Requires len < 240.

A subroutine for CityHash128(). Returns a decent 128-bit hash for strings of any length representable in signed long. Based on City and Murmur.

Hash 128 input bits down to 64 bits of output. This is intended to be a reasonably good hash function.

This probably works well for 16-byte strings as well, but it may be overkill in that case.

Return an 8-byte hash for 33 to 64 bytes.

Equivalent to Rotate(), but requires the second arg to be non-zero. On x86-64, and probably others, it's possible for this to compile to a single inst

Create a graph with n vertices and zero edges. */

* returnes the representative of the equivalence class */

Add a k-mer to this collection. */

Add contiguity stats to database */

Add distance estimates to a path. * @param g0 the original graph * @param g1 the transformed graph */

Add distances to a path. */

* Load the kmers of a given sequence into a Bloom filter. */

Add missing overlap edges. For each vertex u with at least two * outgoing edges, (u,v1) and (u,v2), add the edge (v1,v2) if v1 < v2, * and add the e

Adds all edges described in the vector eds. */

Add the overlaps of vseq to the graph. */

Instantiates a new pipe and adds it to this PipeMux. */

Add prefix overlaps to the graph. */

Add suffix overlaps to the graph. */

Read contigs and add vertices to the graph. */

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

Align multiple sequences. */

Align read pairs. */

Align multiple sequences using DIALIGN-TX. */

Resolve ambiguous region using multiple alignment of all paths in * `solutions'. */

Align the specified pair of sequences. * @return the number of matches and size of the consensus */

Resolve ambiguous region using pairwise alignment * (Needleman-Wunsch) ('solutions' contain exactly two paths, from a * source contig to a dest cont

* adds the given diagional to the given alignment and updates the * datastructure (i.e. frontiers). The given diag must be consistent * to the given

* Return true if a sequence consists entirely of ACGT chars * (case insensitive). */

Return the bitwise-and of the specified ambiguity codes. */

Assemble overlapping paths. */

Assemble the path overlap graph. */

Attach the specified observer. */

Return the last name in this dictionary. */

Find the optimal alignment from the score matrices. * @param[out] align the alignment * @return the number of matches */

Broadcast a message. */

* Build Bloom filter file of type 'konnector', 'rolling-hash' or 'counting', as * per `-t` option. */

* Build a histogram of the lengths of the assembled paths and unused contigs. * Note: This function does not account for the ammount of overlap betwe

Builds the pile up of all reads based on the alignments and * read sequence */

Build a Counting Bloom filter (used by `abyss-bloom-dbg`) */

Build an FM index of the specified file. */

Build an FM index of the specified file. */

Build an FM index of the specified file. */

Build the FM index from the BWT. */

Return the length histogram. */

Build contig overlap graph for paired de Bruijn graph */

Build the path overlap graph. */

Build a rolling-hash based Bloom filter (used by pre 2.2.0 `abyss-bloom-dbg`) */

* Build the scaffold length histogram. * @param g The graph g is destroyed. */

* calculates the score distribution up to the given maximum diaglen * * The pointer returned and the included dist pointer has to be deallocted *

Calculate a k-mer coverage threshold from the given k-mer coverage * histogram. */

Call a consensus base */

Check that the indexes are up to date. */

Check that the indexes are up to date. */

Return the tag of the received message or APM_NONE if no message * has been received. If a message has been received, this call should * be followed

Remove all in edges from vertex v. */

Remove all out edges from vertex u. */

Remove all out edges from vertex u. */

Remove all edges to and from vertex u from this graph. * O(V+E) */