From ba605ceab22645d6ec007a803817a05e158ada67 Mon Sep 17 00:00:00 2001
From: walaj <jwala@broadinstitute.org>
Date: Wed, 22 Mar 2017 21:22:23 -0400
Subject: [PATCH] fixed seq_test issuees with BFC simplification

---
 README.md             | 21 +++++++++++----------
 seq_test/seq_test.cpp |  9 +++++----
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 0a831c0c9..6671ca3b3 100644
--- a/README.md
+++ b/README.md
@@ -301,21 +301,22 @@ w.Close();               // Optional. Will close on destruction
 using namespace SeqLib;
 
 // brv is some set of reads to train the error corrector
-b.TrainCorrection(brv);
+for (BamRecordVector::const_iterator r = brv.begin(); r != brv.end(); ++r)
+    b.AddSequence(r->Sequence().c_str(), r->Qualities().c_str(), r->Qname().c_str());
+b.Train();
+b.clear(); // clear the training sequences. Training parameters saved in BFC object
+
 // brv2 is some set to correct
-b.ErrorCorrect(brv2);
+for (BamRecordVector::const_iterator r = brv2.begin(); r != brv2.end(); ++r)
+    b.AddSequence(r->Sequence().c_str(), r->Qualities().c_str(), r->Qname().c_str());
+b.ErrorCorrect();
 
 // retrieve the sequences
 UnalignedSequenceVector v;
-b.GetSequences(v);
-
-// alternatively, to train and correct the same set of reads
-b.TrainAndCorrect(brv);
-b.GetSequences(v);
+std::string name, seq;
+while (b.GetSequences(seq, name))
+  v.push_back({name, seq});      			   
 
-// alternatively, train and correct, and modify the sequence in-place
-b.TrainCorrection(brv);
-b.ErrorCorrectInPlace(brv);
 ```
 
 Support
diff --git a/seq_test/seq_test.cpp b/seq_test/seq_test.cpp
index 0940a4e65..e692da77c 100644
--- a/seq_test/seq_test.cpp
+++ b/seq_test/seq_test.cpp
@@ -117,9 +117,10 @@ BOOST_AUTO_TEST_CASE( correct_and_assemble ) {
   BamRecordVector brv, brv2;
   size_t count = 0;
   while(br.GetNextRecord(rec) && count++ < 10000) 
-    brv.push_back(rec);
-
-  //b.TrainAndCorrect(brv);
+    b.AddSequence(rec.Sequence().c_str(), rec.Qualities().c_str(), rec.Qname().c_str());
+  
+  b.Train();
+  b.ErrorCorrect();
 
   float kcov = b.GetKCov();
   int   kmer = b.GetKMer();
@@ -990,7 +991,7 @@ BOOST_AUTO_TEST_CASE( set_qualities ) {
   SeqLib::BamRecord r;
   while (br.GetNextRecord(r)) {
     r.SetQualities("", 0);
-    BOOST_CHECK_EQUAL(r.Qualities(), std::string());
+    BOOST_CHECK_EQUAL(r.Qualities().at(0), '!');
     r.SetQualities(std::string(r.Length(), '#'), 33);
     BOOST_CHECK_EQUAL(r.Qualities(), std::string(r.Length(), '#'));    
     BOOST_CHECK_THROW(r.SetQualities(std::string(8, '#'), 0), std::invalid_argument);