From d44eca19ce753bd934a7b9602ccd1e9d4a7e3d3a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Mon, 22 Feb 2016 15:29:22 +0100
Subject: [PATCH] Added the possibility to use standard input as input for
 sequence datasets

---
 libfasta/sequence.c | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/libfasta/sequence.c b/libfasta/sequence.c
index 4f903d9..2cf3d10 100644
--- a/libfasta/sequence.c
+++ b/libfasta/sequence.c
@@ -223,7 +223,13 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
     fastaSeqCount allseqs;
     int32_t discarded=0;
 
-    fp = file_open(fileName, TRUE);
+    if ((fileName == NULL) || (strcmp(fileName, "-") == 0))
+    	fp = stdin;
+    else
+    {
+    	fp = file_open(fileName, TRUE);
+    	exitIfEmptyFile(fp);
+    }
 
     if (fp == NULL)
     {
@@ -231,8 +237,6 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
             exit(1);
     }
 
-    exitIfEmptyFile(fp);
-
     seqPtrAr = (fastaSeqPtr) util_malloc(slots*sizeof(fastaSeq), __FILE__, __LINE__);
 
     seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC);