Changeset 3342

Timestamp:

Nov 6, 2014, 6:26:24 AM (9 years ago)

Author:

Peter

Message:

merge 0.12.2 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• m4/version.m4 (modified) (1 diff)
• test/Makefile.am (modified) (1 diff)
• test/cigar2.cc (copied) (copied from branches/0.12-stable/test/cigar2.cc)
• test/normalization.cc (modified) (2 diffs)
• yat/normalizer/QuantileNormalizer.cc (modified) (2 diffs)
• yat/utility/Aligner.cc (modified) (1 diff)
• yat/utility/SmithWaterman.h (modified) (1 diff)

trunk/NEWS

@@ -12 +12 @@
 
 yat 0.12.x series from http://dev.thep.lu.se/yat/svn/branches/0.12-stable
+
+version 0.12.2 (released 6 November 2014)
+  - Fixed bug in Aligner that internal data was not cleared between
+    alignments resulting in incorrect CIGAR (see bug #820)
+  - Fixed QuantileNormalizer seqfault when input had more columns than
+    rows (see bug #815)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.12.2
 
 version 0.12.1 (released 21 August 2014)

trunk/m4/version.m4

@@ -78 +78 @@
 # yat-0.12   9:0:0
 # yat-0.12.1 9:1:0
+# yat-0.12.2 9:2:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/Makefile.am

@@ -48 +48 @@
   test/bam_pair_iterator.test \
   test/cigar.test \
+  test/cigar2.test \
   test/cigar_iterator.test \
   test/codon.test test/commandline.test \

trunk/test/normalization.cc

@@ -293 +293 @@
 {
   suite.err() << "Testing QuantileNormalizer\n";
-  
   utility::Matrix m(2,2);
   m(0,0) = 0;
@@ -309 +308 @@
   suite.err() << "Testing m(1,1)\n";
   suite.add(suite.equal(m(1,1), 2));
+
+  // testing with landscape-shaped data matrix
+  m.resize(2, 10);
+  qn(m, m);
 }
 

trunk/yat/normalizer/QuantileNormalizer.cc

@@ -4 +4 @@
   Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2012 Peter Johansson
+  Copyright (C) 2012, 2014 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -43 +43 @@
     assert(data.columns()==result.columns());
 
-    std::vector<std::vector<size_t> > index(data.rows());
-    for (size_t column=0; column<data.columns(); ++column)
+    std::vector<std::vector<size_t> > index(data.columns());
+    for (size_t column=0; column<data.columns(); ++column) {
+      assert(column<index.size());
       utility::sort_index(index[column], data.column_const_view(column));
-      
+    }
+
     for (size_t rank=0; rank<data.rows(); ++rank) {
       statistics::Averager a;
-      for (size_t column=0; column<data.columns(); ++column)
+      for (size_t column=0; column<data.columns(); ++column) {
+        assert(column<index.size());
+        assert(rank<index[column].size());
         a.add(data(index[column][rank], column));
+      }
       double mean = a.mean();
-      for (size_t column=0; column<data.columns(); ++column)
+      for (size_t column=0; column<data.columns(); ++column) {
+        assert(column<index.size());
         result(index[column][rank], column) = mean;
+      }
     }
   }

trunk/yat/utility/Aligner.cc

@@ -78 +78 @@
 
     columns_ = x.columns();
-    alignment_.resize(columns_*x.rows(), none);
+    alignment_.assign(columns_*x.rows(), none);
 
     for (size_t i=1; i<x.rows(); ++i)

trunk/yat/utility/SmithWaterman.h

@@ -96 +96 @@
        Calculate a dot-matrix of size query_end-query_begin X
        reference_end-reference_begin where the element ij is 1.0 if
-       query_begin[i] == reference_begin[j] and -mismatch otherwise.
+       reference_begin[i] == query_begin[j] and -mismatch otherwise.
      */
     template<typename RandomAccessIterator1, typename RandomAccessIterator2>
-    double operator()(RandomAccessIterator1 query_begin,
-                      RandomAccessIterator1 query_end,
-                      RandomAccessIterator2 reference_begin,
-                      RandomAccessIterator2 reference_end,
+    double operator()(RandomAccessIterator1 reference_begin,
+                      RandomAccessIterator1 reference_end,
+                      RandomAccessIterator2 query_begin,
+                      RandomAccessIterator2 query_end,
                       double mismatch=0);