From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 1 Sep 2011 14:29:29 +0000 (+0000)
Subject: fixed bug in find_SNPs
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b0bc22d4936b121c63a1abb5a9e2c02912cee700;p=biopieces.git

fixed bug in find_SNPs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1511 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/find_SNPs b/bp_bin/find_SNPs
index 6671144..2b40f32 100755
--- a/bp_bin/find_SNPs
+++ b/bp_bin/find_SNPs
@@ -48,9 +48,9 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
        record[:ALIGN].split(',').each do |snp|
          pos, event = snp.split(':')
 
-         pos += record[:S_BEG]
+         pos = pos.to_i + record[:S_BEG].to_i
 
-         snp_hash[record[:S_ID].to_sym][pos.to_sym][event.to_sym] += 1
+         snp_hash[record[:S_ID].to_sym][pos][event.to_sym] += 1
        end
     end
   end
diff --git a/bp_test/out/find_SNPs.out.1 b/bp_test/out/find_SNPs.out.1
index f92cd4f..2338ec0 100644
--- a/bp_test/out/find_SNPs.out.1
+++ b/bp_test/out/find_SNPs.out.1
@@ -60,21 +60,21 @@ CIGAR: 61M1D39M
 ---
 REC_TYPE: SNP
 S_ID: gi|48994873|gb|U00096.2|
-POS: 632937
+POS: 3000
 EVENT: ->A
 SNP_COUNT: 1
 TYPE: INSERTION
 ---
 REC_TYPE: SNP
 S_ID: gi|48994873|gb|U00096.2|
-POS: 8993
+POS: 1001
 EVENT: G>C
 SNP_COUNT: 2
 TYPE: MISMATCH
 ---
 REC_TYPE: SNP
 S_ID: gi|48994873|gb|U00096.2|
-POS: 615440
+POS: 5501
 EVENT: G>-
 SNP_COUNT: 3
 TYPE: DELETION