From: Daniel Jones Date: Fri, 18 Nov 2011 19:10:00 +0000 (-0800) Subject: Fix inverted match option in fastq-grep. X-Git-Url: https://git.donarmstrong.com/?p=fastq-tools.git;a=commitdiff_plain;h=51c0b6967d832ab84e238a6dd22b6672523ea52b Fix inverted match option in fastq-grep. --- diff --git a/configure.ac b/configure.ac index a1039a0..f106f53 100644 --- 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 3d531e8..7c9e3bf 100644 --- 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); }