Fix inverted match option in fastq-grep.

diff --git a/configure.ac b/configure.ac
index a1039a075350b1d07ba4e1feb0a719cb2fe51a0f..f106f53c7ac1cad9e79a23628dc2d150966d47da 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
 
-AC_INIT( [fastq-tools], [0.3], [dcjones@cs.washington.ed] )
+AC_INIT( [fastq-tools], [0.3], [dcjones@cs.washington.edu] )
 AM_INIT_AUTOMAKE( [foreign -Wall -Werror] )
 m4_ifdef([AM_SILENT_RULES],[AM_SILENT_RULES([yes])])
 

diff --git a/src/fastq-grep.c b/src/fastq-grep.c
index 3d531e863b60116c2d936ed856c516bc86860f11..7c9e3bf60ec844a944719d9e87c03d93dfdf424b 100644 (file)
--- a/src/fastq-grep.c
+++ b/src/fastq-grep.c
@@ -64,7 +64,7 @@ void fastq_grep(FILE* fin, FILE* fout, pcre* re)
     while (fastq_next(fqf, seq)) {
 
         rc = pcre_exec(re,          /* pattern */
-                       NULL,        /* extre data */
+                       NULL,        /* extra data */
                        id_flag ? seq->id1.s : seq->seq.s,
                        id_flag ? seq->id1.n : seq->seq.n,
                        0,           /* subject offset */
@@ -72,7 +72,7 @@ void fastq_grep(FILE* fin, FILE* fout, pcre* re)
                        ovector,     /* output vector */
                        3         ); /* output vector length */
 
-        if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || rc >= 0) {
+        if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || (!invert_flag && rc >= 0)) {
             if (count_flag) count++;
             else            fastq_print(fout, seq);
         }