return true when successful */

* @brief Extract GT from Format field * */

* operators so we can sort blocks */

* update / optimize assignments */

* update / optimise assignments */

Partial-credit-process a VCF file according to our args

put back a variant to the last stage */

Release the object. @warning it is the responsability of the caller to actually destruct the object.

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

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

Calculate SNP and indel ROC. Return a dictionary of variant types and corresponding files. :param filter_handling: can be None, "PASS" or "

GA4GH-VCF field-based ROC counting

Runs scmp, which outputs a file quantify can produce counts on vcf1 and vcf2 must be indexed and only contain a single sample column.

Run VCFEval and convert it's output to something quantify understands

Run quantify and return parsed JSON :param filename: the VCF file name :param output_file: output file name (if None, will use a temp file)

* Set values in a range * * @param val the value * @param start the start position * @param end the end position, or -1 to use the

* @brief Set to use a specific alignment object * * The passed pointer will be deallocated when the HaploCompare object is destroyed. */

* Set the maximum number of paths to enumerate from the Graph reference */

* @brief Reference for shifting * */

* Set region and restart enumeration */

split iterable into list blocks of size n

resolve types to strings */

resolve types to strings */

Unpickle and concatenate sequentially

* BlockAlleleCompare::run doesn't write a header such that * results can be concatenated. This function updates the header once in the beginning

write a VCF header

Haplotype block comparison wrapper function