Append a value.

Iterate over stored values (values will be unpacked into bytes).

Get the value at position `i`.

NewCigarOp returns a CIGAR operation of the specified type with length n.

* * Read data into a record. Return a pointer to the same record */

The length of the DNA string

String representation of BAM alignment flags: 0x001 - p - Paired 0x002 - P - ProperPair 0x004 - u - Unmapped 0x008 - U - MateUnmapped 0x010 - r - Reve

Return regions overlapping the given interval

End returns the highest query-consuming coordinate end of the alignment. The position returned by End is not valid if r.Cigar.IsValid(r.Seq.Length) is

Value returns v containing the value of the auxilliary tag.

Return a new Lmer with position pos set to base val

Method to write a raw record. Useful for outputing a record directly (such as when combining multiple files)

Write writes data to w, which will eventually write the compressed form of data to its underlying writer.

Get the base at position pos

NewWriter returns a new Writer compressing data at the given level. Following zlib, levels range from 1 (BestSpeed) to 9 (BestCompression); higher lev

Tag returns the Tag representation of the Aux tag ID.

Write writes a compressed form of p to the underlying io.Writer. The compressed bytes are not necessarily flushed until the Writer is closed.

Returns the range of breakpoint coordinates supported by this ReadPair. Note that all positions returned at 0-based. Return value:

Iterator that just returns raw records. Useful for writing to output directly w/o doing additional parsing (such as when combining multiple

Log-probability of observing n reads spanning an observed length of obs_len. Inputs: - nreads: number of observed reads - obs

Reset discards any buffered data and resets the Resetter as if it was newly initialized with the given reader.

Gets a list of "bad" positions on the chromosome and returns a list of "good" ranges. Args: - bad_poses: array of bad positions. - chrom_l

Returns true if read1 and read2 are a pair (of primary reads).

Generate the reverse complement Lmer

* * Bsearch a VCF array for chr+position. If chr+position does not occur in the * array, we return the item immediatly before it, or potentially zer

* * Finalize a BlockBuilder. */

! @function Produce CIGAR 32-bit unsigned integer from CIGAR operation and CIGAR length @param length length of CIGAR @param op_letter CIGAR opera

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

Given the bc log prob vectors for haplotype assignment, calculates the overall probability

Average fraction of on-target reads for a fragment with observed area [start_pos, end_pos) and has true length in the distribution given by le

Close flushes and closes the writer.

* * Serialize, compress, and write an object as JSON data to a loupe file. */

Returns the type of SV that the pair of reads supports.

Generate uniformly random DNA sequences

* * Add a single GenericTrackData object to the Blocked JSON index. * This works by adding data to a temporary holding array. When the array * is l