Added docs for fisher test (MLE algorithm).

Added version of VarDict to expected files in integration test.

Author: PolinaBevad

src/main/java/com/astrazeneca/vardict/data/fishertest/FisherExact.java

@@ -54,6 +54,7 @@ public FisherExact(int refFwd, int refRev, int altFwd, int altRev) {
         calculatePValue();
     }
 
+    // Density of the central hypergeometric distribution on its support: store for once as this is needed quite a bit.
     private List<Double> logdcDhyper(int m, int n, int k) {
         List<Double> logdc = new ArrayList<>();
 
@@ -73,6 +74,14 @@ private List<Double> logdcDhyper(int m, int n, int k) {
         return logdc;
     }
 
+    // Determine the MLE for ncp by solving E(X) = x, where the expectation is with respect to H.
+    // Note that in general the conditional distribution of x given the marginals is a non-central hypergeometric
+    // distribution H with non-centrality parameter ncp, the odds ratio.
+    // The null conditional independence is equivalent to the hypothesis that the odds ratio equals one. `Exact`
+    // inference can be based on observing that in general, given all marginal totals fixed, the first element of the
+    // contingency table has a non-central hypergeometric distribution with non-centrality parameter given by odds
+    // ratio (Fisher, 1935). The alternative for a one-sided test is based on the odds ratio, so alternative =
+    // 'greater' is a test of the odds ratio being bigger than or = 1.
     private Double mle(double x) {
         double eps = Math.ulp(1.0);
         if (x == lo) return 0.0;

tests/integration/expected/vardict.paired.vcf

@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.3
+##source=VarDict_v1.8.0
 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

tests/integration/expected/vardict.simple.vcf

@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.3
+##source=VarDict_v1.8.0
 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">