Added comments and doc

align/align.go

@@ -954,6 +954,10 @@ func (a *align) Concat(c Alignment) (err error) {
 	return err
 }
 
+/*
+ Returns the number of variable sites in the alignment.
+It does not take into account gaps and other charactes like "."
+*/
 func (a *align) NbVariableSites() int {
 	nbinfo := 0
 	for site := 0; site < a.Length(); site++ {

cmd/stats.go

@@ -14,8 +14,11 @@ var statsCmd = &cobra.Command{
 	Short: "Prints different characteristics of the alignment",
 	Long: `Prints different characteristics of the alignment.
 
-1 - Length
-2 - Number of sequences
+1. Length of alignment;
+2. Number of sequences;
+3. Average number of alleles per site;
+4. Number of variables sites (does ot take into account gaps or special characters);
+5. Character frequencies.
 
 If the input alignment contains several alignments, will process all of them
 

docs/commands/stats.md

@@ -8,7 +8,8 @@ Without any subcommand, it prints the following information:
 1. Length of alignment;
 2. Number of sequences;
 3. Average number of alleles per site;
-4. Character frequencies.
+4. Number of variables sites (does ot take into account gaps or special characters);
+5. Character frequencies.
 
 Different sub-commands:
 * `goalign stats alleles`: Prints the average number of alleles per site of the alignment;