From 55345d66487f5482a74cc869a2aef484fde017ee Mon Sep 17 00:00:00 2001
From: Rolf Schroeder <rolf.schroeder@centogene.com>
Date: Fri, 30 Jan 2015 12:06:49 +0100
Subject: [PATCH] Add first impl of samtools autocompletion

---
 plugins/samtools/_samtools | 46 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 plugins/samtools/_samtools

diff --git a/plugins/samtools/_samtools b/plugins/samtools/_samtools
new file mode 100644
index 00000000..0a62e2b0
--- /dev/null
+++ b/plugins/samtools/_samtools
@@ -0,0 +1,46 @@
+#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
+    ;;
+  args)
+    case $line[1] in
+      view|tview)
+        _files=(`find . -name \*.sam -o -name \*.bam | grep '\./[^/]*am' | sed 's/\.\///'`)
+        [[ -n "$_files" ]] && _values 'configs' $_files
+        ret=0
+        ;;
+    esac
+    ;;
+esac
+
+return ret