Added a program to adjust quality scores by a fixed offset.

[fastq-tools.git] / src / fastq-grep.c

diff --git a/src/fastq-grep.c b/src/fastq-grep.c
index 3d531e863b60116c2d936ed856c516bc86860f11..994ab587324eb24133baecac8cb75824a4d52f77 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);
         }
@@ -120,7 +120,7 @@ int main(int argc, char* argv[])
     while (1) {
         opt = getopt_long(argc, argv, "ivchV", long_options, &opt_idx);
 
-        if( opt == -1 ) break;
+        if (opt == -1) break;
 
         switch (opt) {
             case 0: