From c9893fdb8525108c2ae0112a899d66b46a994488 Mon Sep 17 00:00:00 2001
From: Christopher Dunn <cdunn@pacificbiosciences.com>
Date: Wed, 26 Sep 2018 08:03:12 -0700
Subject: [PATCH] Fix typo writing to stdout

With "-f" flag, the "rm *.las" lines went to stdout rather
than into ".RM.OPT" script.

https://github.com/PacificBiosciences/pbbioconda/issues/14
---
 HPC.daligner.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/HPC.daligner.c b/HPC.daligner.c
index 656afa3..6a0992d 100644
--- a/HPC.daligner.c
+++ b/HPC.daligner.c
@@ -496,7 +496,7 @@ void daligner_script(int argc, char *argv[])
         for (i = 1; i <= lblock; i++)
           { if (DON)
               fprintf(out,"cd work%d; ",j);
-            printf("rm %s.%d.%s.*.las",root,i,root);
+            fprintf(out,"rm %s.%d.%s.*.las",root,i,root);
             if (DON)
               fprintf(out,"; cd ..");
             fprintf(out,"\n");