* @brief Combine alleles in a single Variants record * */

Convert a pandas dataframe to a PUMA metrics table This is how a metrics table looks like: { id: 'readCounts', label: '

extract chrom / pos / length */

* Use a global alignment to fully transform ref to alt. * * If a local alignment will is used (a'la read realignment), * returned variants will o

* Length difference compared to reference * * min : minimum difference * max : maximum difference * (if multiple insertions/deletions are prese

make a missing float */

https://en.wikipedia.org/wiki/Hamming_weight

query sum over a range */

* @brief Decompose a RefVar into primitive variants (subst / ins / del) by means of realigning * * @param f reference sequence fasta * @param chr t

add single allele */

return if any calls are homref */

keep track of returned types

Extract the VCF header and turn into JSON :param vcfname: VCF file name :return: VCF header in JSON format

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

* @brief Interface to htslib regions functionality * @param regions regions string, see synced_bcf_reader.h * @param isFile True if regions is a fil

* @brief Interface to htslib targets functionality * @param targets targets string, see synced_bcf_reader.h * @param isFile True if targets is a fil

* @brief Return transition partner of base? * * @param base the base * */

* @brief Insert a Variants record into the stream * @details The next record returned will be this one * * @param s Variants to put on top of stack

empty internal buffer */

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

interface to set / get INFO values */

if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)

* Intersect two lanes and return the size of the intersection * @return the number of positions shared by l1 and l2 */

construct DiploidType from het and homref fields in DiploidRef */

* Create a reference graph for a region of a VCF */

* update / optimize assignments */

Preprocess a VCF + create index :param input_filename: the input VCF / BCF / ... :param output_filename: the output VCF :param location:

Free the string duplicated by duplicateStringValue(). */

run a function in parallel on all elements in par :param pool: multiprocessing.Pool or None :param fun: a function :param par: a list of

* @brief Set the region to compare in and reset the enumeration. * */

* Enumerate from set of Variants */

* @brief Add ref block to variant record */

return if any calls are homref */

apply and retrieve modified reference sequence between start and end * Note that _start and _end will be extended if they aren't contained withi

Calculate total length of contigs overlapping a set of locations

* update / optimize assignments * * return < true/false if assignment produces match, number of matched variants > * Total number of va

Read the header lines from a VCF file

Return contig lengths in a fasta file

get stats from a cigar string */

* Test if an assignment produces matching haplotypes * @param a assignment of variants to haplotypes * @return match status -- true

* @return the number of possible assignments */

shared-pointerize */

reset / remove interval range */

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

* @brief Return homref/no-calls * */

write format fields apart from GT */

* @brief Decompose a RefVar into primitive variants (subst / ins / del) * * @param rv the RefVar record * @param vars the primitive records */

total variants reported by query at this level.

* @brief Debug dump, optional */

helper to write values from a single level */

* @brief Add variants from a VariantReader (see above for VariantBufferMode and param) */

Add all intervals from a bed file, attaching a given label :param bed_file: Bed File :param label: either a string label or a functio