Flush the message buffer by sending all messages that are queued

return k-mer at current position */

Return k-mer size used by Bloom filter. */

* print error message and exit */

Return the number of vertices. */

Find the vertex with the specified name. */

Return number of hash functions used by Bloom filter */

Return the number of bytes used by the data and stack segments. * @return -1 on error */

Return the Hamming weight of x. */

Add data to the buffer/queue. */

Return the complement of the specified base. * The reverse of a single base is a no-op. * If the assembly is in colour space, this is a no-op. */

Return a string representation of the k-mer pair, using an accurate number * of Ns to separate the two k-mer. */

Return the base enumeration for the specified character. */

Return the next unique contig name. */

Return the first nucleotides. */

Return the reverse complement of the specified k-mer. */

SIDE EFFECT, releases original memory held by string */

Cast to an integer. */

Remove all the edges and vertices from this graph. */

* frees the memory of the given diagonal and the included seq_parts */

Return the length of a the k-mer pair, including the gap. */

* Read data from a stream with bit-level resolution. * * @param in input byte stream * @param dest destination of copied data (byte array) * @para

Unlock this dictionary. */

Returns an iterator-range to the adjacent vertices. */

Return wheter the specified base is adjacent. */

Clean up by erasing sequences flagged as deleted. * @return the number of sequences erased */

Remove all elements from this set. */

If the specified file is compressed, return a pipe that * uncompresses it. */

Add the object with the specified index to this set. */

Not a network sequence collection. Nothing to do.

Reverse-complement this sequence. */

* Compute hash values for next k-mer to the right and * update internal state. * @param kmer current k-mer * @param nextKmer k-mer we are rollin

* test function that constructs an arbitrary consistent alignment.this function * is used to check the the correctness of adapt_diag() and align_diag

Return the estimated false positive rate */

Return a 16-byte hash for 48 bytes. Quick and dirty. Callers do best to use "random-looking" values for a and b.

Return the SI representation of a number in bytes. */

Return true if checkpoint creation is enabled */

* factory method that creates a diagonal from the given sequence parts * * The pointer returned has to be deallocted explicitely from memory. */

Return the mean of this distribution. */

Return the median of this distribution. */

Return the specified number formatted as a percent. */

Get data and remove it from the buffer. */

Receive and dispatch packets. * @return the number of packets received */

return RollingHash object for current state */

Terminate this branch with the specified reason. */

Return the terminal nucleotides. */

* Convert a quantity with SI units to the equivalent floating * point number. */

Return the state of this branch. */

Return whether any branches of this group are active. */

Return whether this kmer has more than one adjacent kmer. */