added closed? method to filesys.rb

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index f311bf60d3a04ee97009179a1ff2e3fd684992e8..e4b0a947bd5460c5b0a12aa69c63bc84c4b43775 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -452,11 +452,12 @@ class Seq
   def mask_seq_hard!(cutoff)
     raise SeqError, "seq is nil"  if self.seq.nil?
     raise SeqError, "qual is nil" if self.qual.nil?
-    raise SeqError, "Bad cutoff value: #{cutoff}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
+    raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
 
     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
 
@@ -470,11 +471,12 @@ class Seq
   def mask_seq_soft!(cutoff)
     raise SeqError, "seq is nil"  if self.seq.nil?
     raise SeqError, "qual is nil" if self.qual.nil?
-    raise SeqError, "Bad cutoff value: #{cutoff}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
+    raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
 
     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