From df43a5627df2505bf5fc913aa564a7f6428f82b2 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 3 Feb 2012 07:09:49 +0000 Subject: [PATCH] added masks to align.rb git-svn-id: http://biopieces.googlecode.com/svn/trunk@1739 74ccb610-7750-0410-82ae-013aeee3265d --- code_ruby/lib/maasha/align.rb | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/code_ruby/lib/maasha/align.rb b/code_ruby/lib/maasha/align.rb index 85c3490..f7f59f6 100755 --- a/code_ruby/lib/maasha/align.rb +++ b/code_ruby/lib/maasha/align.rb @@ -177,26 +177,31 @@ class Align @entries = entries @cols = entries.first.length @rows = entries.size + + @has_qual = entries.first.qual.nil? ? false : true + @na_seq = NArray.byte(@cols, @rows) - @na_qual = NArray.byte(@cols, @rows) + @na_qual = NArray.byte(@cols, @rows) if @has_qual na_add_entries - m1 = mask_high_qual - m2 = mask_conserved_columns - m3 = mask_conserved_residues + if @has_qual + m1 = mask_high_qual + m2 = mask_conserved_columns + m3 = mask_conserved_residues - @na_seq *= m3 - @na_qual *= m3 + @na_seq *= m3 + @na_qual *= m3 - @na_seq *= (m1 | m2) - @na_qual *= (m1 | m2) + @na_seq *= (m1 | m2) + @na_qual *= (m1 | m2) + end end def to_seq new_seq = Seq.new new_seq.seq = consensus_seq - new_seq.qual = consensus_qual + new_seq.qual = consensus_qual if @has_qual new_seq.type = "dna" new_seq @@ -207,7 +212,7 @@ class Align def na_add_entries @entries.each_with_index do |entry, i| @na_seq[true, i] = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte") - @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_ILLUMINA + @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_ILLUMINA if @has_qual end end -- 2.39.5