Change ',' to '.' everywhere in buffer. * * We had a sophisticated way, but it did not work in WinCE. * @see https://github.com/open-source-parsers

read AD */

* @return all contig names */

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

Split VCF INFO String

Split VCF INFO String

* Get all intersection / extra counts for a given region. By default, will return one * pair with <"Subset.Size", size of the region> * @par

* @return all region names */

return sample names from header */

* Get next pair of haplotype sequences */

* Returns true if regions were loaded. * * Note that this will also return true when an empty bed file was loaded. * This is intentiona

Return all overlapping intervals in chr:[start,end) :param chrom: Chromosome :param start: start (1-based) :param end: end

return number of reference padding bases */

remove values outside region */

fraction of query calls that are UNK */

* @return true if no variants registered */

* Output all buffered variants into a file * @param output HTS file to write to */

relative precision of query */

Preprocess a single VCF file :param vcf_input: input file name :param vcf_output: output file name :param reference: reference fasta nam

wrapper for running in parallel

Run quantify and write tables

get all intervals that overlap a range */

query mean value over a range */

* @brief Read and write from/to JSON files */

recall relative to truth */

Replace all NaNs in the given object with string values :param xobject: a dictionary :return: object, fixed

Replace shebang line / reheader script files

* Reset / remove values from and including position start * * @param start the start position, or -1 for all values */

Return a dictionary with session and run information

* @brief change GTs on chrX/Y to be diploid for matching * */

* Mark one region to intersect with all others. This will * @param base base region (e.g. "CONF") */

* @brief Validate reference alleles * */

If a field is given as an index into a list, split these

Run the unit + integration tests

* @brief Remove unused alleles */

add common quantification args

update command line parser with preprocessing args