* * Load a breakpoints file from disk. */

Multistream controls whether the reader supports multistream files. If enabled (the default), the Reader expects the input to be a sequence of indivi

Reference returns the records reference.

Reset discards the Reader z's state and makes it equivalent to the result of its original state from NewReader, but reading from r instead. This permi

pred_file: BEDPE file with sv calls or pandas DataFrame as returned by tk_sv_io.read_sv_bedpe_to_df true_file: BEDPE file with ground truth v

Determines whether a point is contained in one of the regions

Creates a (BCs X Windows) sparse matrix of barcodes (columns) versus windowed locations

Finds the maximum extension to the left and right of [start_pos, end_pos) such that the probability of observing no reads in the extension is

Gets the specific contig the variant is contained on

Get the go type for the given value. If the value is not one with a good representation in Go, such as a list with inconsistent type, returns

Determine if a data column is leveled

FASTQ read header

Initialize Huffman decoding tables from array of code lengths.

Get a vector of the kmers in the sequence

Combine reads from multiple input FASTQ files, and potentially trim. Demultiplex outputs a series of FASTQ files with filenames of the form:

Takes the other regions and merges

Computes the log-probabilities that two fragments with the same barcode come from the same or different molecules. Args: - As in lr_ta

Get the prefix of a given size.

Extract the rows from the CSV at the specified path. Will throw an error if the file doesn't exist. :type path: string :rtype: list[

Return whether the specified section contains sufficient information to populate bcl2fastq. :type rows: SampleSheetSection :rtype: bo

Set the value as position `i`.

Determine MSP substrings of seq, for given k and p. Returns a vector of tuples indicating the substrings, and the pmer values: (p-mer value, min p-mer

None will remove the info field

* * This assembles data into a single 64-bit integer that we can store */

NewWriterDict is like NewWriter but initializes the new Writer with a preset dictionary. The returned Writer behaves as if the dictionary had been wr

* * Parse a 10X barcode field from a VCF file. This parses a string like * ATTTAAA_12;ACCATA_14,CCCCCCCC_99;GGGGGGGGG_0;ATATATATAT_43 * into a pai

Tag returns an Aux tag whose tag ID matches the first two bytes of tag and true. If no tag matches, nil and false are returned.

Type returns the type of the CIGAR operation for the CigarOp.

Perform the alignment of query against the object reference sequence @param query_seq Query sequence as a python string (case insensi

* * Allocate some bytes from the arena built into each record. */

Find the position in the read of `ref_pos`.

read a single read

Gets the information on called contigs by barcode

Get a list of target regions that are within (ext_start, ext_stop), sorted by their distance from (start, stop)

Number of bases of [start, stop) covered by the targets. Args: - target_coverage: an array with the number of bases covered in bins [0, co

Gets discordant reads in a given st of loci. - chrom, start, stop: a region from which reads will be fetched. loci might be outside this regio

Determines which (if any) region contains a point

Returns list of non-overlapping regions