From 4708cec3da5045e39a7a01f096cb9a5ba9c5206c Mon Sep 17 00:00:00 2001
From: Daniel Park <dpark@broadinstitute.org>
Date: Tue, 12 Dec 2023 11:06:49 -0500
Subject: [PATCH] add multi-file version

---
 scripts/mcp_and_decompress.sh | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100755 scripts/mcp_and_decompress.sh

diff --git a/scripts/mcp_and_decompress.sh b/scripts/mcp_and_decompress.sh
new file mode 100755
index 0000000..5e4d223
--- /dev/null
+++ b/scripts/mcp_and_decompress.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+INFILES=${@:1:$#-1}
+OUTDIR=${@:$#}
+
+for INFILE in $INFILES; do
+    if [[ $INFILE == *.gz ]]; then
+        OUTFNAME=$(basename $INFILE .gz)
+        pigz -dc $INFILE > "$OUTDIR/$OUTFNAME"
+    elif [[ $INFILE == *.zst ]]; then
+        OUTFNAME=$(basename $INFILE .zst)
+        zstd -d $INFILE -o "$OUTDIR/$OUTFNAME"
+    else
+        OUTFNAME=$(basename $INFILE)
+        cp $INFILE "$OUTDIR/$OUTFNAME"
+    fi
+done