From 39422dfc6100f9955c6263a0a8eb5f62a665ea4f Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 6 Sep 2011 08:19:10 +0000
Subject: [PATCH] fixed bug in remove_mids

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1520 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/remove_mids            | 12 ------------
 bp_test/out/remove_mids.out.4 | 12 ++++++------
 2 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/bp_bin/remove_mids b/bp_bin/remove_mids
index 39f575c..74846c1 100755
--- a/bp_bin/remove_mids
+++ b/bp_bin/remove_mids
@@ -213,8 +213,6 @@ pos        = options[:pos]
 mismatches = options[:mismatches]
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  aux_hash = {}
-
   input.each_record do |record|
     if record.has_key? :SEQ
       found_tag    = nil
@@ -230,12 +228,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       end
 
       if mismatches > 0 and found_tag.nil?
-        if aux_hash.has_key? tag10
-          found_tag = tag10
-        elsif aux_hash.has_key? tag11
-          found_tag = tag11
-        end
-
         if found_tag.nil?
           gsmid_hash.each_pair do |mid, mid_name|
             hamming_dist = tag10.to_s.hamming_distance(mid.to_s)
@@ -243,8 +235,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
             if hamming_dist <= mismatches
               found_tag = mid
 
-              aux_hash[tag10] = mid_name
-
               break
             end
           end
@@ -257,8 +247,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
             if hamming_dist <= mismatches
               found_tag = mid
 
-              aux_hash[tag11] = mid_name
-
               break
             end
           end
diff --git a/bp_test/out/remove_mids.out.4 b/bp_test/out/remove_mids.out.4
index 319808a..9dbc8fd 100644
--- a/bp_test/out/remove_mids.out.4
+++ b/bp_test/out/remove_mids.out.4
@@ -28,11 +28,11 @@ MID_MISMATCHES: 2
 SEQ_NAME: test_RL12_2_mismatches_repeat
 SEQ: gtgactgact
 SEQ_LEN: 10
-MID: ACTCACCTCGT
-MID_NAME: 
+MID: ACTCGCGTCGT
+MID_NAME: RL12
 MID_POS: 4
 MID_LEN: 11
-MID_MISMATCHES: 0
+MID_MISMATCHES: 2
 ---
 SEQ_NAME: test_GS99_0_mismatches
 SEQ: gtagtagtagt
@@ -64,9 +64,9 @@ MID_MISMATCHES: 2
 SEQ_NAME: test_GS99_2_mismatches_repeat
 SEQ: gtagtagtagt
 SEQ_LEN: 11
-MID: CTGTTCAGAC
-MID_NAME: 
+MID: CTGTACATAC
+MID_NAME: MID99
 MID_POS: 4
 MID_LEN: 10
-MID_MISMATCHES: 0
+MID_MISMATCHES: 2
 ---
-- 
2.39.5