X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fbwa_seq;h=fd807821dac3dfe3728a8b34dae9f7ee1ec25fc3;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=80c5b5cc87385d4eeb032b1229cb1722bd26b095;hpb=fca741e13da6009c9cb34c34b4f00f1f256350f1;p=biopieces.git

diff --git a/bp_bin/bwa_seq b/bp_bin/bwa_seq
index 80c5b5c..fd80782 100755
--- a/bp_bin/bwa_seq
+++ b/bp_bin/bwa_seq
@@ -102,7 +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
@@ -116,7 +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