Updated doc for --ignore-identical

evolbioinfo · May 3, 2021 · 891777d · 891777d
1 parent 22cee62
commit 891777d
Show file tree

Hide file tree

Showing 11 changed files with 146 additions and 146 deletions.
diff --git a/docs/commands/append.md b/docs/commands/append.md
@@ -34,16 +34,16 @@ Flags:
   -o, --output string   Alignment output file (default "stdout")
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical  int Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 #### Examples

diff --git a/docs/commands/consensus.md b/docs/commands/consensus.md
@@ -20,18 +20,18 @@ Flags:
   -o, --output string   Alignment output file (default "stdout")
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --ignore-gaps        Ignore gaps (except if only gaps on the column)
-      --ignore-n           Ignore Ns  (except if only N on the column)
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --ignore-gaps           Ignore gaps (except if only gaps on the column)
+      --ignore-n              Ignore Ns  (except if only N on the column)
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 #### Examples

diff --git a/docs/commands/extract.md b/docs/commands/extract.md
@@ -57,16 +57,16 @@ Flags:
       --translate int        Wether the extracted sequence will be translated (only if input alignment is nucleotide). <0: No translation, 0: Std code, 1: Vertebrate mito, 2: Invertebrate mito (default -1)
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 #### Examples

diff --git a/docs/commands/mask.md b/docs/commands/mask.md
@@ -60,16 +60,16 @@ Flags:
                          (start and length are ignored)
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical  int Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 #### Examples

diff --git a/docs/commands/revcomp.md b/docs/commands/revcomp.md
@@ -22,16 +22,16 @@ Flags:
       --unaligned       Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored)
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 

diff --git a/docs/commands/sample.md b/docs/commands/sample.md
@@ -22,17 +22,17 @@ Flags:
   -h, --help   help for sample
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
-      --seed int           Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
+      --seed int              Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
 ```
 * seqs command
 ```
@@ -47,17 +47,17 @@ Flags:
       --unaligned        Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored)
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
-      --seed int           Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical  int Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
+      --seed int              Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
 ```
 
 * sites command
@@ -73,17 +73,17 @@ Flags:
   -o, --output string   Alignment output file (default "stdout")
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
-      --seed int           Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
+      --seed int              Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
 ```
 
 * rarefy command
@@ -100,17 +100,17 @@ Flags:
       --unaligned        Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored)
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
-      --seed int           Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
+      --seed int              Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
 ```
 
 #### Examples

diff --git a/docs/commands/split.md b/docs/commands/split.md
@@ -21,16 +21,16 @@ Flags:
       --partition string    File containing definition of the partitions (default "none")
 
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string     int  Alignment input file (default "stdin")
+      --auto-detect      int  Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal          int  Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict     int  Strict phylip input format (only used with -p)
+  -x, --nexus            int  Alignment is in nexus? default fasta
+      --no-block         int  Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line         int  Write Phylip sequences on 1 line (only used with -p)
+      --output-strict    int  Strict phylip output format (only used with -p)
+  -p, --phylip           int  Alignment is in phylip? default fasta
 ```
 
 #### Examples

diff --git a/docs/commands/stats.md b/docs/commands/stats.md
@@ -88,16 +88,16 @@ Available Commands:
   taxa        Prints index (position) and name of taxa of the alignment file
 			  
 Global Flags:
-  -i, --align string       Alignment input file (default "stdin")
-      --auto-detect        Auto detects input format (overrides -p, -x and -u)
-  -u, --clustal            Alignment is in clustal? default fasta
-      --ignore-identical   Ignore duplicated sequences that have the same name and same sequences
-      --input-strict       Strict phylip input format (only used with -p)
-  -x, --nexus              Alignment is in nexus? default fasta
-      --no-block           Write Phylip sequences without space separated blocks (only used with -p)
-      --one-line           Write Phylip sequences on 1 line (only used with -p)
-      --output-strict      Strict phylip output format (only used with -p)
-  -p, --phylip             Alignment is in phylip? default fasta
+  -i, --align string          Alignment input file (default "stdin")
+      --auto-detect           Auto detects input format (overrides -p, -x and -u)
+  -u, --clustal               Alignment is in clustal? default fasta
+      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
+      --input-strict          Strict phylip input format (only used with -p)
+  -x, --nexus                 Alignment is in nexus? default fasta
+      --no-block              Write Phylip sequences without space separated blocks (only used with -p)
+      --one-line              Write Phylip sequences on 1 line (only used with -p)
+      --output-strict         Strict phylip output format (only used with -p)
+  -p, --phylip                Alignment is in phylip? default fasta
 ```
 
 #### Examples