[BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.8,1.9

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv1262

Modified Files:
	report.rb 
Log Message:
Changed some documents.
Reference: http://genome.ucsc.edu/goldenPath/help/blatSpec.html


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	20 Jun 2006 14:21:34 -0000	1.8
--- report.rb	20 Jun 2006 14:34:38 -0000	1.9
***************
*** 21,25 ****
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # 
  
  require 'bio'
--- 21,25 ----
  #   Genome Research, 12, 656--664, 2002.
  #   http://www.genome.org/cgi/content/abstract/12/4/656
! # * http://genome.ucsc.edu/goldenPath/help/blatSpec.html
  
  require 'bio'
***************
*** 262,268 ****
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
!         # rep. match (???)
          def rep_match;   @data[2].to_i;  end
!         # N's (???)
          def n_s;         @data[3].to_i;  end
  
--- 262,272 ----
          # Mismatch nucleotides.
          def mismatch;    @data[1].to_i;  end
! 
!         # "rep. match".
!         # Number of bases that match but are part of repeats.
!         # Note that current version of BLAT always set 0.
          def rep_match;   @data[2].to_i;  end
! 
!         # "N's". Number of 'N' bases.
          def n_s;         @data[3].to_i;  end