From 2f5b5f513a71b88e241bd917dd9107270959f8d6 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 17 Nov 2011 16:53:31 +0000 Subject: [PATCH] fixed remove_primers git-svn-id: http://biopieces.googlecode.com/svn/trunk@1661 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/remove_primers | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers index 4e4e2e7..108f585 100755 --- a/bp_bin/remove_primers +++ b/bp_bin/remove_primers @@ -52,14 +52,16 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| record[:FORWARD_POS] = forward.last.pos record[:FORWARD_LEN] = forward.last.length pos = forward.last.pos + forward.last.length - seq.subseq!(pos) + len = seq.length - pos + seq.subseq!(pos, len) if len > 0 end - if reverse = seq.patscan(options[:reverse].to_s, pos, options[:mismatches], options[:insertions], options[:deletions]) + if pos < seq.length && reverse = seq.patscan(options[:reverse].to_s, pos, options[:mismatches], options[:insertions], options[:deletions]) record[:REVERSE_POS] = reverse.first.pos record[:REVERSE_LEN] = reverse.first.length - pos = reverse.first.pos - seq.subseq!(0, pos) + pos = 0 + len = reverse.first.pos + seq.subseq!(pos, len) if len > 0 end if pos > 0 -- 2.39.2