* * Parse (very simply) a VCF file into SimpleVCFRow structs. * This parses a file that looks like: * * [chromosome] [offset] [reference-id] [refe

* * This is a rediculously simple VCF parser that only knows how to parse the * first three elements of each line to produce a chr+offset-->rsid map

Reset discards the writer's state and makes it equivalent to the result of NewWriter or NewWriterDict called with dst and w's level and dictionary.

Reset discards the Writer z's state and makes it equivalent to the result of its original state from NewWriter or NewWriterLevel, but writing to w ins

* * Search an interval tree. Calls |callback| for each interval found that * overlaps with location. */

* Sort an array of GenericTrackData objects. This returns an array of pointers, sorted by the chromosome and start. */

* * Compare sort-order of an VCF entry with what we're looking for. * We return less-than-zero, zero, or greater-than-zero depending * on how they

* * This copies a file into the compressed Loupe file and returns * loupesection object for that file. No transformations (compression or * otherwi

* * Write the index part to a file */

* * Serialize a StructuralVariant array to JSON */

* * Write summary data to the given path. */

Free the space alocated for the matrix used by align

Calls haplotypes and outputs the variant file

Convert cigar and cigarLen into an human readable Cigar string as in SAM files

Compute the yield (number of bases passing filter) from a populated metrics object generated by get_illumina_sequencing_metrics()

Compute the number of bases passing filter + Q30 from a populated metrics dictionary generated by get_illumina_sequencing_metrics()

Compute raw yield (number of bases total) from a populated metrics object generated by get_illumina_sequencing_metrics()

Recursively gets teh go type name for the given value for sets, lists, or maps.

Free the space alocated for the matrix used by init

Whether to split bcl2fastq into a number of stages by tile.

Returns 'string' unless the value is a paths based on the runtime path of the module, since those will not be accurite.

Add an average quality score to the stats :param average: The average quality score of the bases :param total_bases: The numb

Update the barcode state in with the new read. If this read should actually create a new fragment, we should return the old fragment and set the state

Convert a BAM alignment into a sequence of `AlignedSegments`

Look at the leaves and assign them a bit count and an encoding as specified in RFC 1951 3.2.2

Convert an ASCII-encoded DNA base to a 2-bit representation

Return the number of literals assigned to each bit size in the Huffman encoding This method is only called when list.length >= 3 The cases of 0, 1, a

send each item in the source generator to each consumer in the list

* * Clear out the arena in each record. */

buildAux constructs a single byte slice that represents a slice of Aux.

Runs bwa paired-end aligner on reads using paired-end information Algorithm choices are currently MEM: Maximal Exact Matching (better for long

Runs bwa aligner on reads without using paired-information (using bam as input format).

Calculate the posterior distribution of the haplotype state of each fragment

Evaluate a pair of loci (c1, s1, e1), (c2, s2, e2) for distal SV calls. Return value: a list of SvCall objects.

Evaluate a pair of loci (c1, s1, e1), (c1, s2, e2) for proximal SV calls. Return value: A tuple (results, reads). results is a list of SvCall

Given the value of the lanes in the cell and a lane count from the flowcell, generate the set of lanes represented by the cell value. Fo

MSP a random string & verify that the BSPs match the original string

Compare two sets of phase blocks - what's shared and what's different. The max_allowable_overhang parameters allow one to ignore minor diffe

Attempt to correct an incorrect BC sequence by computing the probability that a Hamming distance=1 BC generated the observed sequence, a

This assumes that the spreadsheet and runinfo have been validated already.

Validate that the path and fastqprefix arguments are compatible and allowed. Return the input_mode and sample_name that should be sent downs