Raw, uncorrected barcode sequence

Returns an interator over a fastq file tha produces (name, seq, qual) If paired_end, returns both reads (assuming interleaving fastq)

Yields groups of rows corresponding to each section of an Illumina sample sheet. The format will be { 'section': (name of sectio

Updates the new log probabilities

write a single read

Writes a single read to a fastq file

* * .Loupe-ify a BAM file. This involves copying the "interesting" data from the bam * file into the .loupe data section using the BlockedIndex mec

* * Compare the (correct) sorting order of two chromosomes. The order that this * yields is: * chr1, chr2, ... chr10, chr11, .. chr20, chr21, .. ch

@Function: Calculate the length of the previous cigar operator and store it in new_cigar and new_cigar_string. Clean up in_M (false), in_X (false), le

Consumes returns the CIGAR operation alignment consumption characteristics for the CigarOpType.

to make reading easy

Len returns the number of positions affected by the CigarOp CIGAR operation.

* Create a new loupe file. |headerspace| is the number of bytes to reserve at the begining of the file for the preamble */

* * Open a file to store the data section of a blocked index and prepare a BlockIndexBuilder * data structure. * The generate approach here is to c

* * Implement a "ReRead" function. It reads from a Reader and it retries * if it gets fewer bytes than it wanted. It will always completely fill *

* * Read a generic bed file into a GenericTrackData array. * fieldnames is an array of strings that specify the names of the fields * after the fir

* * Sort (destructively) an array of pointers to intervals. */

to make writing reads easy

* * Write a BundledTrackData instance to a file. */

Either: -- overwrite the cell at row[idx] if it exists -- pad the row until you can append the idx col, and then write it

Calculates the log probability matrices for blocks

Creates a bam file with given chromosome names and lengths. template is an existing bam file. If it is specified, chrom_names and chrom_lengths

Creates the initial data structure to hold the bc log probabilities for a given hap assignment Stored as: key: tuple of haplotype ass

Build a key from a flowcell and lane

Find the longest prefix of read such that all bases in the final kmer have qv >= min_qual Should implement https://github.com/10XDev/supernova/blob/ma

Return a fresh Dir with the opposite direction

Returns a tuple (P, S) where: P is an array with log-probability of length being L for all L in frag_sizes that are > min_frag_len S[i] i

Update this Huffman Code object to be the minimum code for the specified frequency count. freq An array of frequencies, in which frequency[i] gives

GZIP (RFC 1952) is little-endian, unlike ZLIB (RFC 1950).

Returns the best haplotype assignments over all blocks Potential improvement: Calculate on larger (overlapping) blocks and only retai

Log-probability of a ReadPair being mapped correctly

Converts the HAPS info field into a VCF commpatible genotype call

Read the next Huffman-encoded symbol from f according to h.

Decode a single Huffman block from f. hl and hd are the Huffman states for the lit/length values and the distance values, respectively. If hd == nil,

Clusters reads within window distance of each other.