From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 29 Jan 2011 16:21:40 +0000 (+0000)
Subject: fixed bug in shred_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=15bee5c1f1a081fa2924c65cc89e4683be6b2c45;p=biopieces.git

fixed bug in shred_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1227 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/shred_seq b/bp_bin/shred_seq
index a59b688..2a70b1a 100755
--- a/bp_bin/shred_seq
+++ b/bp_bin/shred_seq
@@ -47,7 +47,12 @@ class Seq
     strand  = '+'
 
     while (sum / self.seq.length) < max_cov
-      start    = rand(self.seq.size - size)
+      if self.seq.size - size == 0
+        start = 0
+      else
+        start    = rand(self.seq.size - size)
+      end
+
       stop     = start + size - 1
       seq_name = self.seq_name + "[#{start + 1}-#{stop + 1}:#{strand}]"
       seq      = self.seq[start .. stop]
@@ -79,7 +84,7 @@ bp = Biopieces.new
 options = bp.parse(ARGV, casts)
 
 bp.each_record do |record|
-  if record.has_key? :SEQ
+  if record.has_key? :SEQ and record[:SEQ].length >= options[:size]
     entry = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:SCORES])
 
     entry.shred(options[:size], options[:coverage]) do |subentry|