From dae2e0bf49297310be0ca6a5a626de196691557f Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 21 Sep 2012 09:09:50 +0000 Subject: [PATCH] slight polish of read_fastq git-svn-id: http://biopieces.googlecode.com/svn/trunk@1935 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/read_fastq | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq index a1206f5..c2f74cd 100755 --- a/bp_bin/read_fastq +++ b/bp_bin/read_fastq @@ -57,9 +57,9 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| Fastq.open(file, mode='r') do |fastq| fastq.each do |entry| if encoding == 'auto' - if entry.qual.match(/[!-:]/) # sanger or illumina18 + if entry.qual_base33? # sanger or illumina18 encoding = 'illumina18' - elsif entry.qual.match(/[K-h]/) # solexa or illumina13 or illumina15 + elsif entry.qual_base64? # solexa or illumina13 or illumina15 encoding = 'illumina13' else raise SeqError, "Could not auto-detect quality score encoding" -- 2.39.5