Merge pull request #13 from jermp/dev

Dev

README.md

@@ -17,18 +17,23 @@ Please, cite these papers if you use SSHash.
 For a dictionary of n k-mers,
 two basic queries are supported:
 
-- i = Lookup(g), where i is in [0,n) if the k-mer g is found in the dictionary or i = -1 otherwise;
-- g = Access(i), where g is the k-mer associated to the identifier i.
+- i = **Lookup**(g), where i is in [0,n) if the k-mer g is found in the dictionary or i = -1 otherwise;
+- g = **Access**(i), where g is the k-mer associated to the identifier i.
 
 If also the weights of the k-mers (their frequency counts) are stored in the dictionary, then the dictionary is said to be *weighted* and it also supports:
 
-- w = Weight(i), where i is a given k-mer identifier and w is the weight of the k-mer.
+- w = **Weight**(i), where i is a given k-mer identifier and w is the weight of the k-mer.
 
-A membership query (determine if a given k-mer is present in the dictionary or not) is, therefore, supported by means of the Lookup query.
-The dictionary can also stream through all k-mers of a given DNA file
+Other supported queries are:
+
+- **Membership Queries**: determine if a given k-mer is present in the dictionary or not.
+- **Streaming Queries**: stream through all k-mers of a given DNA file
 (.fasta or .fastq formats) to determine their membership to the dictionary.
+- **Navigational Queries**: given a k-mer g[1..k] determine if g[2..k]+x is present (forward neighbourhood) and if x+g[1..k-1] is present (backward neighbourhood), for x = A, C, G, T ('+' here means string concatenation).
+SSHash internally stores a set of strings, called *contigs* in the following, each associated to a distinct identifier.
+If a contig identifier is specified for a navigational query (rather than a k-mer), then the backward neighbourhood of the first k-mer and the forward neighbourhood of the last k-mer in the contig are returned.
 
-**NOTE**: The Lookup query assumes that two k-mers being the *reverse complement* of each other are the same.
+**NOTE**: It is assumed that two k-mers being the *reverse complement* of each other are the same.
 
 #### Table of contents
 * [Compiling the Code](#compiling-the-code)
@@ -357,7 +362,7 @@ Below the complete query reports.
 Author
 ------
 
-Giulio Ermanno Pibiri - <giulio.ermanno.pibiri@isti.cnr.it>
+[Giulio Ermanno Pibiri](https://jermp.github.io) - <giulioermanno.pibiri@unive.it>
 
 References
 -----