* Align reads from single BAM file to graph and disambiguate reads * to produce counts. * * @param parameters alignment parameters * @param output

* High-level read extraction interface * @param reader An open bam reader * @param target_regions list of target regions * @param max_reads maximum

Tag a piece of reference with a haplotype Don't apply haplotype label to leading padding sequence shared by all alleles :param start:

* Convert a CIGAR string to a list of variants * * @param ref reference sequence string * @param alt alt sequence string * @param cigar cigar for

Delete node and all its edges from graph

* Helper function to return JSON object from a file or from a string * @param file_or_value filename or string value * @return JSON value */

TODO: the suboptimal alignments this produces are all anchored to the end point of the optimal alignment this is valid for the pinned alignment, but i

* Initialize a logger. * @param name logger name * @param async log asynchronously (use true when there are many messages) * @param level minim

* @brief Parse coordinates * * @param input input string, e.g. "chr1:1,000-2000" * @param chr the contig name, e.g. "chr1" * @para

* Pile up reads at pos * @param pos position to calculuate pileup for * @param processor function that is called successively for every read that ov

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

allele depths for alt

* Add a genotype for a particular sample * @param allele_names names of all alleles in GT * @param gt genotype of the sample * @return sample index

Add one alt allele to the graph Trim of leading padding bases (shared with ref) For insertions add a 'bypass allele' parallel to the

* Create parameterized read filter * @param graph the graph the read was aligned to * @param remove_nonuniq remove reads that don't have a unique be

* Update sequence labels in read according to nodes the read has traversed * @param g graph structure * @param reads list of aligned reads * @param

Record the length as a prefix. */

* * return true if this aligned read or its mate overlaps >= 1 base with the target region * @param read The single read to be checked * @param reg

Parse a region string into chrom, start, end :param region_string: string like "chrom:start-end" :type region_string: str :return: ch

* Read paths from JSON * @param graph graph to use for the paths * @param in_paths Input JSON node with paths */

* upper-case a string */

allele depths for others

allele depths for reference

* Append coverage values to JSON value * * This will append to arrays like this: * * { * "ref": <ref-matching depth> * "ref:FWD": <...> *

* return the size of a contig. Sum of all contig sizes if contig == 0 * @param contig name of contig, or empty * @return number of bases in the cont

* @brief Test if string has given suffix * * @return true if str ends with suffix */

* Fit the observed data with a naive Gaussian (i.e. simple mean and variance) */

* Format genomic coordinates */

Returns the total probability in the distribution of aligned characters with a given logarithm base */

if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)

Load JSON from text file or gzip

* Get the mean of the fitted distribution * @return double */

** \brief Retrieve the next k-mer hat does not contain any N. ** ** \param kmer the next kmer if any ** ** \param start position o

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