From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 21 Sep 2012 09:09:50 +0000 (+0000)
Subject: slight polish of read_fastq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=dae2e0bf49297310be0ca6a5a626de196691557f;p=biopieces.git

slight polish of read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1935 74ccb610-7750-0410-82ae-013aeee3265d
---

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"