empty internal buffer */

empty internal buffer */

empty internal buffer */

empty internal buffer */

empty internal buffer */

empty internal buffer */

empty internal buffer */

decide how to aggregate */

* @brief Enable / disable returning of homref intervals * */

* @brief Enable / disable reference padding * * RefVars can be trimmed to include / not include reference bases */

read a format field as a single int. */

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 g

* @brief Enable / disable returning of homref intervals * * TODO : output homref as intervals */

* Get region intersection sizes in NT * @param region_name base region to intersect all others with (e.g. "CONF") * @return mapping of size

* Get level for a region (0 for top-level, 1 for regions specified in a bed file) * @param region_name * @return level for the given region

* Get total region sizes in NT * @param region_name * @return the region size */

Run gvcf2bed and return temporary region bed file in temp folder

Modified Jeffreys confidence interval for binomial proportions: Brown, Cai and DasGupta: Interval Estimation for a Binomial Proportion. 2001,

list all quantification methods */

merge two intervals

mkdir -p path

translate name to count key */