Determine whether the rows comprise a readable simple CSV, with a lane number, sample and index (in that order) :type rows: list[list[str

Return a minimal sam line = by default return an undetermined sam line. Check the document [SAM Format Specification](http://samtools.sourcef

Test for a very high-quality read. Only reads satisfying this predicate are used when computing summary dup rates to avoid spurious duplicate

Striped Smith-Waterman Record the highest score of each reference position. Return the alignment score and ending position of the best alignment

Decide whether or not to try and phase a variant. Currently this just ignores homozygous variants

Returns the type of a token

Creates an alignedRead object and writes it to the corresponding bam file. If cigar is unspecified, the alignment is defaulted to a perfect align

Write a dictionary of named values to a R 'dump file' for consumption by stan

* * This computes a global track positions for all genes. The results are filled in * as the "row" field in the GeneExtraData structure. This attemp

Bin returns the BAM index bin of the record.

* This converts a "contig index" from the "fai" index in the reference data package to a JSON encoding that loupe understands. */

* * Compute the data that goes into a single SNP record in a loupe * file. */

* * Build an interval tree from an (sorted) array of intervals. */

* * This is a trivially simple interval search. We try to confirm * that this has the same behavior as the faster-better-probably-more-buggy * vers

* * Extract all of the optional fields in a bed file into a map. * filenmaes is an array of strings that specifies what to call them */

* * This extracts data from the genotype field and returns the sequence information. * The genotype string is a string that looks like <integer>|<in

* This function takes a "variant format specifier" string and a variant string * and parses out the useful fields. * a variant format specifier is a

* * Implement an "uncompressing" reader that uses the system's * gunzip program to uncompress the input file. We do this * because the system gzip

** * Generate a BarcodeValidator object using the existing barcode count and * whitelist as the basis for barcode correction. */

* * This is just a wrapper around looking up something in a map */

* * Compute a md5 hash of a bunch or files. We use this to compute a reference * hash so that Loupe will only have to load the reference once, even

next several functions for heap interface

* * Load a file of structural variants breakpoints and return a * list of SVs. */

* * Load a file of structural variants breakpoints and return a * list of SVs. Short SVs are encoded like SVs in the bedpe file. */

* * Make a new ReReader from any Reader object */

Calculates the N50 for a given set of lengths

NewReaderDict is like NewReader but initializes the reader with a preset dictionary. The returned Reader behaves as if the uncompressed data stream s

NewWriterLevel is like NewWriter but specifies the compression level instead of assuming DefaultCompression. The compression level can be DefaultComp

Overlap returns the length of the overlap between the alignment of the BAM record and the interval specified. Note that this will count repeated matc

* * This function decides of a row from a VCF file is compatible with a phase * block summary or not. * SNP's that share: chromosome, and phase id