Added option --pos to goalign shuffle swap

cmd/swap.go

@@ -8,6 +8,7 @@ import (
 )
 
 var swapRate float64
+var swapPos float64
 
 // swapCmd represents the swap command
 var swapCmd = &cobra.Command{
@@ -18,7 +19,13 @@ It may take Fasta or Phylip input alignment.
 
 If the input alignment contains several alignments, will process all of them
 
-The only option is to specify the rate of swap.
+It will exchange sequences from one seq to another of the alignment.
+if rate>=0 and rate<=1 then it takes rate/2 sequences and exchanges sequences
+with rate/2 other sequences, from a random position.
+
+If given pos >=0 and <=1 then take this position (relative to align length)
+ instead of a random one.
+
 A rate of 0.5 will swap 25% of the sequences with 
 other 25% of the sequences at a random position.
 
@@ -50,7 +57,10 @@ goalign shuffle swap -i align.fasta -r 0.5
 		defer utils.CloseWriteFile(f, shuffleOutput)
 
 		for al := range aligns.Achan {
-			al.Swap(swapRate)
+			if err = al.Swap(swapRate, swapPos); err != nil {
+				io.LogError(err)
+				return
+			}
 			writeAlign(al, f)
 		}
 
@@ -66,4 +76,5 @@ func init() {
 	shuffleCmd.AddCommand(swapCmd)
 
 	swapCmd.PersistentFlags().Float64VarP(&swapRate, "rate", "r", 0.5, "Rate of Swap sequences (>=0 and <=1)")
+	swapCmd.PersistentFlags().Float64Var(&swapPos, "pos", -1, "Position of the break point (0<pos<1, relative to alignment length), default: -1 (means random)")
 }

docs/commands/shuffle.md

@@ -23,7 +23,7 @@ This command adds different type of noises in an input alignment, with these sub
 	```
 * `goalign shuffle seqs` : Shuffles sequence order in alignment. It does not add any noise in the alignment.
 * `goalign shuffle sites`: Shuffles vertically a given proportion of the alignment sites. Optionnaly, it is possible to shuffle vertically an additional (same) proportion of the remaining intact sites for a given proportion of the sequences (~rogues)
-* `goalign shuffle swap` : Swaps a given portion of the sequences in the input alignment. The only option to specify is the swap rate. A rate of 0.5 will swap 25% of the sequences with other 25% of the sequences from a random position to the end. Example swaping 50% of sequences:
+* `goalign shuffle swap` : Swaps a given portion of the sequences in the input alignment. The option `-r` specifies the swap rate. A rate of 0.5 will swap 25% of the sequences with other 25% of the sequences from a random position to the end. The option `--pos` specifies the position from which to swap the sequences. If pos <0 or >1, the, the position is random. Example swaping 50% of sequences at a random position:
   ```
   s1 CCCCCCCCCCCCCC    s1 CCCCCCCCCCCCCC
   s2 AAAAAAAAAAAAAA => s2 AAAAAATTTTTTTT
@@ -137,6 +137,7 @@ Usage:
   goalign shuffle swap [flags]
 
 Flags:
+  --pos float    Position of the break point (0<pos<1, relative to alignment length), default: -1 (means random) (default -1)
   -r, --rate float   Rate of Swap sequences (>=0 and <=1) (default 0.5)
 
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