line 1004) | std::shared_ptr class OptionAdder (line 1010) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) class OptionDetails (line 1012) | class OptionDetails method OptionDetails (line 1015) | OptionDetails method OptionDetails (line 1031) | OptionDetails(const OptionDetails& rhs) method OptionDetails (line 1038) | OptionDetails(OptionDetails&& rhs) = default; method CXXOPTS_NODISCARD (line 1040) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1047) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1053) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1060) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1067) | CXXOPTS_NODISCARD method hash (line 1074) | size_t type HelpOptionDetails (line 1090) | struct HelpOptionDetails type HelpGroupDetails (line 1104) | struct HelpGroupDetails class OptionValue (line 1111) | class OptionValue method parse (line 1114) | void method parse_default (line 1127) | void method CXXOPTS_NODISCARD (line 1143) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1157) | CXXOPTS_NODISCARD method T (line 1165) | const T& method ensure_value (line 1181) | void class KeyValue (line 1199) | class KeyValue method KeyValue (line 1202) | KeyValue(std::string key_, std::string value_) method CXXOPTS_NODISCARD (line 1208) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1215) | CXXOPTS_NODISCARD method T (line 1223) | T class ParseResult (line 1239) | class ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& type Option (line 1315) | struct Option method Option (line 1317) | Option class OptionParser (line 1341) | class OptionParser method OptionParser (line 1344) | OptionParser(const OptionMap& options, const PositionalList& positio... class Options (line 1395) | class Options method Options (line 1399) | explicit Options(std::string program, std::string help_string = "") method Options (line 1412) | Options& method Options (line 1419) | Options& method Options (line 1426) | Options& method Options (line 1433) | Options& method Options (line 1440) | Options& method Options (line 1447) | Options& method parse_positional (line 1496) | void class OptionAdder (line 1552) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function String (line 1587) | String function String (line 1633) | String function OptionAdder (line 1779) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function OptionAdder (line 1786) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function ParseResult (line 1962) | inline method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function ParseResult (line 1971) | inline ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function String (line 2212) | inline function HelpGroupDetails (line 2374) | inline type cxxopts (line 83) | namespace cxxopts function String (line 87) | inline class UnicodeStringIterator (line 94) | class UnicodeStringIterator : public method UnicodeStringIterator (line 99) | UnicodeStringIterator(const icu::UnicodeString* string, int32_t pos) method value_type (line 105) | value_type method UnicodeStringIterator (line 123) | UnicodeStringIterator& method UnicodeStringIterator (line 130) | UnicodeStringIterator function String (line 141) | inline function String (line 148) | inline function String (line 161) | String& function stringLength (line 173) | inline function toUTF8String (line 180) | inline function empty (line 190) | inline function T (line 223) | T function stringLength (line 229) | inline function String (line 236) | inline function String (line 243) | inline function String (line 251) | String& function toUTF8String (line 258) | std::string function empty (line 264) | inline class Value (line 295) | class Value : public std::enable_shared_from_this class OptionException (line 341) | class OptionException : public std::exception method OptionException (line 344) | explicit OptionException(std::string message) method CXXOPTS_NODISCARD (line 349) | CXXOPTS_NODISCARD class OptionSpecException (line 360) | class OptionSpecException : public OptionException method OptionSpecException (line 364) | explicit OptionSpecException(const std::string& message) class OptionParseException (line 370) | class OptionParseException : public OptionException method OptionParseException (line 373) | explicit OptionParseException(const std::string& message) class option_exists_error (line 379) | class option_exists_error : public OptionSpecException method option_exists_error (line 382) | explicit option_exists_error(const std::string& option) class invalid_option_format_error (line 388) | class invalid_option_format_error : public OptionSpecException method invalid_option_format_error (line 391) | explicit invalid_option_format_error(const std::string& format) class option_syntax_exception (line 397) | class option_syntax_exception : public OptionParseException { method option_syntax_exception (line 399) | explicit option_syntax_exception(const std::string& text) class option_not_exists_exception (line 406) | class option_not_exists_exception : public OptionParseException method option_not_exists_exception (line 409) | explicit option_not_exists_exception(const std::string& option) class missing_argument_exception (line 415) | class missing_argument_exception : public OptionParseException method missing_argument_exception (line 418) | explicit missing_argument_exception(const std::string& option) class option_requires_argument_exception (line 426) | class option_requires_argument_exception : public OptionParseException method option_requires_argument_exception (line 429) | explicit option_requires_argument_exception(const std::string& option) class option_not_has_argument_exception (line 437) | class option_not_has_argument_exception : public OptionParseException method option_not_has_argument_exception (line 440) | option_not_has_argument_exception class option_not_present_exception (line 454) | class option_not_present_exception : public OptionParseException method option_not_present_exception (line 457) | explicit option_not_present_exception(const std::string& option) class option_has_no_value_exception (line 463) | class option_has_no_value_exception : public OptionException method option_has_no_value_exception (line 466) | explicit option_has_no_value_exception(const std::string& option) class argument_incorrect_type (line 475) | class argument_incorrect_type : public OptionParseException method argument_incorrect_type (line 478) | explicit argument_incorrect_type class option_required_exception (line 489) | class option_required_exception : public OptionParseException method option_required_exception (line 492) | explicit option_required_exception(const std::string& option) function throw_or_mimic (line 501) | void throw_or_mimic(const std::string& text) type values (line 519) | namespace values type detail (line 531) | namespace detail type SignedCheck (line 534) | struct SignedCheck type SignedCheck (line 537) | struct SignedCheck type SignedCheck (line 561) | struct SignedCheck function check_signed_range (line 569) | void function checked_negate (line 577) | void function checked_negate (line 587) | void function integer_parser (line 594) | void function stringstream_parser (line 664) | void stringstream_parser(const std::string& text, T& value) function parse_value (line 673) | inline function parse_value (line 680) | inline function parse_value (line 687) | inline function parse_value (line 694) | inline function parse_value (line 701) | inline function parse_value (line 708) | inline function parse_value (line 715) | inline function parse_value (line 722) | inline function parse_value (line 729) | inline function parse_value (line 752) | inline function parse_value (line 763) | void function parse_value (line 769) | void function parse_value (line 783) | void function parse_value (line 792) | inline type type_is_container (line 804) | struct type_is_container type type_is_container> (line 810) | struct type_is_container> class abstract_value (line 816) | class abstract_value : public Value method abstract_value (line 821) | abstract_value() method abstract_value (line 827) | explicit abstract_value(T* t) method abstract_value (line 834) | abstract_value& operator=(const abstract_value&) = default; method abstract_value (line 836) | abstract_value(const abstract_value& rhs) method parse (line 854) | void method is_container (line 860) | bool method parse (line 866) | void method has_default (line 872) | bool method has_implicit (line 878) | bool method default_value (line 884) | std::shared_ptr method implicit_value (line 892) | std::shared_ptr method no_implicit_value (line 900) | std::shared_ptr method get_default_value (line 907) | std::string method get_implicit_value (line 913) | std::string method is_boolean (line 919) | bool method T (line 925) | const T& class standard_value (line 947) | class standard_value : public abstract_value method override (line 954) | const override class standard_value (line 961) | class standard_value : public abstract_value method standard_value (line 966) | standard_value() method standard_value (line 971) | explicit standard_value(bool* b) method clone (line 977) | std::shared_ptr method set_default_and_implicit (line 985) | void function value (line 997) | std::shared_ptr function value (line 1004) | std::shared_ptr class OptionAdder (line 1010) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) class OptionDetails (line 1012) | class OptionDetails method OptionDetails (line 1015) | OptionDetails method OptionDetails (line 1031) | OptionDetails(const OptionDetails& rhs) method OptionDetails (line 1038) | OptionDetails(OptionDetails&& rhs) = default; method CXXOPTS_NODISCARD (line 1040) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1047) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1053) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1060) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1067) | CXXOPTS_NODISCARD method hash (line 1074) | size_t type HelpOptionDetails (line 1090) | struct HelpOptionDetails type HelpGroupDetails (line 1104) | struct HelpGroupDetails class OptionValue (line 1111) | class OptionValue method parse (line 1114) | void method parse_default (line 1127) | void method CXXOPTS_NODISCARD (line 1143) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1157) | CXXOPTS_NODISCARD method T (line 1165) | const T& method ensure_value (line 1181) | void class KeyValue (line 1199) | class KeyValue method KeyValue (line 1202) | KeyValue(std::string key_, std::string value_) method CXXOPTS_NODISCARD (line 1208) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1215) | CXXOPTS_NODISCARD method T (line 1223) | T class ParseResult (line 1239) | class ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& type Option (line 1315) | struct Option method Option (line 1317) | Option class OptionParser (line 1341) | class OptionParser method OptionParser (line 1344) | OptionParser(const OptionMap& options, const PositionalList& positio... class Options (line 1395) | class Options method Options (line 1399) | explicit Options(std::string program, std::string help_string = "") method Options (line 1412) | Options& method Options (line 1419) | Options& method Options (line 1426) | Options& method Options (line 1433) | Options& method Options (line 1440) | Options& method Options (line 1447) | Options& method parse_positional (line 1496) | void class OptionAdder (line 1552) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function String (line 1587) | String function String (line 1633) | String function OptionAdder (line 1779) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function OptionAdder (line 1786) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function ParseResult (line 1962) | inline method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function ParseResult (line 1971) | inline ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function String (line 2212) | inline function HelpGroupDetails (line 2374) | inline type std (line 198) | namespace std function begin (line 200) | inline function end (line 207) | inline type cxxopts (line 218) | namespace cxxopts function String (line 87) | inline class UnicodeStringIterator (line 94) | class UnicodeStringIterator : public method UnicodeStringIterator (line 99) | UnicodeStringIterator(const icu::UnicodeString* string, int32_t pos) method value_type (line 105) | value_type method UnicodeStringIterator (line 123) | UnicodeStringIterator& method UnicodeStringIterator (line 130) | UnicodeStringIterator function String (line 141) | inline function String (line 148) | inline function String (line 161) | String& function stringLength (line 173) | inline function toUTF8String (line 180) | inline function empty (line 190) | inline function T (line 223) | T function stringLength (line 229) | inline function String (line 236) | inline function String (line 243) | inline function String (line 251) | String& function toUTF8String (line 258) | std::string function empty (line 264) | inline class Value (line 295) | class Value : public std::enable_shared_from_this class OptionException (line 341) | class OptionException : public std::exception method OptionException (line 344) | explicit OptionException(std::string message) method CXXOPTS_NODISCARD (line 349) | CXXOPTS_NODISCARD class OptionSpecException (line 360) | class OptionSpecException : public OptionException method OptionSpecException (line 364) | explicit OptionSpecException(const std::string& message) class OptionParseException (line 370) | class OptionParseException : public OptionException method OptionParseException (line 373) | explicit OptionParseException(const std::string& message) class option_exists_error (line 379) | class option_exists_error : public OptionSpecException method option_exists_error (line 382) | explicit option_exists_error(const std::string& option) class invalid_option_format_error (line 388) | class invalid_option_format_error : public OptionSpecException method invalid_option_format_error (line 391) | explicit invalid_option_format_error(const std::string& format) class option_syntax_exception (line 397) | class option_syntax_exception : public OptionParseException { method option_syntax_exception (line 399) | explicit option_syntax_exception(const std::string& text) class option_not_exists_exception (line 406) | class option_not_exists_exception : public OptionParseException method option_not_exists_exception (line 409) | explicit option_not_exists_exception(const std::string& option) class missing_argument_exception (line 415) | class missing_argument_exception : public OptionParseException method missing_argument_exception (line 418) | explicit missing_argument_exception(const std::string& option) class option_requires_argument_exception (line 426) | class option_requires_argument_exception : public OptionParseException method option_requires_argument_exception (line 429) | explicit option_requires_argument_exception(const std::string& option) class option_not_has_argument_exception (line 437) | class option_not_has_argument_exception : public OptionParseException method option_not_has_argument_exception (line 440) | option_not_has_argument_exception class option_not_present_exception (line 454) | class option_not_present_exception : public OptionParseException method option_not_present_exception (line 457) | explicit option_not_present_exception(const std::string& option) class option_has_no_value_exception (line 463) | class option_has_no_value_exception : public OptionException method option_has_no_value_exception (line 466) | explicit option_has_no_value_exception(const std::string& option) class argument_incorrect_type (line 475) | class argument_incorrect_type : public OptionParseException method argument_incorrect_type (line 478) | explicit argument_incorrect_type class option_required_exception (line 489) | class option_required_exception : public OptionParseException method option_required_exception (line 492) | explicit option_required_exception(const std::string& option) function throw_or_mimic (line 501) | void throw_or_mimic(const std::string& text) type values (line 519) | namespace values type detail (line 531) | namespace detail type SignedCheck (line 534) | struct SignedCheck type SignedCheck (line 537) | struct SignedCheck type SignedCheck (line 561) | struct SignedCheck function check_signed_range (line 569) | void function checked_negate (line 577) | void function checked_negate (line 587) | void function integer_parser (line 594) | void function stringstream_parser (line 664) | void stringstream_parser(const std::string& text, T& value) function parse_value (line 673) | inline function parse_value (line 680) | inline function parse_value (line 687) | inline function parse_value (line 694) | inline function parse_value (line 701) | inline function parse_value (line 708) | inline function parse_value (line 715) | inline function parse_value (line 722) | inline function parse_value (line 729) | inline function parse_value (line 752) | inline function parse_value (line 763) | void function parse_value (line 769) | void function parse_value (line 783) | void function parse_value (line 792) | inline type type_is_container (line 804) | struct type_is_container type type_is_container> (line 810) | struct type_is_container> class abstract_value (line 816) | class abstract_value : public Value method abstract_value (line 821) | abstract_value() method abstract_value (line 827) | explicit abstract_value(T* t) method abstract_value (line 834) | abstract_value& operator=(const abstract_value&) = default; method abstract_value (line 836) | abstract_value(const abstract_value& rhs) method parse (line 854) | void method is_container (line 860) | bool method parse (line 866) | void method has_default (line 872) | bool method has_implicit (line 878) | bool method default_value (line 884) | std::shared_ptr method implicit_value (line 892) | std::shared_ptr method no_implicit_value (line 900) | std::shared_ptr method get_default_value (line 907) | std::string method get_implicit_value (line 913) | std::string method is_boolean (line 919) | bool method T (line 925) | const T& class standard_value (line 947) | class standard_value : public abstract_value method override (line 954) | const override class standard_value (line 961) | class standard_value : public abstract_value method standard_value (line 966) | standard_value() method standard_value (line 971) | explicit standard_value(bool* b) method clone (line 977) | std::shared_ptr method set_default_and_implicit (line 985) | void function value (line 997) | std::shared_ptr function value (line 1004) | std::shared_ptr class OptionAdder (line 1010) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) class OptionDetails (line 1012) | class OptionDetails method OptionDetails (line 1015) | OptionDetails method OptionDetails (line 1031) | OptionDetails(const OptionDetails& rhs) method OptionDetails (line 1038) | OptionDetails(OptionDetails&& rhs) = default; method CXXOPTS_NODISCARD (line 1040) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1047) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1053) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1060) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1067) | CXXOPTS_NODISCARD method hash (line 1074) | size_t type HelpOptionDetails (line 1090) | struct HelpOptionDetails type HelpGroupDetails (line 1104) | struct HelpGroupDetails class OptionValue (line 1111) | class OptionValue method parse (line 1114) | void method parse_default (line 1127) | void method CXXOPTS_NODISCARD (line 1143) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1157) | CXXOPTS_NODISCARD method T (line 1165) | const T& method ensure_value (line 1181) | void class KeyValue (line 1199) | class KeyValue method KeyValue (line 1202) | KeyValue(std::string key_, std::string value_) method CXXOPTS_NODISCARD (line 1208) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1215) | CXXOPTS_NODISCARD method T (line 1223) | T class ParseResult (line 1239) | class ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& type Option (line 1315) | struct Option method Option (line 1317) | Option class OptionParser (line 1341) | class OptionParser method OptionParser (line 1344) | OptionParser(const OptionMap& options, const PositionalList& positio... class Options (line 1395) | class Options method Options (line 1399) | explicit Options(std::string program, std::string help_string = "") method Options (line 1412) | Options& method Options (line 1419) | Options& method Options (line 1426) | Options& method Options (line 1433) | Options& method Options (line 1440) | Options& method Options (line 1447) | Options& method parse_positional (line 1496) | void class OptionAdder (line 1552) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function String (line 1587) | String function String (line 1633) | String function OptionAdder (line 1779) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function OptionAdder (line 1786) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function ParseResult (line 1962) | inline method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function ParseResult (line 1971) | inline ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function String (line 2212) | inline function HelpGroupDetails (line 2374) | inline type cxxopts (line 275) | namespace cxxopts function String (line 87) | inline class UnicodeStringIterator (line 94) | class UnicodeStringIterator : public method UnicodeStringIterator (line 99) | UnicodeStringIterator(const icu::UnicodeString* string, int32_t pos) method value_type (line 105) | value_type method UnicodeStringIterator (line 123) | UnicodeStringIterator& method UnicodeStringIterator (line 130) | UnicodeStringIterator function String (line 141) | inline function String (line 148) | inline function String (line 161) | String& function stringLength (line 173) | inline function toUTF8String (line 180) | inline function empty (line 190) | inline function T (line 223) | T function stringLength (line 229) | inline function String (line 236) | inline function String (line 243) | inline function String (line 251) | String& function toUTF8String (line 258) | std::string function empty (line 264) | inline class Value (line 295) | class Value : public std::enable_shared_from_this class OptionException (line 341) | class OptionException : public std::exception method OptionException (line 344) | explicit OptionException(std::string message) method CXXOPTS_NODISCARD (line 349) | CXXOPTS_NODISCARD class OptionSpecException (line 360) | class OptionSpecException : public OptionException method OptionSpecException (line 364) | explicit OptionSpecException(const std::string& message) class OptionParseException (line 370) | class OptionParseException : public OptionException method OptionParseException (line 373) | explicit OptionParseException(const std::string& message) class option_exists_error (line 379) | class option_exists_error : public OptionSpecException method option_exists_error (line 382) | explicit option_exists_error(const std::string& option) class invalid_option_format_error (line 388) | class invalid_option_format_error : public OptionSpecException method invalid_option_format_error (line 391) | explicit invalid_option_format_error(const std::string& format) class option_syntax_exception (line 397) | class option_syntax_exception : public OptionParseException { method option_syntax_exception (line 399) | explicit option_syntax_exception(const std::string& text) class option_not_exists_exception (line 406) | class option_not_exists_exception : public OptionParseException method option_not_exists_exception (line 409) | explicit option_not_exists_exception(const std::string& option) class missing_argument_exception (line 415) | class missing_argument_exception : public OptionParseException method missing_argument_exception (line 418) | explicit missing_argument_exception(const std::string& option) class option_requires_argument_exception (line 426) | class option_requires_argument_exception : public OptionParseException method option_requires_argument_exception (line 429) | explicit option_requires_argument_exception(const std::string& option) class option_not_has_argument_exception (line 437) | class option_not_has_argument_exception : public OptionParseException method option_not_has_argument_exception (line 440) | option_not_has_argument_exception class option_not_present_exception (line 454) | class option_not_present_exception : public OptionParseException method option_not_present_exception (line 457) | explicit option_not_present_exception(const std::string& option) class option_has_no_value_exception (line 463) | class option_has_no_value_exception : public OptionException method option_has_no_value_exception (line 466) | explicit option_has_no_value_exception(const std::string& option) class argument_incorrect_type (line 475) | class argument_incorrect_type : public OptionParseException method argument_incorrect_type (line 478) | explicit argument_incorrect_type class option_required_exception (line 489) | class option_required_exception : public OptionParseException method option_required_exception (line 492) | explicit option_required_exception(const std::string& option) function throw_or_mimic (line 501) | void throw_or_mimic(const std::string& text) type values (line 519) | namespace values type detail (line 531) | namespace detail type SignedCheck (line 534) | struct SignedCheck type SignedCheck (line 537) | struct SignedCheck type SignedCheck (line 561) | struct SignedCheck function check_signed_range (line 569) | void function checked_negate (line 577) | void function checked_negate (line 587) | void function integer_parser (line 594) | void function stringstream_parser (line 664) | void stringstream_parser(const std::string& text, T& value) function parse_value (line 673) | inline function parse_value (line 680) | inline function parse_value (line 687) | inline function parse_value (line 694) | inline function parse_value (line 701) | inline function parse_value (line 708) | inline function parse_value (line 715) | inline function parse_value (line 722) | inline function parse_value (line 729) | inline function parse_value (line 752) | inline function parse_value (line 763) | void function parse_value (line 769) | void function parse_value (line 783) | void function parse_value (line 792) | inline type type_is_container (line 804) | struct type_is_container type type_is_container> (line 810) | struct type_is_container> class abstract_value (line 816) | class abstract_value : public Value method abstract_value (line 821) | abstract_value() method abstract_value (line 827) | explicit abstract_value(T* t) method abstract_value (line 834) | abstract_value& operator=(const abstract_value&) = default; method abstract_value (line 836) | abstract_value(const abstract_value& rhs) method parse (line 854) | void method is_container (line 860) | bool method parse (line 866) | void method has_default (line 872) | bool method has_implicit (line 878) | bool method default_value (line 884) | std::shared_ptr method implicit_value (line 892) | std::shared_ptr method no_implicit_value (line 900) | std::shared_ptr method get_default_value (line 907) | std::string method get_implicit_value (line 913) | std::string method is_boolean (line 919) | bool method T (line 925) | const T& class standard_value (line 947) | class standard_value : public abstract_value method override (line 954) | const override class standard_value (line 961) | class standard_value : public abstract_value method standard_value (line 966) | standard_value() method standard_value (line 971) | explicit standard_value(bool* b) method clone (line 977) | std::shared_ptr method set_default_and_implicit (line 985) | void function value (line 997) | std::shared_ptr function value (line 1004) | std::shared_ptr class OptionAdder (line 1010) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) class OptionDetails (line 1012) | class OptionDetails method OptionDetails (line 1015) | OptionDetails method OptionDetails (line 1031) | OptionDetails(const OptionDetails& rhs) method OptionDetails (line 1038) | OptionDetails(OptionDetails&& rhs) = default; method CXXOPTS_NODISCARD (line 1040) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1047) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1053) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1060) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1067) | CXXOPTS_NODISCARD method hash (line 1074) | size_t type HelpOptionDetails (line 1090) | struct HelpOptionDetails type HelpGroupDetails (line 1104) | struct HelpGroupDetails class OptionValue (line 1111) | class OptionValue method parse (line 1114) | void method parse_default (line 1127) | void method CXXOPTS_NODISCARD (line 1143) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1157) | CXXOPTS_NODISCARD method T (line 1165) | const T& method ensure_value (line 1181) | void class KeyValue (line 1199) | class KeyValue method KeyValue (line 1202) | KeyValue(std::string key_, std::string value_) method CXXOPTS_NODISCARD (line 1208) | CXXOPTS_NODISCARD method CXXOPTS_NODISCARD (line 1215) | CXXOPTS_NODISCARD method T (line 1223) | T class ParseResult (line 1239) | class ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& type Option (line 1315) | struct Option method Option (line 1317) | Option class OptionParser (line 1341) | class OptionParser method OptionParser (line 1344) | OptionParser(const OptionMap& options, const PositionalList& positio... class Options (line 1395) | class Options method Options (line 1399) | explicit Options(std::string program, std::string help_string = "") method Options (line 1412) | Options& method Options (line 1419) | Options& method Options (line 1426) | Options& method Options (line 1433) | Options& method Options (line 1440) | Options& method Options (line 1447) | Options& method parse_positional (line 1496) | void class OptionAdder (line 1552) | class OptionAdder method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function String (line 1587) | String function String (line 1633) | String function OptionAdder (line 1779) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function OptionAdder (line 1786) | inline method OptionAdder (line 1556) | OptionAdder(Options& options, std::string group) function ParseResult (line 1962) | inline method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function ParseResult (line 1971) | inline ParseResult method ParseResult (line 1243) | ParseResult() = default; method ParseResult (line 1244) | ParseResult(const ParseResult&) = default; method ParseResult (line 1246) | ParseResult(NameHashMap&& keys, ParsedHashMap&& values, std::vector<... method ParseResult (line 1254) | ParseResult& operator=(ParseResult&&) = default; method ParseResult (line 1255) | ParseResult& operator=(const ParseResult&) = default; method count (line 1257) | size_t method OptionValue (line 1276) | const OptionValue& function String (line 2212) | inline function HelpGroupDetails (line 2374) | inline FILE: src/draft_mapping.h function namespace (line 6) | namespace chromap { FILE: src/draft_mapping_generator.cc type chromap (line 7) | namespace chromap { FILE: src/draft_mapping_generator.h function namespace (line 12) | namespace chromap { FILE: src/feature_barcode_matrix.cc type chromap (line 10) | namespace chromap { FILE: src/feature_barcode_matrix.h function namespace (line 19) | namespace chromap { FILE: src/feature_barcode_matrix_writer.h function namespace (line 16) | namespace chromap { FILE: src/hit_utils.h function namespace (line 6) | namespace chromap { FILE: src/index.cc type chromap (line 10) | namespace chromap { FILE: src/index.h function namespace (line 17) | namespace chromap { function Destroy (line 40) | void Destroy() { function Save (line 51) | void Save() const; FILE: src/index_parameters.h function namespace (line 4) | namespace chromap { FILE: src/index_utils.h function namespace (line 19) | namespace chromap { FILE: src/khash.h type khint32_t (line 135) | typedef unsigned int khint32_t; type khint32_t (line 137) | typedef unsigned long khint32_t; type khint64_t (line 141) | typedef unsigned long khint64_t; type khint64_t (line 143) | typedef unsigned long long khint64_t; type khint32_t (line 162) | typedef khint32_t khint_t; type khint_t (line 163) | typedef khint_t khiter_t; function kh_inline (line 426) | static kh_inline khint_t __ac_X31_hash_string(const char *s) function kh_inline (line 443) | static kh_inline khint_t __ac_Wang_hash(khint_t key) FILE: src/kseq.h type kstring_t (line 83) | typedef struct __kstring_t { function ks_getuntil (line 145) | static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *s... FILE: src/ksw.cc type _kswq_t (line 47) | struct _kswq_t { function kswq_t (line 64) | kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const... function kswr_t (line 112) | kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, in... function kswr_t (line 233) | kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _o_del, i... function revseq (line 337) | static inline void revseq(int l, uint8_t *s) function kswr_t (line 344) | kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, i... function kswr_t (line 368) | kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, in... function ksw_extend2 (line 381) | int ksw_extend2(int qlen, const uint8_t *query, int tlen, const uint8_t ... function ksw_extend (line 482) | int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *... function ksw_semi_global3 (line 505) | int ksw_semi_global3(int qlen, const char *query, int tlen, const char *... function ksw_semi_global (line 628) | int ksw_semi_global(int qlen, const char *query, int tlen, const char *t... function ksw_semi_global2 (line 633) | int ksw_semi_global2(int qlen, const char *query, int tlen, const char *... function ksw_global2 (line 638) | int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t ... function ksw_global (line 742) | int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *... function main (line 778) | int main(int argc, char *argv[]) FILE: src/ksw.h type _kswq_t (line 11) | struct _kswq_t type kswq_t (line 12) | typedef struct _kswq_t kswq_t; type kswr_t (line 14) | typedef struct { FILE: src/mapping.h function namespace (line 4) | namespace chromap { FILE: src/mapping_generator.cc type chromap (line 3) | namespace chromap { FILE: src/mapping_generator.h function namespace (line 25) | namespace chromap { FILE: src/mapping_in_memory.h function namespace (line 10) | namespace chromap { FILE: src/mapping_metadata.h function namespace (line 13) | namespace chromap { FILE: src/mapping_parameters.h function namespace (line 7) | namespace chromap { FILE: src/mapping_processor.h function namespace (line 22) | namespace chromap { FILE: src/mapping_writer.cc type chromap (line 3) | namespace chromap { FILE: src/mapping_writer.h function namespace (line 26) | namespace chromap { function AppendMappingOutput (line 80) | inline void AppendMappingOutput(const std::string &line) { function OutputTempMapping (line 94) | inline void OutputTempMapping( FILE: src/minimizer.h function namespace (line 9) | namespace chromap { FILE: src/minimizer_generator.cc type chromap (line 5) | namespace chromap { FILE: src/minimizer_generator.h function namespace (line 11) | namespace chromap { FILE: src/mmcache.hpp type chromap (line 13) | namespace chromap { type _mm_cache_entry (line 14) | struct _mm_cache_entry { class mm_cache (line 27) | class mm_cache { type _mm_cache_entry (line 30) | struct _mm_cache_entry method IsMinimizersMatchCache (line 41) | int IsMinimizersMatchCache(const std::vector &minimizers, method mm_cache (line 84) | mm_cache(int size) { method SetKmerLength (line 116) | void SetKmerLength(int kl) { kmer_length = kl; } method Query (line 119) | int Query(MappingMetadata &mapping_metadata, uint32_t read_len) { method Update (line 187) | void Update(const std::vector &minimizers, method DirectUpdateWeight (line 341) | void DirectUpdateWeight(int idx, int weight) { cache[idx].weight += ... method GetMemoryBytes (line 343) | uint64_t GetMemoryBytes() { method GetUpdateThreshold (line 358) | uint32_t GetUpdateThreshold(uint32_t num_loaded_reads, method PrintStats (line 371) | void PrintStats() { FILE: src/paf_mapping.h function namespace (line 8) | namespace chromap { FILE: src/paired_end_mapping_metadata.h function namespace (line 10) | namespace chromap { function SetMinSumErrors (line 95) | inline void SetMinSumErrors(int min_sum_errors) { function SetSecondMinSumErrors (line 98) | inline void SetSecondMinSumErrors(int second_min_sum_errors) { function SetNumBestMappings (line 101) | inline void SetNumBestMappings(int num_best_mappings) { function SetNumSecondBestMappings (line 104) | inline void SetNumSecondBestMappings(int num_second_best_mappings) { FILE: src/pairs_mapping.h function namespace (line 8) | namespace chromap { FILE: src/sam_mapping.h function namespace (line 10) | namespace chromap { function GetSequenceLength (line 259) | uint32_t GetSequenceLength() const { function WriteToFile (line 293) | size_t WriteToFile(FILE *temp_mapping_output_file) const { function LoadFromFile (line 345) | size_t LoadFromFile(FILE *temp_mapping_output_file) { FILE: src/sequence_batch.cc type chromap (line 7) | namespace chromap { FILE: src/sequence_batch.h function namespace (line 15) | namespace chromap { FILE: src/sequence_effective_range.h function namespace (line 11) | namespace chromap { FILE: src/strand.h function namespace (line 4) | namespace chromap { FILE: src/summary_metadata.h function namespace (line 15) | namespace chromap { FILE: src/temp_mapping.h function namespace (line 19) | namespace chromap { FILE: src/utils.h function namespace (line 16) | namespace chromap {