docs: fix docs

Author: omatheuspimenta

docs/api/philogenics.md

@@ -1,24 +1,21 @@
 <div class="termy" data-termynal data-ty-macos data-ty-title="shell"><span data-ty="input" data-ty-prompt="$">gramep get-mutations --help</span><span data-ty>                                                                                                                                                                                              
-    Usage: gramep get-mutations [OPTIONS]                                                                                                       
+ Usage: gramep get-mutations [OPTIONS]                                                                                                       
 
-    Perform k-mers analysis and optionally generate a report.                                                                                   
-                                                                                                                                                
-   ╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-   │ *  --rpath                         TEXT     📂 Path to reference sequence. [default: None] [required]                                     │
-   │ *  --spath                         TEXT     📂 Path to sequence. [default: None] [required]                                               │
-   │ *  --save-path                     TEXT     📂 Path to save results. [default: None] [required]                                           │
-   │ *  --word                  -w      INTEGER  📏 Word size. [default: None] [required]                                                      │
-   │ *  --step                  -s      INTEGER  ⏭ Step size. [default: None] [required]                                                       │
-   │    --apath                         TEXT     📂 Path to annotation file. [default: None]                                                   │
-   │    --snps-max                      INTEGER  ✔ Max number of SNPs allowed. [default: 1]                                                    │
-   │    --dictonary             -d      TEXT     🧬📖 DNA dictionary. [default: DNA]                                                           │
-   │    --create-report                          📋 Create report.                                                                             │
-   │    --save-kmers                             💾 Save exclusive k-mers.                                                                     │
-   │    --load-exclusive-kmers                   📂 Load exclusive k-mers.                                                                     │
-   │    --exclusive-kmers               TEXT     📂 Path to exclusive k-mers, in .sav format or plain text with one k-mer per line.            │
-   │                                             [default: None]                                                                               │
-   │    --chunk-size                    INTEGER  📦 Chunk size for loading sequences. [default: 100]                                           │
-   │    --help                                   Show this message and exit.                                                                   │
-   ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+ Perform k-mers analysis and optionally generate a report.                                                                                   
+                                                                                                                                             
+╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ *  --rpath                  TEXT     📂 Path to reference sequence. [default: None] [required]                                            │
+│ *  --spath                  TEXT     📂 Path to sequence. [default: None] [required]                                                      │
+│ *  --save-path              TEXT     📂 Path to save results. [default: None] [required]                                                  │
+│ *  --word           -w      INTEGER  📏 Word size. [default: None] [required]                                                             │
+│ *  --step           -s      INTEGER  ⏭ Step size. [default: None] [required]                                                              │
+│    --apath                  TEXT     📂 Path to annotation file. [default: None]                                                          │
+│    --snps-max               INTEGER  ✔ Max number of SNPs allowed. [default: 1]                                                           │
+│    --dictonary      -d      TEXT     🧬📖 DNA dictionary. [default: DNA]                                                                  │
+│    --create-report                   📋 Create report.                                                                                    │
+│    --chunk-size             INTEGER  📦 Chunk size for loading sequences. [default: 100]                                                  │
+│    --help                            Show this message and exit.                                                                          │
+╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+
 
    <br></span></div>

docs/basic_usage.md

@@ -219,7 +219,7 @@ def classify(
     get_kmers: Annotated[
         bool,
         Option(
-            '--should-get-kmers',
+            '--get-kmers',
             help=':straight_ruler: Get only k-mers.',
         ),
     ] = False,

docs/index.md

@@ -78,7 +78,7 @@ def test_classify_get_kmers(caplog):
             SAVE_PATH,
             '--dir-path',
             DIR_PATH,
-            '--should-get-kmers',
+            '--get-kmers',
             '--reference-path',
             REF_PATH,
             '--dictonary',