* Convert double to string with a fixed precision */

* Check bcf records for equality * Equality is determined via chrom, pos, alleles * @param a first bcf record * @param b second bcf record * @retu

* \brief find next suitable executor for the current thread */

* Fit the observed data using the 1D Minimum covariance determinant method * @param nums a vector of doubles */

update manifest data from generated idxdepth results dump manifest into the new path

Generate idxdepth JSON for all samples :param bam_manifest: list of BAM file information records :type bam_manifest: list of grm.graph_t

* return genotype likelihood given genotype (using Poisson model with internal parameters) * @param lambda Poisson distribution parameter * @param g

read AD */

* @return allele frequencies */

* Get the names of all alleles * @return vector of allele names */

* @return fraction of samples with unfiltered calls */

read DP(I) -- will use in this order: DP, DPI, -1 */

* Get depth standard deviation for a sample * @param sample_index * @return std deviation of average depth. if not available, return 0 */

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

read a format field as a single int. */

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

Deprecated. Preserved for backward compatibility

read GQ(X) -- will use in this order: GQX, GQ, -1 * * This is somewhat Illumina-specific, TODO: refactor to avoid using this function in a general s

* @brief Read the GT field */

* Get the genotype for a particular sample * * @param samplename sample name * @param breakpointname name of breakpoint ("" for combined GT) * @re

* @brief Retrieve an info flag * * @return true of the flag is set */

* @brief Retrieve an info field as a double * * @return the value or NaN */

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

* Get the length of the shortest ALT allele for a vector of refVars * @param rv * @return */

* \return uppercase base or N for bcl N */

* \brief reverse-complements the base bits of a bcl byte * * \returns 0 for 0, reverse-complemented lower bits with quality bits unchanged */

return sample names from header */

* Get sex integer for a sample */

* \return uppercase base or N for bcl N */

make variants from a cigar string */

automatically adds 0-scoring N to the final row and column

* Check if variant has any symbolic alleles */