* Write a header to a loupe file. Many '\n' will be appended to the header to make things more intelligable. */

* * Write single chink of VCF entries as a complete JSON blob to a file. Additionally, * update "index" to include an index record for those entries

* * Add a single datum to a histogram. We quantize everything by the quantization * factor and add the "end-start" to said histogram. */

Cast a python DNA string into a Ctype int8 matrix

Read rows from the HDF5 data frame that match the tabix query. A tabix query is in the form ('chr1', 100, 200). query_cols is a list of colum

Render the elements of a list.

Given a base position, deletion range and coverage, returns P(Base Deletion | Coverage) if the base position is withing deletion range Otherwise retur

Convert a 2-bit representation of a base to a char

Calculates the probability that the variant was on haplotype 1 or haplotype 2 given the assignment at all other locations.

Get the set of canditate alleles: If this variant is phased, it's the allele corresponding to this phasing state. If unphased, then it's

Find cases where adjacent phase blocks overlap. Ignore overlaps that are less than max_allowable_overlap (useful when working with canoni

Compute the BC-BC overlap matrix, threshold it and convert to a graph, and report large clusters

Given the parent and child genotypes, and which alleles are supposedly being inherited, see if the actual haplotypes are consistent.

Convert within-tile coords to lane coords

copyHist copies f.copyLen bytes from f.hist (f.copyDist bytes ago) to itself. It reports whether the f.hist buffer is full.

Count the number of sequences in a fastq or a fastq file @param filename Path to a valid readeable file @param file_type Should be either

Return a function for filtering groups of barcodes. The returned function will only keep reads that satisfy the following: - their barcode is

Get the first kmer in the sequence

forwardCopy is like the built-in copy function except that it always goes forward from the start, even if the dst and src overlap. It is equivalent to

Read from a dict

Return a BC id for a BC string. bc_id = bc_number + (gem_group - 1) * num_bcs + 1 BC ID 0 is reserved, so the bc_is offset by 1. The GEM group increme

Returns the start and end of the closest region, and whether the region contains the point

Closest region to a given region and distance. direction: 1 means try to get the closest upstream region, -1 means closest downstream,

Get closest variant to target, looking in specified direction (-1 = before target, 1 = after target)

Get logical type of column

Computes the distance between the breakpoints of the BEDPE (read as dataframe) and a set of regions. region_names is a dict (start, stop) -> n

get_ec_table takes a list of codes (either the left 7-mer or the right 9-mer) to generate error correction table, wwhich is a HashMap of n-mer, Correc

Get the data structures required for fragment-based sv-calling. Args: - frag_hist_file: histogram json like the one produced by REPORT_SINGLE_

Return a dataframe with coverage per haplotype. Args: - in_bam: reader for a position sorted bam - ps_h5: HDF5 with phase set coordinates

Get the kmer starting at position pos