Add documentation for truncate-msa

README.md

@@ -56,10 +56,20 @@ create-samplesheet --directory /home/nathan/experiment/fastas --msa-dir /home/na
 ├── A1.fasta
 ├── A2.fasta
 └── msas
-    ├── A1.m3a
-    └── A2.m3a
+    ├── A1.a3m
+    └── A2.a3m
 ```
-> **_NOTE:_** Assume that each FASTA file contains a sample with the same name as the file itself. `create-samplesheet` will search for m3a files based on the **sample name** in the FASTA file, not the FASTA filename itself.
+> **_NOTE:_** Assume that each FASTA file contains a sample with the same name as the file itself. `create-samplesheet` will search for a3m files based on the **sample name** in the FASTA file, not the FASTA filename itself.
+
+### truncate-msa
+This command can be used to edit an a3m file to target a specific region of the alignment for special use cases. The module will preserve the first sample of the file, and truncate the remaining entries. 
+```bash
+truncate-msa [ARGS] [INPUT_FILE] [REGION_START] [REGION_END]
+```
+- `-i --in-place` Modify the input file directly, instead of making a new file.
+- `-r --inverse` Invert the output, removing the target region instead.
+- `--version` Output version information.
+- `--debug` Display debug information.
 
 ### TODO
 - [ ] Finish documentation