! @return a string representation of the last read byte */

Copy constructor.

* SequenceFeatureCollection::getFeatureListContaining * returns a pointer to a feature of type 'type' which starts at or before 'startPosition' and e

! @brief return whether value is an array This function returns true if and only if the JSON value is an array. @return `true` if type i

! @brief return whether value is null This function returns true if and only if the JSON value is null. @return `true` if type is null,

boost::hash_combine

! @brief internal implementation of the serialization function This function is called by the public member function dump and organizes t

* running external commands * returns stdout */

return the last read token (for errors only). Will never contain EOF (an arbitrary value that is not a valid char value, often -1), because 255 may l

* SequenceFeatureCollection::getFeatureListOvlpingRange * returns a pointer to a feature of type 'type' whose inverval overlaps the interval * going

Returns string with name of the reference of an alignment sequence. */

* convert int to string */

casts node to StateType

Gets the elapsed time, in milliseconds.

Routine for aborting the program which is safe to call from an exec-style death test child process, in which case the error message is propagated back

* */

saves the alignment to the alignment archive */

! @brief return the value of an iterator @pre The iterator is initialized; i.e. `m_object != nullptr`. */

Converts the buffer in a stringstream to an std::string, converting NUL bytes to "\\0" along the way.

* expand the ~ to the $Home directory */

apply a power function, more efficient through above precomputation and by using exponents that are a fraction of 8 (3 'std::sqrt' calls take about 52

* SegProbs::setEmiProbs */

Reads and returns the Boolean environment variable corresponding to the given flag; if it's not set, returns default_value. The value is considered t

Parses a string for a bool flag, in the form of either "--flag=value" or "--flag". In the former case, the value is taken as true as long as it does

by oddRatio

! @brief get next character from the input This function provides the interface to the used input adapter. It does not throw in case the