Close closes the Reader. It does not close the underlying io.Reader.

* * Index and generate a BdundledTrackData from an array of GenericTrackData * objects. */

Type returns a byte corresponding to the type of the auxilliary tag. Returned values are in {'A', 'c', 'C', 's', 'S', 'i', 'I', 'f', 'Z', 'H', 'B'}.

Shift the base v into the left end of the kmer

Converts a list of positions to a list of ranges. Args: - min_gap: minimum length of output region. Return value: A list of tuples (st

Get the level index for a dataset

Wrapper to get around the fact that tk_io.get_variant_iterator() takes a locus string instead of a tuple.

Push values read from a byte array. # Arguments `bytes`: byte array to read values from `seq_length`: how many values to read from the byte array. No

Handles 0 division and conversion to floats automatically

Find the sets containing the objects and merge them all.

Start returns the lower-coordinate end of the alignment.

Adds single region to set while removing overlap

Args: loci: list of tuples (chrom, start, stop, name) win: distance between loci to cluster together max_range: used to avoid overmer

Returns the barcode indices that computation needs to be performed on for the relevant positions.

Computes the log-LR of the two hypotheses that there was an SV vs there was no SV: logP(observed fragments | SV) - logP(observed fragments | n

Coverage of regions in bins. Bins a locus (eg. a chromosome) into bins and computes the number of bases in each bin that are covered by the gi

Close closes the Writer, flushing any unwritten data to the underlying io.Writer, but does not close the underlying io.Writer.

Len returns the length of the alignment.

NewReader returns a new ReadCloser that can be used to read the uncompressed version of r. If r does not also implement io.ByteReader, the decompresso

NewWriter returns a new Writer. Writes to the returned writer are compressed and written to w. It is the caller's responsibility to call Close on the

* * Search a BundledTrackData instance for all of the ranges that overlap * a given position on a chromosome */

* Compress and write a chunk of data to a loupe file. This returns a LoupeSection object for the new data. */

Flush any buffered output to the underlying writer.

Returns true iff read1/read2 are a pair of split reads. Only considers a pair of a primary and a secondary read as a split pair.

Position within the read where mapping starts. Eg. if the first 4 bases of the read are soft-clipped, the position returned will be 5 (4th positio

Merges a set of SVs into a non-redundant set. Args: - bedpe_df: Either a bedpe file or a DataFrame like the one returned by tk_sv_io.read_

* * Add a new barcode annotation */

NewReader creates a new Reader reading the given reader. If r does not also implement io.ByteReader, the decompressor may read more data than necessar

Clear the sequence.

Get the log-probability of the reads assuming that there is an SV of the same type as the pair at positions b1 and b2. Args:

Distance from breakpoint to beginning of read.

Compute P(nr reads in [start_pos, end_pos); alpha, alpha_corr_factor, mean_target_ratio)

easy to deal with closing all of those files

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

* * Find a ident number for this barcode. If we've seen the barcode before * recycle the number that we've used. Otherwise allocate a new one and w