From 09595b199d09cef2bc5916d997fc22f9308de1fb Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 18 May 2021 21:31:06 +0200
Subject: [PATCH] closes #151

---
 HISTORY.md     |  1 +
 paste/paste.go | 32 ++++++++++++++++++++++----------
 2 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/HISTORY.md b/HISTORY.md
index 85dccf3..af921be 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -2,6 +2,7 @@ v0.2.7
 ======
 + use csi index for bams to support larger organisms
 + fix ordering of error-checking (#146)
++ support for longer file-lists (#151)
 
 v0.2.6
 ======
diff --git a/paste/paste.go b/paste/paste.go
index a7321e2..163ae53 100644
--- a/paste/paste.go
+++ b/paste/paste.go
@@ -98,17 +98,27 @@ func Main() {
 
 	cli := cliargs{OutDir: "./"}
 	arg.MustParse(&cli)
-
-	wg := &sync.WaitGroup{}
-	wg.Add(len(cli.VCFs))
-	procs := 5
-
-	go count(wg, procs, cli.VCFs)
-
 	outvcf := fmt.Sprintf(filepath.Join(cli.OutDir, cli.Name) + ".smoove.square.vcf.gz")
-	shared.Slogger.Printf("squaring %d files to %s", len(cli.VCFs), outvcf)
+	var wg *sync.WaitGroup
+
+	// TODO: check files in list
+	if !strings.HasSuffix(cli.VCFs[0], ".list") {
+		wg = &sync.WaitGroup{}
+		wg.Add(len(cli.VCFs))
+		procs := 5
+
+		go count(wg, procs, cli.VCFs)
+		shared.Slogger.Printf("squaring %d files to %s", len(cli.VCFs), outvcf)
+	} else {
+		shared.Slogger.Printf("squaring files from %s to %s", cli.VCFs[0], outvcf)
+	}
+
 	args := []string{"merge", "-o", outvcf, "-O", "z", "--threads", "3"}
-	args = append(args, cli.VCFs...)
+	if strings.HasSuffix(cli.VCFs[0], ".list") && len(cli.VCFs) == 1 {
+		args = append(args, []string{"-l", cli.VCFs[0]}...)
+	} else {
+		args = append(args, cli.VCFs...)
+	}
 
 	p := exec.Command("bcftools", args...)
 	p.Stderr = shared.Slogger
@@ -118,5 +128,7 @@ func Main() {
 		log.Fatal(err)
 	}
 	shared.Slogger.Printf("wrote squared file to %s", outvcf)
-	wg.Wait()
+	if wg != nil {
+		wg.Wait()
+	}
 }