Update samtools

yamaton · Oct 30, 2024 · 468095d · 468095d
1 parent 93baa36
commit 468095d
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Showing 6 changed files with 19 additions and 11 deletions.
diff --git a/bio.json.gz b/bio.json.gz
diff --git a/bio/bash b/bio/bash
diff --git a/bio/fish b/bio/fish
diff --git a/bio/json/samtools.json b/bio/json/samtools.json
diff --git a/bio/yaml/samtools.yaml b/bio/yaml/samtools.yaml
@@ -2256,12 +2256,20 @@ subcommands:
         description: provide the sample tag name from the @RG line [SM].
       - names:
           - -o
-        argument: FILE output file .
-        description: -f FILE load an indexed fasta file in the collection of references. Can be used multiple times. Add an extra column with the path to the reference file.
+        argument: FILE
+        description: output file [stdout].
       - names:
-          - -o
-        argument: FILE output file stdout.
-        description: -f FILE load an indexed fasta file in the collection of references. Can be used multiple times. Add an extra column with the path to the reference file.
+          - -f
+        argument: FILE
+        description:  load an indexed fasta file in the collection of references. Can be used multiple times. Add an extra column with the path to the reference file.
+      - names:
+          - -F
+        argument: FILE
+        description:  read a file containing the paths to indexed fasta files. One path per line.
+      - names:
+          - -X
+        argument: ""
+        description:  use a custom index file.
 version: samtools 1.21
 tldr: |
   > Tools for handling high-throughput sequencing (genomics) data.

diff --git a/bio/zsh b/bio/zsh