Corrected doc

cmd/stats.go

@@ -35,19 +35,29 @@ If --per-sequences is given, then it will print the following stats, for each se
 2. Number of consecutive gaps at the beginning of the sequence;
 3. Number of consecutive gaps at the end of the sequence;
 4. Number of gaps unique to the sequence (present in no other sequence);
-	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	If --count-profile is given along, then the output will be : unique\tnew\tboth, with:
 	- 4a unique: # gaps that are unique in each sequence in the alignment
 	- 4b new: # gaps that are new in each sequence compared to the profile
 	- 4c both: # gaps that are unique in each sequence in the alignment and that are new compared the profile
 5. Number of gap opennings (streches of gaps are counted once);
 6. Number of Unique mutations;
-	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	If --count-profile is given along, then the output will be : unique\tnew\tboth, with:
 	- 6a unique: # mutations that are unique in each sequence in the alignment
 	- 6b new: # mutations that are new in each sequence compared to the profile
 	- 6c both: # mutations that are unique in each sequence in the alignment and that are new compared the profile
 7. Number of mutations compared to a reference sequence (given with --ref-sequence, otherwise, no column);
 8. Length of the sequence without gaps;
 9..n Number of occurence of each character (A,C,G, etc.).
+
+Note that --count-profile takes a tab separated file such as given by the command 
+goalign stats char --per-sites
+
+site  A C G T
+0 nA  nC  nG  nT
+1...
+...
+n...
+
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var aligns *align.AlignChannel

cmd/stats_gaps.go

@@ -27,14 +27,22 @@ var statGapsCmd = &cobra.Command{
 	- If --from-start is specified, then counts only gaps at sequence starts;
 	- If --from-end is specified, then counts only gaps at sequence ends;
 	- If --unique is specified, then counts only gaps that are unique in their column. 
-	  If --profile is given along --unique, then the output will be : unique\tnew\tboth, with:
+	  If --count-profile is given along with --unique, then the output will be : unique\tnew\tboth, with:
 		- unique: # gaps that are unique in each sequence in the alignment
 		- new: # gaps that are new in each sequence compared to the profile
 		- both: # gaps that are unique in each sequence in the alignment and that are new compared the profile
 	- If --openning is specified, then counts only gap openning (streches of gaps are counted once)
 	- Otherwise, counts total number of gaps
 	for the given sequence.
 
+	Note that --count-profile takes a tab separated file such as the one given by the command 
+	goalign stats char --per-sites
+
+	site  A C G T
+	0 nA  nC  nG  nT
+	1...
+	...
+	n...
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var aligns *align.AlignChannel

cmd/stats_mutations.go

@@ -21,7 +21,7 @@ var statMutationsCmd = &cobra.Command{
 
 	- If --unique is specified, then counts only mutations (characters) that are unique in their column
 	for the given sequence.
-	If --profile is given along --unique, then the output will be : unique\tnew\tboth, with:
+	If --count-profile is given along with --unique, then the output will be : unique\tnew\tboth, with:
 		- unique: # mutations that are unique in each sequence in the alignment
 		- new: # mutations that are new in each sequence compared to the profile
 		- both: # mutations that are unique in each sequence in the alignment and that are new compared the profile
@@ -32,6 +32,16 @@ var statMutationsCmd = &cobra.Command{
 
 	It does not take into account '-' and 'N' as unique mutations, and does not take into account '-' and 'N' as mutations compared 
 	to a reference sequence.
+
+	Note that --count-profile takes a tab separated file such as the one given by the command 
+	goalign stats char --per-sites
+
+	site  A C G T
+	0 nA  nC  nG  nT
+	1...
+	...
+	n...
+
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var aligns *align.AlignChannel

docs/commands/stats.md

@@ -19,15 +19,15 @@ If `--per-sequences` option is given, then prints statistics for all sequences i
 4. gapsend: Number of consecutive gaps at the end;
 5. gapsuniques: Number of gaps unique to that sequence;
 
-	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	If --count-profile is given, then the output will be : unique\tnew\tboth, with:
 	- 5a unique: # gaps that are unique in each sequence in the alignment
 	- 5b new: # gaps that are new in each sequence compared to the profile
 	- 5c both: # gaps that are unique in each sequence in the alignment and that are new compared the profile
 
 6. gapsopenning: Number of streches of gaps;
 7. mutuniques: Number of unique mutations;
 
-	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	If --count-profile is given, then the output will be : unique\tnew\tboth, with:
 	- 7a unique: # mutations that are unique in each sequence in the alignment
 	- 7b new: # mutations that are new in each sequence compared to the profile
 	- 7c both: # mutations that are unique in each sequence in the alignment and that are new compared the profile
@@ -36,6 +36,15 @@ If `--per-sequences` option is given, then prints statistics for all sequences i
 8. length: Lenght of the unaligned sequence;
 9. A	C	G	T...: Number of occurence of each character.
 
+Note that `--count-profile`takes a tab separated file such as given by the command `goalign stats char --per-sites`:
+
+```
+site  A C G T
+0 nA  nC  nG  nT
+1...
+...
+n
+```
 
 Different sub-commands:
 * `goalign stats alleles`: Prints the average number of alleles per site of the alignment;