From 295169d0054ed934aaac2f694ae007aa5d752719 Mon Sep 17 00:00:00 2001
From: Thomas Flouris <flouris@gmail.com>
Date: Tue, 11 Jul 2017 17:09:54 +0100
Subject: [PATCH] fixed issue with phylip parsing when header (seqs length)
 ends with CRLF

---
 src/phylip.c | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/src/phylip.c b/src/phylip.c
index 3b0bea4..fa3b74d 100644
--- a/src/phylip.c
+++ b/src/phylip.c
@@ -175,13 +175,14 @@ static int args_getint(const char * arg, int * len)
   return temp;
 }
 
-static int whitechar(char c)
+static int whitespace(char c)
 {
-  if (c == ' ' || c == '\t') return 1;
-
+  if (c == ' ' || c == '\t' || c == '\n' || c == '\r')
+    return 1;
   return 0;
 }
 
+
 static int parse_header(const char * line,
                         int * seq_count,
                         int * seq_len,
@@ -210,7 +211,7 @@ static int parse_header(const char * line,
   line += len;
 
   /* go through all white spaces */
-  while (*line && whitechar(*line)) ++line;
+  while (*line && whitespace(*line)) ++line;
 
   /* if end of line then return successfully */
   if (!*line)
@@ -224,7 +225,7 @@ static int parse_header(const char * line,
     return 0;
 
   /* go through all white spaces */
-  while (*line && whitechar(*line)) ++line;
+  while (*line && whitespace(*line)) ++line;
 
   /* if end of line then return successfully */
   if (!*line)
@@ -233,13 +234,6 @@ static int parse_header(const char * line,
   return 0;
 }
 
-static int whitespace(char c)
-{
-  if (c == ' ' || c == '\t' || c == '\n' || c == '\r')
-    return 1;
-  return 0;
-}
-
 static char * parse_oneline_sequence(pll_phylip_t * fd,
                                      pll_msa_t * msa,
                                      char * p,