Initialize Huffman decoding tables from array of code lengths.

Efficiently iterate over the kmers in the sequence

Mark exact duplicate reads in the BAM file. Duplicates have the same read1 start site and read2 start site

Returns the extra offset of a match token

Open a reference fasta and rename the contigs to strip any fasta comments

Determines whether a region described by start and end overlaps any of the regions.

Full raw R1 QVs

Full raw R1 sequence

calculate bin given an alignment covering [beg,end) (zero-based, half-close-half-open)

Returns whether or not the row of strings is an Illumina data header line. :type row: list[string] :rtype: bool

Determine whether the rows comprise an Illumina Experiment Manager (IEM) sample sheet by checking for the presence of a [Data] section with

Rename or supplant all the keys generated by the get_illumina_sequencing_metrics method from their original names (dictated by the ANALYZ

Sorts and merges list of tuples (chrom, start, stop). Args: - regions: list of tuples (chrom, start, stop). - extend: non-negative integer

writeString writes a UTF-8 string s in GZIP's format to z.w. GZIP (RFC 1952) specifies that strings are NUL-terminated ISO 8859-1 (Latin-1).

Write the go source package to the given writer.

* Build a block index for an array of GenericTrackData object. * data_path must be the path of the "data file" that goes at the end of the loupe file

* * Return a map of phase-block-size to freequency. */

* * Build an interval tree by (destructively) sorting the input and then using * DoBuildIntervalTree to build the tree its self. */

* Convert a 4-byte array to a float32 */

* * Convert a little-endiat byte array to an integer. */

@Function: 1. Calculate the number of mismatches. 2. Modify the cigar string: differentiate matches (M) and mismatches(X). Note that SSW does not diff

remember guys, its just one file now, many reads, one file

* * This function iterates through a "vcf-like" file that defines rsIDs for * genomic coordinates and associates those with the SNPs in the run VCF.

* Extend a PhaseBlockSummary struct to include another row of VCF data */

* * Search the auxilary tags for the barcode tag, BX. */

* * Write the final chunk of data for a chromosome (and update the index) */

Flush flushes any pending compressed data to the underlying writer. It is useful mainly in compressed network protocols, to ensure that a remote read

* * Flush the contents of bib.Buffer to the data file. If force==false, * we only flush data if we're out of space. */

IsValid returns whether the CIGAR string is valid for a record of the given sequence length. Validity is defined by the sum of query consuming operati

* * Load a breakpoint details file from disk. */

* Convert a raw gene entry into a GenericTrackData object */

* * Use SearchIntervalTree and an internal callback to compute an array of all * intervals that overlap |location| and return that array. */