From b1fadc0ce9224b6a13f8deae332bb902a54c65af Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 23 Sep 2013 12:29:14 +0000 Subject: [PATCH] fixed isseu in find_orphans git-svn-id: http://biopieces.googlecode.com/svn/trunk@2207 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/find_orphans | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/bp_bin/find_orphans b/bp_bin/find_orphans index d8f2e4e..20cc9c2 100755 --- a/bp_bin/find_orphans +++ b/bp_bin/find_orphans @@ -24,7 +24,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -# Identify paired end orphan in records with sequence data. +# Find paired end orphan in records with sequence data. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -48,22 +48,24 @@ records = [] Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| input.each_record do |record| - records << record + if record[:SEQ_NAME] + records << record - if records.size == 2 - if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME]) - records.first[:TYPE] = "paired" - records.last[:TYPE] = "paired" + if records.size == 2 + if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME]) + records.first[:TYPE] = "paired" + records.last[:TYPE] = "paired" - output.puts records.first - output.puts records.last + output.puts records.first + output.puts records.last - records = [] - else - records.first[:TYPE] = "orphan" - output.puts records.first + records = [] + else + records.first[:TYPE] = "orphan" + output.puts records.first - records.shift + records.shift + end end end end -- 2.39.2