From e701fa49e7fc5f8aaef4ba680e012a14bce00c4b Mon Sep 17 00:00:00 2001
From: Rolf Schröder <rolf.schr@gmail.com>
Date: Sat, 12 Jun 2021 16:12:07 +0200
Subject: feat(plugins): New plugins for samtools and bedtools (#3574)

* Add first impl of samtools autocompletion

* Just autocomplete with files all the time

* Add init impl of bedtools completion

* Add readme.md for bedtools plugin

* Add readme for samtools

Co-authored-by: Rolf Schroeder <rolf.schroeder@centogene.com>
---
 plugins/samtools/README.md |  5 +++++
 plugins/samtools/_samtools | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 plugins/samtools/README.md
 create mode 100644 plugins/samtools/_samtools

(limited to 'plugins/samtools')

diff --git a/plugins/samtools/README.md b/plugins/samtools/README.md
new file mode 100644
index 000000000..f4baf41f7
--- /dev/null
+++ b/plugins/samtools/README.md
@@ -0,0 +1,5 @@
+# Samtools plugin
+
+This plugin adds support for [samtools](http://www.htslib.org/):
+
+* Adds autocomplete options for all samtools sub commands.
diff --git a/plugins/samtools/_samtools b/plugins/samtools/_samtools
new file mode 100644
index 000000000..ddb002ae2
--- /dev/null
+++ b/plugins/samtools/_samtools
@@ -0,0 +1,40 @@
+#compdef samtools
+#autoload
+
+local curcontext="$curcontext" state line ret=1
+local -a _files
+
+_arguments -C \
+  '1: :->cmds' \
+  '2:: :->args' && ret=0
+
+case $state in
+  cmds)
+    _values "samtools command" \
+        "view[SAM<->BAM conversion]" \
+        "sort[sort alignment file]" \
+        "mpileup[multi-way pileup]" \
+        "depth[compute the depth]" \
+        "faidx[index/extract FASTA]" \
+        "tview[text alignment viewer]" \
+        "index[index alignment]" \
+        "idxstats[BAM index stats (r595 or later)]" \
+        "fixmate[fix mate information]" \
+        "flagstat[simple stats]" \
+        "calmd[recalculate MD/NM tags and '=' bases]" \
+        "merge[merge sorted alignments]" \
+        "rmdup[remove PCR duplicates]" \
+        "reheader[replace BAM header]" \
+        "cat[concatenate BAMs]" \
+        "bedcov[read depth per BED region]" \
+        "targetcut[cut fosmid regions (for fosmid pool only)]" \
+        "phase[phase heterozygotes]" \
+        "bamshuf[shuffle and group alignments by name]"
+    ret=0
+    ;;
+  *)
+    _files
+    ;;
+esac
+
+return ret
-- 
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