From 1a741c85652e2b1e5543701499b6125d96deee3d Mon Sep 17 00:00:00 2001
From: Albert Kim <alkim1234@gmail.com>
Date: Mon, 7 May 2012 18:05:05 -0700
Subject: [PATCH] Do not modify contigs KmerContigMap

---
 contig.cpp          | 6 ++++++
 contig.h            | 1 +
 kmer_contig_map.cpp | 7 ++++---
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/contig.cpp b/contig.cpp
index b6510cd..6c5ceb4 100644
--- a/contig.cpp
+++ b/contig.cpp
@@ -26,6 +26,12 @@ Contig::Contig(kmer_t init_kmer)
     s = kmer_str;
 }
 
+Contig::Contig(Contig* contig)
+    : id(id_generator++), s(contig->s), left_ext(contig->left_ext),
+    right_ext(contig->right_ext)
+{
+}
+
 bool Contig::check_next_left_ext(base next_left_ext)
 {
     return char2base(s[s.size() - k]) == next_left_ext;
diff --git a/contig.h b/contig.h
index 717dc54..89d8ad2 100644
--- a/contig.h
+++ b/contig.h
@@ -15,6 +15,7 @@ class Contig {
 
     Contig();
     Contig(kmer_t init_kmer);
+    Contig(Contig* contig);
 
     /* Checks the given base 'next_left_ext' against the s[size - k] to see if
      * they're the same. If the kmer overlaps properly, these bases should be
diff --git a/kmer_contig_map.cpp b/kmer_contig_map.cpp
index cb469a5..e89bd8c 100644
--- a/kmer_contig_map.cpp
+++ b/kmer_contig_map.cpp
@@ -41,14 +41,15 @@ void KmerContigMap::join_contigs(ContigStore& contig_store)
     for (map_type_t::iterator it = forward_map.map.begin();
             it != forward_map.map.end();
             it++) {
-        Contig* contig = it->second;
-
-        if (contig->s.size() == 0) continue;
+        if (it->second->s.size() == 0) continue;
 
+        Contig* contig = new Contig(it->second);
         walk(contig);
         contig->revcmp();
         walk(contig);
         contig_store.add(contig);
+
+        it->second->s.clear();
     }
 }