From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 24 Jan 2012 08:34:23 +0000 (+0000)
Subject: fixed indels in methods mask_seq_hard/soft
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=9fd75d58f7cfb8611a344017f527a10dff0bf0b5;p=biopieces.git

fixed indels in methods mask_seq_hard/soft

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1734 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index d22bfd1..e4b0a94 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -457,6 +457,7 @@ class Seq
     na_seq  = NArray.to_na(self.seq, "byte")
     na_qual = NArray.to_na(self.qual, "byte")
     mask    = (na_qual - SCORE_ILLUMINA) < cutoff
+    mask   *= na_seq.ne("-".ord)
 
     na_seq[mask] = 'N'.ord
 
@@ -475,6 +476,7 @@ class Seq
     na_seq  = NArray.to_na(self.seq, "byte")
     na_qual = NArray.to_na(self.qual, "byte")
     mask    = (na_qual - SCORE_ILLUMINA) < cutoff
+    mask   *= na_seq.ne("-".ord)
 
     na_seq[mask] ^= ' '.ord