Number of values in array or object

Read variants from a block into a list */

add observations from second ROC

get the full haplotype sequence */

* @brief Add a sample to read from * @param filename file name * @param sname name of sample to read from * @return sample number to retrieve rec

Wraps runShellCommand for compatibility. :param args: :return:

set up processing */

* @brief Split a string along separators */

* @brief Check if interval is fully covered in a given lane */

* @brief Get a cigar string */

read a format field as a single double. result will not be overwritten on failure */

* @brief Add an interval to a lane * * @param start interval coordinates * @param end interval coordinates * @param lane lane to a

add variant */

* @brief Report SNV type * * @param refBase the reference base * @param altBase the variant base * * Return true if SNV is tr

* Helper to aggregate reference variants base by base * * Refpos must be > vars.back().end * */

* Compare all buffered variants */

* @brief set target sequence */

* Format genomic coordinates */

* @brief Classify a variant's GT type * */

* @brief Debug dump, optional */

* @brief Parse coordinates * * @param input input string, e.g. "chr1:1,000-2000" * @param chr the contig name, e.g. "chr1" * @para

* @brief set query sequence */

* @brief Retrieve an info field as an integer * * @param result the default to return if the field is not present */

* reset/initialize an assignment */

* @brief Advance buffer, discarding all intervals with start < to * * @param to interval minimum end position */

* @brief Test if string has given suffix * * @return true if str ends with suffix */

shortcut to get chromosome name */

* @brief Rewind / set region to read * * @param chr chromosome/contig name * @param startpos start position on chr (or -1 for entire chr) */

update format string for a single sample. */

* @brief Read the GT field */

* @brief Is base a valid uppercase non-N base? * * @param base the base * */

Register a ROC calculator :param name: the name of the calculator :param ftname: the features / feature table name

process a Variant Reader */

Compute ROC table from TP/FP/FN classification table. :param tbl: table with label and feature :type tbl: pandas.DataFrame :param label_c

Return a data frame with features collected from the given VCF, tagged by given type

* return the non-N padded size of a contig. This is calculated * as the size of the contig minus any N's at the beginning or * at the end. * * Ret

Duplicates the specified string value. * @param value Pointer to the string to duplicate. Must be zero-terminated if * length is "unkno

* @brief Get the alignment score */

* @brief Check if interval is partially covered in a given lane */

http://graphics.stanford.edu/~seander/bithacks.html#NextBitPermutation

* @brief Replace all instances of find with replace in str */

* @brief Canonical representation w.r.t. reference */

Run a shell command (e.g. bcf tools), and return output

Given a list of VCF features, get tab-separated list from VCF file :param vcfname: the vcf file name :param features: list of features to ex

* return the size of a contig. Sum of all contig sizes if contig == 0 * @param contig name of contig, or empty * @return number of bases in the cont

read a format field as a single float. default return value is NaN */

Parse BCFTOOLS Stats Output

* @brief Reference for shifting * */