removed debug message

[biopieces.git] / bp_bin / bwa_seq

diff --git a/bp_bin/bwa_seq b/bp_bin/bwa_seq
index 43637ca5e9677e275c6e1ea037b74378f5cd122c..fd807821dac3dfe3728a8b34dae9f7ee1ec25fc3 100755 (executable)
--- a/bp_bin/bwa_seq
+++ b/bp_bin/bwa_seq
@@ -43,7 +43,6 @@ casts << {:long=>'cpus',       :short=>'c', :type=>'uint',   :mandatory=>false,
 options = Biopieces.options_parse(ARGV, casts)
 
 tmp_dir = Biopieces.mktmpdir
-tmp_dir = "Sletmig"
 tmp_fq  = File.join(tmp_dir, "bwa.fq")
 tmp_sai = File.join(tmp_dir, "bwa.sai")
 tmp_sam = File.join(tmp_dir, "bwa.sam")
@@ -103,7 +102,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     input.each_record do |record|
       output.puts record
 
-      if record.has_key? :SEQ_NAME and record.has_key? :SEQ and record.has_key? :SCORES
+      if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
         entry = Seq.new_bp(record)
 
         io_fq.puts entry.to_fastq
@@ -117,7 +116,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
   Sam.open(tmp_sam, 'r') do |io_sam|
     io_sam.each do |entry|
-      output.puts Sam.to_bp(entry)
+      output.puts Sam.to_bp(entry) unless entry[:RNAME] == '*'
     end
   end
 end