! @brief return whether value is a binary array This function returns true if and only if the JSON value is a binary array. @return `tru

* Get the position furthest to the left of base such that with respect to * frame at position base there is no stop codon in the window from * lef

output GFF for noncoding genes

* reverseComplement * * allocates a new character array and fills it with the reverse complement of 'dna' * eg agcngt -> acngct * doesn't change

Returns the current time in milliseconds.

Returns true iff the unit test passed (i.e. all test suites passed).

Iterates over a vector of TestSuites, keeping a running sum of the results of calling a given int-returning method on each. Returns the sum.

! @brief checks whether the container is empty. Checks if a JSON value has no elements (i.e. whether its @ref size is `0`). @return The

Gets the number of failed tests.

keys encodes all of: chrStart chrEnd type lenMod3

returns position (0-based) where alignment starts */

* computes the probability of the emission of the sequence from left to right * left and right included * DEPRECATED: this is done with SegProbs now

returns the explanatory string

Formats a source file path and a line number as they would appear in an error message from the compiler used to compile this code.

Creates a TestSuite with the given name. Arguments: name: name of the test suite a_type_param: the name of the test suite's type parameter,

* */

returns ID number for reference sequence */

* @brief Get the last coordinate in the relative coordinate system with a corresponding scaffold position. * @return Returns the last coordinate in

Provides access to the event listener list.

* ViterbiSubmapType::merge(other, mult): * merge two maps and take the maximum entries, after multiplying * entries of other map with _mult_ * note

Returns the current OS stack trace getter if it is not NULL; otherwise, creates an OsStackTraceGetter, makes it the current getter, and returns it.

* PredictionRun::print */

! @brief add an object to an array Appends the given element @a val to the end of the JSON value. If the function is called on a JSON nul

! @brief exchanges the values Exchanges the contents of the JSON value with those of @a other. Does not invoke any move, copy, or swap op

Chops off the n lowest bits from a bit pattern. Returns the n lowest bits. As a side effect, the original bit pattern will be shifted to the right b

Helper function used by ValidateRegex() to format error messages.

Returns the i-th test among all the tests. i can range from 0 to total_test_count() - 1. If i is not in that range, returns NULL.

Gets the i-th test suite among all the test suites. i can range from 0 to total_test_suite_count() - 1. If i is not in that range, returns NULL.

Returns true iff ch appears anywhere in str (excluding the terminating '\0' character).

Returns whether the given character is a valid path separator.

return on/off value for a flag

If *pstr starts with the given prefix, modifies *pstr to be right past the prefix and returns true; otherwise leaves *pstr unchanged and returns false

Returns true iff the test was skipped.

Reads and returns the string environment variable corresponding to the given flag; if it's not set, returns default_value.

* SequenceFeatureCollection::computeHintedSites */

* Precompute and store the array of matrices. * Takes approximate k * m * 0.015 seconds on greif1: Time for eigendecompose is small compared to time

computes the score for the splice sites of an exon candidate