From 52e94bbea7bf66eebdc23873e8a1768306c7443e Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Mon, 22 Feb 2016 16:46:13 +0100
Subject: [PATCH] Fixed bug with the parser and n's

---
 libfasta/fasta_header_parser.c | 50 +++++++++++++++++-----------------
 libfasta/fasta_header_parser.l |  4 +--
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/libfasta/fasta_header_parser.c b/libfasta/fasta_header_parser.c
index 9af575c..ad18723 100644
--- a/libfasta/fasta_header_parser.c
+++ b/libfasta/fasta_header_parser.c
@@ -406,9 +406,9 @@ static yyconst flex_int32_t yy_ec[256] =
         4,    5,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
-        1,    6,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
 
-        1,    1,    1,    1,    1,    1,    1,    1,    1,    6,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
@@ -427,41 +427,41 @@ static yyconst flex_int32_t yy_ec[256] =
         1,    1,    1,    1,    1
     } ;
 
-static yyconst flex_int32_t yy_meta[7] =
+static yyconst flex_int32_t yy_meta[6] =
     {   0,
-        1,    2,    3,    3,    4,    4
+        1,    2,    3,    3,    4
     } ;
 
-static yyconst flex_int16_t yy_base[35] =
+static yyconst flex_int16_t yy_base[36] =
     {   0,
-        0,    0,   23,   22,    6,    0,   12,    0,   26,    0,
+        0,    4,   23,    0,    9,    0,   14,    0,   27,    0,
         0,   29,   29,    0,    0,   29,   29,    0,    0,   29,
-       29,    0,    0,    0,    0,    0,    0,   29,   18,   23,
-       23,   21,   21,   18
+       29,    0,    0,    0,    0,    0,    0,   29,   19,   23,
+       23,    7,    5,    3,    1
     } ;
 
-static yyconst flex_int16_t yy_def[35] =
+static yyconst flex_int16_t yy_def[36] =
     {   0,
-       28,    1,    1,    1,   28,    5,   28,    7,   28,   29,
-       30,   28,   28,   31,   32,   28,   28,   33,   34,   28,
-       28,   29,   30,   31,   32,   33,   34,    0,   28,   28,
+       29,   29,    2,    3,   28,    5,   28,    7,   28,   30,
+       31,   28,   28,   32,   33,   28,   28,   34,   35,   28,
+       28,   30,   31,   32,   33,   34,   35,    0,   28,   28,
+       28,   28,   28,   28,   28
+    } ;
+
+static yyconst flex_int16_t yy_nxt[35] =
+    {   0,
+       28,   11,   27,   26,   12,   11,   25,   24,   12,   14,
+       15,   16,   17,   13,   18,   19,   20,   21,   13,   10,
+       10,   10,   10,   22,   23,   22,   28,   13,    9,   28,
        28,   28,   28,   28
     } ;
 
-static yyconst flex_int16_t yy_nxt[36] =
+static yyconst flex_int16_t yy_chk[35] =
     {   0,
-       10,   11,   10,   10,   12,   13,   14,   15,   16,   17,
-       13,   13,   18,   19,   20,   21,   13,   13,   22,   27,
-       22,   26,   25,   24,   23,   28,   13,   13,    9,   28,
-       28,   28,   28,   28,   28
-    } ;
-
-static yyconst flex_int16_t yy_chk[36] =
-    {   0,
-        1,    1,    1,    1,    1,    1,    5,    5,    5,    5,
-        5,    5,    7,    7,    7,    7,    7,    7,   29,   34,
-       29,   33,   32,   31,   30,    9,    4,    3,   28,   28,
-       28,   28,   28,   28,   28
+        0,    1,   35,   34,    1,    2,   33,   32,    2,    5,
+        5,    5,    5,    5,    7,    7,    7,    7,    7,   29,
+       29,   29,   29,   30,   31,   30,    9,    3,   28,   28,
+       28,   28,   28,   28
     } ;
 
 static yy_state_type yy_last_accepting_state;
diff --git a/libfasta/fasta_header_parser.l b/libfasta/fasta_header_parser.l
index 12ba444..c270c64 100644
--- a/libfasta/fasta_header_parser.l
+++ b/libfasta/fasta_header_parser.l
@@ -21,8 +21,8 @@
 	
 %}
 
-WORD                [^>\\n[:blank:]=;]+
-WORDID              [^>\\n[:blank:]]+
+WORD                [^>[:blank:]=;]+
+WORDID              [^>[:blank:]]+
 SUP					>
 EOL                	\n
 SEP                 ;