From 9135b8d371fd98be85b7cfa36c4a942832043696 Mon Sep 17 00:00:00 2001 From: earonesty Date: Thu, 4 Sep 2014 17:24:25 +0000 Subject: [PATCH] max-n-pct default needs to be -1 --- clipper/fastq-mcf.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/clipper/fastq-mcf.cpp b/clipper/fastq-mcf.cpp index 5d3aa77..2813600 100644 --- a/clipper/fastq-mcf.cpp +++ b/clipper/fastq-mcf.cpp @@ -82,7 +82,7 @@ const char *cmd_align_pe = "bowtie -S %i -1 %1 -2 %2"; // quality filter args int qf_mean=0, qf_max_ns=-1, qf_xgt_num=0, qf_xgt_min=0, qf_max_n_pct=-1; -int qf2_mean=0, qf2_max_ns=-1, qf2_xgt_num=0, qf2_xgt_min=0, qf2_max_n_pct=0; +int qf2_mean=0, qf2_max_ns=-1, qf2_xgt_num=0, qf2_xgt_min=0, qf2_max_n_pct=-1; // qual adjust class adjustment {