Changeset 4038

Timestamp:

Jan 25, 2021, 5:33:35 AM (2 years ago)

Author:

Peter

Message:

merge trunk into branch

Location:

branches/kendall-score

Files:

• . (modified) (1 prop)
• NEWS (modified) (2 diffs)
• build_support/Makefile.am (modified) (1 diff)
• doc/Makefile.am (modified) (1 diff)
• m4/version.m4 (modified) (2 diffs)
• m4/yat_check_htslib.m4 (modified) (3 diffs)
• m4/yat_check_libs.m4 (modified) (2 diffs)
• test/Makefile.am (modified) (4 diffs)
• test/cigar.cc (modified) (3 diffs)
• test/deleter.cc (modified) (2 diffs)
• test/percentile_confidence_interval.cc (copied) (copied from trunk/test/percentile_confidence_interval.cc)
• test/random_distribution.cc (deleted)
• test/rnd.cc (modified) (1 diff)
• test/segment.cc (modified) (7 diffs)
• test/vcf.cc (modified) (4 diffs)
• test/yat_pc_test.sh (modified) (1 diff)
• yat/classifier/KernelLookup.h (modified) (3 diffs)
• yat/classifier/MatrixLookup.h (modified) (3 diffs)
• yat/classifier/MatrixLookupWeighted.h (modified) (3 diffs)
• yat/omic/BamPair.cc (modified) (1 diff)
• yat/omic/BamPair.h (modified) (1 diff)
• yat/omic/BamPairIterator.h (modified) (2 diffs)
• yat/omic/BamPairIterator2.h (modified) (2 diffs)
• yat/omic/BamReadIterator.cc (modified) (6 diffs)
• yat/omic/BamReadIterator.h (modified) (4 diffs)
• yat/omic/Fasta.cc (modified) (1 diff)
• yat/omic/Fasta.h (modified) (3 diffs)
• yat/omic/Pileup.h (modified) (2 diffs)
• yat/omic/VCF.h (modified) (2 diffs)
• yat/random/ContinuousDistribution.h (deleted)
• yat/random/DiscreteDistribution.h (deleted)
• yat/random/Distribution.h (deleted)
• yat/random/Makefile.am (modified) (1 diff)
• yat/random/random.cc (modified) (3 diffs)
• yat/random/random.h (modified) (4 diffs)
• yat/statistics/Makefile.am (modified) (2 diffs)
• yat/statistics/PercentileConfidenceInterval.cc (copied) (copied from trunk/yat/statistics/PercentileConfidenceInterval.cc)
• yat/statistics/PercentileConfidenceInterval.h (copied) (copied from trunk/yat/statistics/PercentileConfidenceInterval.h)
• yat/utility/Aligner.cc (modified) (3 diffs)
• yat/utility/Aligner.h (modified) (2 diffs)
• yat/utility/Cigar.cc (copied) (copied from trunk/yat/utility/Cigar.cc)
• yat/utility/Cigar.h (modified) (2 diffs)
• yat/utility/Deleter.h (modified) (2 diffs)
• yat/utility/Exception.cc (modified) (1 diff)
• yat/utility/Exception.h (modified) (1 diff)
• yat/utility/Makefile.am (modified) (1 diff)
• yat/utility/Segment.h (modified) (1 diff)
• yat/utility/SegmentSet.h (modified) (9 diffs)
• yat/utility/SegmentTree.h (modified) (5 diffs)

branches/kendall-score/NEWS

@@ -10 +10 @@
 yat 0.18.x series from http://dev.thep.lu.se/yat/svn/branches/0.18-stable
 
-version 0.18 (released NOT YET)
+version 0.18.1 (released 21 January 2021)
+  - SegmentTree::key_comp() and ::value_comp() now compile (bug #970).
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.18.1
+
+version 0.18 (released 6 November 2020)
   - regression::NegativeBinomial now inherits from
     regression::Multivariate (ticket #957)
@@ -558 +564 @@
 Copyright (C) 2010, 2011 Peter Johansson
 Copyright (C) 2012 Jari Häkkinen, Peter Johansson
-Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Peter Johansson
+Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Peter Johansson
 
 This file is part of yat library, http://dev.thep.lu.se/yat

branches/kendall-score/build_support/Makefile.am

@@ -89 +89 @@
   --exec-prefix="$(exec_prefix)" \
   --libdir="$(libdir)" --includedir="$(includedir)" \
-  --input="../$(srcdir)/build_support/yat.pc.in" > yat.pc-t \
+  --input="$(abs_srcdir)/build_support/yat.pc.in" > yat.pc-t \
   && mv yat.pc-t yat.pc

branches/kendall-score/doc/Makefile.am

@@ -47 +47 @@
 EXTRA_DIST += doc/doxygen.config.in
 
-doc/doxygen.config: doc/doxygen.config.in
+# config file needs to be updated when $(DOXYGEN_INPUT) is
+# changed. That variable is set in various Makefile.am, but instead we
+# depend on Makefile.in, since that dependency is easier to maintain.
+doc/doxygen.config: doc/doxygen.config.in $(srcdir)/Makefile.in
   $(AM_V_GEN)echo "# $@ generated by make from doc/doxygen.config.in." \
   > $@-t \

branches/kendall-score/m4/version.m4

@@ -2 +2 @@
 #
 # Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2020 Peter Johansson
+# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2020, 2021 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -95 +95 @@
 # yat-0.17.1 14:1:0
 # yat-0.17.2 14:2:0
+# yat-0.18   15:0:0
+# yat-0.18.1 15:1:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

branches/kendall-score/m4/yat_check_htslib.m4

@@ -1 +1 @@
 ## $Id$
 #
-# serial 7 (yat 0.18)
+# serial 8 (yat 0.19)
 #
 #   Copyright (C) 2016, 2018, 2020 Peter Johansson
@@ -45 +45 @@
   _YAT_CHECK_ZLIB
   _YAT_CHECK_HTSLIB
+  YAT_VAR_BAM_CIGAR_TABLE([
+    AC_DEFINE([HAVE_BAM_CIGAR_TABLE], [1],
+              [Define to 1 if bam_cigar_table is available])
+  ])
 ])
 _YAT_PROG_SAMTOOLS
@@ -110 +114 @@
                 [$2])
 ]) # YAT_LIB_HTS
+
+
+# YAT_VAR_BAM_CIGAR_TABLE([action-if-found], [action-if-not-found])
+# =====================
+# Check if variable bam_cigar_table is available.
+AC_DEFUN([YAT_VAR_BAM_CIGAR_TABLE],
+[
+  AC_CACHE_CHECK([if bam_cigar_table is available],
+    [yat_cv_var_bam_cigar_table],
+    [AC_COMPILE_IFELSE([
+        AC_LANG_PROGRAM([@%:@include <htslib/sam.h>],
+                        [int8_t x = bam_cigar_table@<:@0@:>@;])
+      ], [
+        yat_cv_var_bam_cigar_table=yes
+      ], [
+        yat_cv_var_bam_cigar_table=no
+      ])
+    ])
+  AS_VAR_IF([yat_cv_var_bam_cigar_table], [yes], [$1], [$2])
+])
 
 

branches/kendall-score/m4/yat_check_libs.m4

@@ -1 +1 @@
 ## $Id$
 #
-# serial 2 (yat 0.18)
+# serial 3 (yat 0.18)
 #
 # see http://www.gnu.org/software/automake/manual/automake.html#Serials
@@ -42 +42 @@
 AC_DEFUN([YAT_CHECK_LIBS],
 [
-  m4_pushdef([yat_message], [$1])
-  m4_pushdef([yat_cache], [$2])
-  m4_pushdef([yat_search_libs], [$3])
+  m4_pushdef([yat_MESSAGE], [$1])
+  m4_pushdef([yat_CACHE], [$2])
+  m4_pushdef([yat_SEARCH_LIBS], [$3])
+  m4_pushdef([yat_DEFAULT_RESULT], ["none required"])
   AC_LANG_CONFTEST([$4])
-  AC_CACHE_CHECK([yat_message], [$2], [
+  AC_CACHE_CHECK([yat_MESSAGE], [yat_CACHE], [
     save_LIBS=$LIBS
-    for yat_lib in '' yat_search_libs; do
+    for yat_lib in '' yat_SEARCH_LIBS; do
       AS_VAR_IF([yat_lib], [''],[
-        yat_result="non required"
+        yat_result=yat_DEFAULT_RESULT
       ], [
         yat_result=-l$yat_lib
         LIBS="-l$yat_lib $save_LIBS"
       ])
-      AC_LINK_IFELSE([], [yat_cache=$yat_result])
-      AS_VAR_SET_IF([yat_cache], [break])
+      AC_LINK_IFELSE([], [yat_CACHE=$yat_result])
+      AS_VAR_SET_IF([yat_CACHE], [break])
     done
-    AS_VAR_SET_IF([yat_cache], [], [yat_cache=no])
+    AS_VAR_SET_IF([yat_CACHE], [], [yat_CACHE=no])
     rm conftest.$ac_ext
     LIBS=$save_LIBS
   ])
-  yat_result=$yat_cache
+  yat_result=$yat_CACHE
 
   # action
   AS_VAR_IF([yat_result], [no], [$6], [
-    AS_VAR_IF([yat_result], ["none required"], [], [LIBS="$yat_result $LIBS"])
+    AS_VAR_IF([yat_result], [yat_DEFAULT_RESULT], [],
+              [LIBS="$yat_result $LIBS"])
     $5
   ])
 
-
-  m4_popdef([yat_message])
-  m4_popdef([yat_cache])
-  m4_popdef([yat_search_libs])
+  m4_popdef([yat_MESSAGE])
+  m4_popdef([yat_CACHE])
+  m4_popdef([yat_SEARCH_LIBS])
+  m4_popdef([yat_DEFAULT_RESULT])
 ])

branches/kendall-score/test/Makefile.am

@@ -33 +33 @@
 EXTRA_DIST += test/init.sh
 
-EXTRA_PROGRAMS = test/alignment.test \
+CXX_TESTS = test/alignment.test \
   test/alignment2.test \
   test/averager.test \
@@ -94 +94 @@
   test/ostream_iterator.test \
   test/pca.test \
+  test/percentile_confidence_interval.test \
   test/perceptron.test \
   test/phred.test \
@@ -131 +132 @@
   test/view.test
 
+EXTRA_PROGRAMS = $(CXX_TESTS)
+
 CLEANFILES += $(EXTRA_PROGRAMS)
 
@@ -162 +165 @@
 test/yat_use_libtool_tag_test.sh
 
-TESTS = $(DISTRIBUTED_TESTS) $(EXTRA_PROGRAMS)
+TESTS = $(DISTRIBUTED_TESTS) $(CXX_TESTS)
 EXTRA_DIST += $(DISTRIBUTED_TESTS)
 

branches/kendall-score/test/cigar.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2014, 2019 Peter Johansson
+  Copyright (C) 2014, 2019, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -25 +25 @@
 
 #include "yat/utility/Aligner.h"
-
+#include "yat/utility/Exception.h"
 #include "yat/utility/Matrix.h"
+#include "yat/utility/utility.h"
 
 #include <sstream>
@@ -83 +84 @@
   }
   suite.out() << "\n";
+  utility::Aligner::Cigar cig2(os.str());
+  if (std::distance(cig.begin(), cig.end())!=
+      std::distance(cig2.begin(), cig2.end()) ||
+      !std::equal(cig.begin(), cig.end(), cig2.begin())) {
+    suite.add(false);
+    suite.err() << "error: incorrect construction from Cigar(string)\n";
+    suite.err() << ": " << cig2 << "\nexpected:" << cig << "\n";
+  }
+  try {
+    utility::Aligner::Cigar cig3("BANANA");
+    suite.add(false);
+    suite.err() << "error: Cigar(\"BANANA\") did not throw\n";
+    suite.err() << "cigar: " << cig3 << "\n";
+  }
+  catch (utility::invalid_argument& e) {
+    suite.out() << "expected exception: ";
+    utility::print_what(e, suite.out());
+    suite.out() << "\n";
+  }
 
   if (!suite.add(cig.length()==17))

branches/kendall-score/test/deleter.cc

@@ -26 +26 @@
 #include "yat/utility/Deleter.h"
 
-#include <boost/shared_ptr.hpp>
+#include <memory>
 
 using namespace theplu::yat;
@@ -41 +41 @@
 
   int* p0 = new int(2);
-  boost::shared_ptr<int> smartp(p0, del);
+  std::shared_ptr<int> smartp(p0, del);
 
   Deleter del2(false);
   int* p = new int(3);
   if (true) {
-    boost::shared_ptr<int> sp(p, del2);
+    std::shared_ptr<int> sp(p, del2);
     suite.out() << *sp << "\n";
   }

branches/kendall-score/test/rnd.cc

@@ -54 +54 @@
   suite.err() << "Checking that all random generators can be constructed\n";
   theplu::yat::statistics::Histogram histogram(0,100,1000);
+  std::vector<DiscreteGeneral> discrete(10);
   DiscreteGeneral dg(histogram);
   DiscreteUniform du;

branches/kendall-score/test/segment.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2010, 2011, 2012, 2014, 2015, 2016, 2017 Peter Johansson
+  Copyright (C) 2010, 2011, 2012, 2014, 2015, 2016, 2017, 2021 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -30 +30 @@
 using namespace theplu::yat;
 using namespace utility;
+void test_comp(test::Suite& suite);
 void test_compare(test::Suite& suite);
 void test_count(test::Suite&);
@@ -41 +42 @@
 void test_operator(test::Suite& suite);
 void test_segment_map(test::Suite& suite);
+void test_segment_set(test::Suite& suite);
 void test_set_bound(test::Suite&);
 void test_union(test::Suite&);
@@ -51 +53 @@
   test::Suite suite(argc, argv);
 
+  test_comp(suite);
   test_compare(suite);
   test_count(suite);
@@ -64 +67 @@
 
   test_segment_map(suite);
+  test_segment_set(suite);
 
   return suite.return_value();
+}
+
+
+void test_comp(test::Suite& suite)
+{
+  Segment<double> key;
+  {
+    SegmentSet<double> set;
+    SegmentSet<double>::key_compare kcompare = set.key_comp();
+    if (kcompare(key, key))
+      suite.add(false);
+    test::avoid_compiler_warning(kcompare);
+    SegmentSet<double>::value_compare vcompare = set.value_comp();
+    if (vcompare(key, key))
+      suite.add(false);
+    test::avoid_compiler_warning(vcompare);
+  }
+
+  {
+    SegmentMap<double, std::string> map;
+    std::pair<const Segment<double>, std::string> value(key, "hello");
+    SegmentMap<double, std::string>::key_compare kcompare = map.key_comp();
+    if (kcompare(key, key))
+      suite.add(false);
+    test::avoid_compiler_warning(kcompare);
+    SegmentMap<double, std::string>::value_compare vcompare = map.value_comp();
+    if (vcompare(value, value))
+      suite.add(false);
+    test::avoid_compiler_warning(vcompare);
+  }
 }
 
@@ -267 +301 @@
 }
 
+
 void test_segment_map(test::Suite& suite)
 {
@@ -303 +338 @@
 }
 
+
+void test_segment_set(test::Suite& suite)
+{
+  SegmentSet<double> set;
+  Segment<double> segment(0.12,23.2);
+  set.insert_merge(segment);
+  set.insert_merge(Segment<double>(0.12,23.2));
+  SegmentSet<double>::iterator hint = set.begin();
+  set.insert_merge(hint, segment);
+  set.insert_merge(hint, Segment<double>(0.12,23.2));
+  SegmentSet<double>::const_iterator chint = set.begin();
+  set.insert_merge(chint, segment);
+  set.insert_merge(chint, Segment<double>(0.12,23.2));
+  std::vector<Segment<double>> vec(set.begin(), set.end());
+  set.insert_merge(vec.begin(), vec.end());
+
+  // test functions inherited from SegmentTree
+  SegmentSet<double>::const_iterator citer = set.begin();
+  SegmentSet<double>::const_iterator iter = set.begin();
+
+  citer = set.end();
+  iter = set.end();
+
+  if (set.count(0.13)!=1) {
+    suite.add(false);
+    suite.err() << "error: expected count = 1\n";
+  }
+  if (set.count(0.02)!=0) {
+    suite.add(false);
+    suite.err() << "error: expected count = 0\n";
+  }
+  if (set.empty()) {
+    suite.add(false);
+    suite.err() << "error: expected empty() return false";
+  }
+  if (set.find(0.15) == set.end()) {
+    suite.add(false);
+    suite.err() << "error: find returned end()";
+  }
+  set.erase(set.begin());
+  set.clear();
+  set.erase(set.begin(), set.end());
+
+  set.insert(segment);
+  set.insert(Segment<double>(102, 200));
+
+  iter = set.lower_bound(1.0);
+  citer = set.lower_bound(1.0);
+  iter = set.upper_bound(1.0);
+  citer = set.upper_bound(1.0);
+  SegmentSet<double>::size_type s = set.size();
+  test::avoid_compiler_warning(s);
+}
+
+
 void test_segment(test::Suite& suite)
 {

branches/kendall-score/test/vcf.cc

@@ -24 +24 @@
 
 #include "yat/omic/VCF.h"
+#include "yat/utility/utility.h"
 
 #include <fstream>
@@ -41 +42 @@
     if (false) {
       std::ifstream is("nonsense.vcf");
-      VCF vcf;
+      VCF vcf(is);
       test::avoid_compiler_warning(vcf);
     }
@@ -121 +122 @@
     }
 
+    // test getting int when value is a String
+    try {
+      double x;
+      vcf.info().get(x, "FOO");
+      suite.add(false);
+    }
+    catch (utility::runtime_error& e) {
+      std::ostringstream os;
+      utility::print_what(e, os);
+      suite.out() << "expected exception: what: " << os.str();
+      if (os.str().find("FOO")==std::string::npos) {
+        suite.add(false);
+        suite.err() << "error: expected 'FOO' mentioned in what()\n";
+      }
+    }
+
     suite.out() << "test data\n";
     std::vector<std::string> GT;
@@ -148 +165 @@
     ID.push_back("baz");
     vcf.data().add("ID", ID);
+
+    // test unknown key
+    try {
+      vcf.data().get("banana", GT);
+    }
+    catch (utility::runtime_error& e) {
+      std::ostringstream os;
+      utility::print_what(e, os);
+      suite.out() << "expected exception: what: " << os.str();
+      std::vector<std::string> tags = { "unknown key", "banana"};
+      for (size_t i=0; i<tags.size(); ++i)
+        if (os.str().find(tags[i]) == std::string::npos) {
+          suite.add(false);
+          suite.err() << "error: expected '" << tags[i]
+                      << "' in error message\n";
+        }
+    }
+
+    // test getting int when value is a String
+    try {
+      std::vector<int> p;
+      vcf.data().get("ID", p);
+    }
+    catch (utility::runtime_error& e) {
+      std::ostringstream os;
+      utility::print_what(e, os);
+      suite.out() << "expected exception: what: " << os.str();
+      if (os.str().find("ID")==std::string::npos) {
+        suite.add(false);
+        suite.err() << "error: expected 'ID' mentioned in what()\n";
+      }
+    }
   }
   catch (std::exception& e) {

branches/kendall-score/test/yat_pc_test.sh

@@ -81 +81 @@
 CXX = `yat-config --cxx`
 # add -I flags to include local header files; 2nd term needed for VPATH build
-CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir/yat/utility \
+CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir \
+-I$abs_top_builddir/yat/utility \
 `$PKG_CONFIG yat --cflags-only-I`
 CXXFLAGS = `$PKG_CONFIG yat --cflags-only-other`

branches/kendall-score/yat/classifier/KernelLookup.h

@@ -8 +8 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2010, 2012 Peter Johansson
+  Copyright (C) 2010, 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -32 +32 @@
 #include "yat/utility/StrideIterator.h"
 
-#include <boost/shared_ptr.hpp>
+#include <memory>
 
 namespace theplu {
@@ -324 +324 @@
 
     utility::Index column_index_;
-    boost::shared_ptr<const Kernel> kernel_;
+    std::shared_ptr<const Kernel> kernel_;
     utility::Index row_index_;
   }; // class KernelLookup

branches/kendall-score/yat/classifier/MatrixLookup.h

@@ -8 +8 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2012 Peter Johansson
+  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -33 +33 @@
 
 #include <boost/iterator/permutation_iterator.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iosfwd>
+#include <memory>
 #include <vector>
 
@@ -327 +327 @@
 
     utility::Index column_index_;
-    typedef boost::shared_ptr<const utility::Matrix> MatrixP;
+    typedef std::shared_ptr<const utility::Matrix> MatrixP;
     MatrixP data_;
     utility::Index row_index_;

branches/kendall-score/yat/classifier/MatrixLookupWeighted.h

@@ -7 +7 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2012 Peter Johansson
+  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -33 +33 @@
 
 #include <boost/iterator/permutation_iterator.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iosfwd>
+#include <memory>
 #include <utility>
 #include <vector>
@@ -296 +296 @@
 
   private:
-    typedef boost::shared_ptr<const utility::MatrixWeighted> MatrixWP;
+    typedef std::shared_ptr<const utility::MatrixWeighted> MatrixWP;
     utility::Index column_index_;
     MatrixWP data_;

branches/kendall-score/yat/omic/BamPair.cc

@@ -37 +37 @@
   BamPair::BamPair(const BamRead& first, const BamRead& second)
     : first_(first), second_(second) {}
+
+
+  BamPair::BamPair(BamRead&& first, BamRead&& second)
+    : first_(std::move(first)), second_(std::move(second)) {}
 
 

branches/kendall-score/yat/omic/BamPair.h

@@ -46 +46 @@
      */
     BamPair(const BamRead& first, const BamRead& second);
+
+    /**
+       \brief Move constructor
+
+       \since New in yat 0.19
+     */
+    BamPair(BamRead&& first, BamRead&& second);
 
     /**

branches/kendall-score/yat/omic/BamPairIterator.h

@@ -32 +32 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iterator>
 #include <map>
+#include <memory>
 #include <utility>
 
@@ -115 +115 @@
     Base end_;
     const BamRead* mate_;
-    boost::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
+    std::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
     typedef std::pair<int32_t, int32_t> Position;
-    boost::shared_ptr<std::multimap<Position, BamRead> > reads_;
+    std::shared_ptr<std::multimap<Position, BamRead> > reads_;
     friend class boost::iterator_core_access;
 

branches/kendall-score/yat/omic/BamPairIterator2.h

@@ -32 +32 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iterator>
 #include <map>
+#include <memory>
 #include <utility>
 
@@ -118 +118 @@
     // multimap with reads' position as key
     typedef std::multimap<Position, BamRead> MultiMap;
-    boost::shared_ptr<MultiMap> reads_;
+    std::shared_ptr<MultiMap> reads_;
     MultiMap::iterator first_;
     MultiMap::iterator second_;

branches/kendall-score/yat/omic/BamReadIterator.cc

@@ -28 +28 @@
 #include "yat/utility/Exception.h"
 
+#include <cassert>
 #include <cstddef>
 #include <sstream>
@@ -36 +37 @@
 
   BamReadIterator::BamReadIterator(void)
+    : actor_(new AllActor)
   {
-    actor_ = boost::shared_ptr<Actor>(new AllActor);
+    assert(actor_);
   }
 
 
   BamReadIterator::BamReadIterator(InBamFile& in)
+    : actor_(new AllActor(in))
   {
-    actor_ = boost::shared_ptr<Actor>(new AllActor(in));
+    assert(actor_);
     increment();
   }
@@ -50 +53 @@
   BamReadIterator::BamReadIterator(InBamFile& bf, int32_t tid, int32_t start,
                                    int32_t end)
+    : actor_(new IndexActor(bf, tid, start, end))
   {
-    actor_ = boost::shared_ptr<Actor>(new IndexActor(bf, tid, start, end));
     assert(actor_);
     increment();
@@ -58 +61 @@
 
   BamReadIterator::BamReadIterator(InBamFile& bf, int32_t tid, int32_t start)
+    : actor_(new IndexActor(bf, tid, start, bf.header().target_length(tid)))
   {
-    actor_ =
-      boost::shared_ptr<Actor>(new IndexActor(bf, tid, start,
-                                              bf.header().target_length(tid)));
     assert(actor_);
     increment();
@@ -83 +84 @@
     actor_->increment();
   }
+
+
+  void BamReadIterator::IndexDestroyer::operator()(hts_itr_t* i) const
+  {
+    bam_itr_destroy(i);
+  }
+
 
 
@@ -120 +128 @@
   BamReadIterator::IndexActor::IndexActor(InBamFile& bf, int32_t tid,
                                           int32_t begin,int32_t end)
-    : Actor(&bf)
+    : Actor(&bf),
+      iter_(sam_itr_queryi(bf.index(), tid, begin, end), IndexDestroyer())
   {
-    using boost::shared_ptr;
-    iter_ = shared_ptr<hts_itr_t>(sam_itr_queryi(bf.index(), tid, begin, end),
-                                  IndexDestroyer());
     if (!iter_.get()) {
       std::stringstream ss;

branches/kendall-score/yat/omic/BamReadIterator.h

@@ -29 +29 @@
 
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iterator>
+#include <memory>
 
 namespace theplu {
@@ -118 +118 @@
     void increment(void);
 
+
     /*
        Interface class for the actor that handles difference between
@@ -142 +143 @@
     };
 
+    // functor calling bam_itr_destroy
+    struct IndexDestroyer
+    {
+      void operator()(hts_itr_t* i) const;
+    };
+
     // class used when iterating over a sub-region of the bam file
     class IndexActor : public Actor
@@ -149 +156 @@
       void increment(void);
     private:
-      boost::shared_ptr<hts_itr_t> iter_;
+      std::unique_ptr<hts_itr_t, IndexDestroyer> iter_;
     };
 
-    boost::shared_ptr<Actor> actor_;
+    std::shared_ptr<Actor> actor_;
 
-    struct IndexDestroyer
-    {
-      void operator()(hts_itr_t* i) const
-      {
-        bam_itr_destroy(i);
-      }
-    };
   };
 }}}

branches/kendall-score/yat/omic/Fasta.cc

@@ -166 +166 @@
   {
     // allocate a new char*
-    boost::shared_array<char> ptr(new char[seq.size()+1]);
+    std::shared_ptr<char> ptr(new char[seq.size()+1],
+                              std::default_delete<char[]>());
     std::copy(seq.seq_.get(), seq.seq_.get()+seq.size(), ptr.get());
     // calculate reverse complement

branches/kendall-score/yat/omic/Fasta.h

@@ -21 +21 @@
 #include <htslib/faidx.h>
 
-#include <boost/shared_array.hpp>
-#include <boost/shared_ptr.hpp>
-
 #include <iosfwd>
 #include <map>
+#include <memory>
 #include <string>
 #include <vector>
@@ -114 +112 @@
       friend class Fasta;
       friend Sequence reverse_complement(const Fasta::Sequence&);
-      boost::shared_array<const char> seq_;
+      std::shared_ptr<char> seq_;
       int size_;
     };
@@ -134 +132 @@
 
   private:
-    boost::shared_ptr<faidx_t> faidx_;
+    std::shared_ptr<faidx_t> faidx_;
     // using compiler generated copy
     //FastaIndex(const FastaIndex& other);

branches/kendall-score/yat/omic/Pileup.h

@@ -31 +31 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/concept/assert.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <algorithm>
 #include <list>
+#include <memory>
 
 namespace theplu {
@@ -139 +139 @@
       size_t qpos(void) const { return qpos_; }
     private:
-      boost::shared_ptr<BamRead> bam_;
+      std::shared_ptr<BamRead> bam_;
       // index of base pointed to
       size_t qpos_;

branches/kendall-score/yat/omic/VCF.h

@@ -600 +600 @@
     size_t begin = str_.find(k);
 
-    if (begin == std::string::npos) {
-      converter(value, result);
-      return;
-    }
-
-    if (begin && str_[begin-1]!=';') {
-      k = ";" + key + "=";
-      begin = str_.find(k, begin+key.size());
+    try {
       if (begin == std::string::npos) {
         converter(value, result);
         return;
       }
+
+      if (begin && str_[begin-1]!=';') {
+        k = ";" + key + "=";
+        begin = str_.find(k, begin+key.size());
+        if (begin == std::string::npos) {
+          converter(value, result);
+          return;
+        }
+      }
+
+      begin += k.size();
+      int end = str_.find(";", begin);
+      value = str_.substr(begin, end-begin);
+      converter(value, result);
     }
-
-    begin += k.size();
-    int end = str_.find(";", begin);
-    value = str_.substr(begin, end-begin);
-    converter(value, result);
+    catch (utility::runtime_error& e) {
+      std::ostringstream msg;
+      msg << "invalid VCF::Info format for key '" << key << "'";
+      std::throw_with_nested(utility::runtime_error(msg.str()));
+    }
   }
 
@@ -642 +649 @@
     detail::Converter<T> converter;
     data.resize(data_.size());
-    for (size_t i=0; i<data.size(); ++i)
-      converter(data_[i][idx], data[i]);
-  }
-
-
-  /*
-  template<typename T>
-  void VCF::add_data(const std::string& key, const std::vector<T>& val)
-  {
-    if (format() != "")
-      format() += ":";
-    format() += key;
-
-
-    YAT_ASSERT(val.size()+9 == vec_.size());
-    for (size_t i=0; i<val.size(); ++i) {
-      std::string& data = vec_[i+9];
-      if (data != "")
-        data += ":";
-      append(data, val[i]);
+    try {
+      for (size_t i=0; i<data.size(); ++i)
+        converter(data_[i][idx], data[i]);
+    }
+    catch (utility::runtime_error& e) {
+      std::ostringstream msg;
+      msg << "invalid VCF::Data format for key '" << key << "'";
+      std::throw_with_nested(utility::runtime_error(msg.str()));
     }
   }
-  */
+
+
 }}}
 #endif

branches/kendall-score/yat/random/Makefile.am

@@ -22 +22 @@
 yat_libyat_la_SOURCES += yat/random/random.cc
 
-nobase_include_HEADERS += $(srcdir)/yat/random/ContinuousDistribution.h
 nobase_include_HEADERS += $(srcdir)/yat/random/copy_k_of_n.h
-nobase_include_HEADERS += $(srcdir)/yat/random/DiscreteDistribution.h
-nobase_include_HEADERS += $(srcdir)/yat/random/Distribution.h
 nobase_include_HEADERS += $(srcdir)/yat/random/random.h

branches/kendall-score/yat/random/random.cc

@@ -219 +219 @@
 
 
+  DiscreteGeneral::DiscreteGeneral(void)
+    : gen_(nullptr)
+  {}
+
+
   DiscreteGeneral::DiscreteGeneral(const statistics::Histogram& hist)
     : gen_(NULL)
@@ -233 +238 @@
   {
     preproc();
+  }
+
+
+  DiscreteGeneral::DiscreteGeneral(DiscreteGeneral&& other)
+    : Discrete(std::move(other)), gen_(nullptr), p_(std::move(other.p_))
+  {
+    gen_ = std::move(other.gen_);
   }
 
@@ -262 +274 @@
   DiscreteGeneral& DiscreteGeneral::operator=(const DiscreteGeneral& rhs)
   {
-    free();
-    p_ = rhs.p_;
-    preproc();
+    DiscreteGeneral tmp(rhs);
+    swap(*this, tmp);
     return *this;
   }
 
 
+  DiscreteGeneral& DiscreteGeneral::operator=(DiscreteGeneral&& rhs)
+  {
+    DiscreteGeneral tmp(std::move(rhs));
+    swap(*this, tmp);
+    return *this;
+  }
+
+
   unsigned long DiscreteGeneral::operator()(void) const
   {
     return gsl_ran_discrete(rng_->rng(), gen_);
+  }
+
+
+  void swap(DiscreteGeneral& lhs, DiscreteGeneral& rhs)
+  {
+    std::swap(lhs.gen_, rhs.gen_);
+    std::swap(lhs.p_, rhs.p_);
   }
 

branches/kendall-score/yat/random/random.h

@@ -341 +341 @@
   {
   public:
+    /**
+       Default constructor leaves the object uninitialized and
+       behaviour of operator() is undefined.
+
+       \since New in yat 0.19
+     */
+    DiscreteGeneral(void);
+
     ///
     /// @brief Constructor
@@ -354 +362 @@
      */
     DiscreteGeneral(const DiscreteGeneral&);
+
+    /**
+       \brief Move constructor
+
+       \since New in yat 0.19
+     */
+    DiscreteGeneral(DiscreteGeneral&&);
 
     ///
@@ -377 +392 @@
     DiscreteGeneral& operator=(const DiscreteGeneral&);
 
+    /**
+       \brief Move assignment operator
+
+       \since New in yat 0.19
+     */
+    DiscreteGeneral& operator=(DiscreteGeneral&&);
+
   private:
     void free(void);
@@ -383 +405 @@
     gsl_ran_discrete_t* gen_;
     std::vector<double> p_;
-  };
+    friend void swap(DiscreteGeneral& lhs, DiscreteGeneral& rhs);
+  };
+
+  /**
+     \relates DiscreteGeneral
+
+     \since Specialisation new in yat 0.19
+   */
+  void swap(DiscreteGeneral& lhs, DiscreteGeneral& rhs);
 
   /**

branches/kendall-score/yat/statistics/Makefile.am

@@ -36 +36 @@
   yat/statistics/LikelihoodRatioTestBinomial.cc \
   yat/statistics/Pearson.cc \
-  yat/statistics/PearsonCorrelation.cc yat/statistics/Percentiler.cc \
+  yat/statistics/PearsonCorrelation.cc \
+  yat/statistics/PercentileConfidenceInterval.cc \
+  yat/statistics/Percentiler.cc \
   yat/statistics/ROC.cc \
   yat/statistics/SAMScore.cc yat/statistics/Score.cc \
@@ -73 +75 @@
   $(srcdir)/yat/statistics/PearsonCorrelation.h \
   $(srcdir)/yat/statistics/PearsonDistance.h \
+  $(srcdir)/yat/statistics/PercentileConfidenceInterval.h \
   $(srcdir)/yat/statistics/Percentiler.h \
   $(srcdir)/yat/statistics/ROC.h \

branches/kendall-score/yat/utility/Aligner.cc

@@ -28 +28 @@
 #include <algorithm>
 #include <cassert>
+#include <cctype>
 #include <limits>
 #include <ostream>
 
+#include <iostream>
 namespace theplu {
 namespace yat {
@@ -158 +160 @@
   // ================ Cigar =======================
 
+  Aligner::Cigar::Cigar(const std::string& s)
+  {
+    try {
+      std::cerr << "Cigar: " << s << "\n";
+      std::istringstream is(s);
+      while (parse_element(is));
+    }
+    catch (invalid_argument& e) {
+      std::ostringstream msg;
+      msg << "Aligner::Cigar: " << s;
+      std::throw_with_nested(invalid_argument(msg.str()));
+    }
+  }
+
+
   Aligner::Cigar::const_iterator Aligner::Cigar::begin(void) const
   {
@@ -210 +227 @@
     assert(i<cigar_.size());
     return bam_cigar_oplen(cigar_[i]);
+  }
+
+
+  bool Aligner::Cigar::parse_element(std::istream& is)
+  {
+    char c = is.get();
+    if (!is.good())
+      return false;
+    if (!isdigit(c)) {
+      std::string msg("not a digit: '");
+      msg += c;
+      msg += "'";
+      throw invalid_argument(msg);
+    }
+    uint32_t len = c - '0';
+
+    while (is.get(c).good()) {
+      if (isdigit(c))
+        len = 10 * len + (c - '0');
+      else {
+        push_back(cigar_table(static_cast<uint8_t>(c)), len);
+        return true;
+      }
+    }
+    throw invalid_argument("Cigar::parse_element: missing operator");
+    return true;
   }
 

branches/kendall-score/yat/utility/Aligner.h

@@ -190 +190 @@
 
       /**
+         Default constructor
+       */
+      Cigar(void) = default;
+
+      /**
+         \param s string in same format as output from operator<<,
+         i.e., an concatenated string of integer followed by one of
+         "MIDNSHP=XB".
+
+         \since New in yat 0.19
+       */
+      explicit Cigar(const std::string& s);
+
+      /**
          \return iterator pointing to first element
 
@@ -302 +316 @@
     private:
       std::deque<uint32_t> cigar_;
+
+      // parse a string of type 12M and push_back into cigar. Format
+      // is is first an integer followed by a 1-char describing the
+      // operation (see Cigar.h)
+      bool parse_element(std::istream& is);
 
       // calculate length only counting operations whose type is set

branches/kendall-score/yat/utility/Cigar.h

@@ -30 +30 @@
 // allow inclusion of config_bam.h so this file is available also without bam.h
 #ifdef YAT_HAVE_HTSLIB
-#include "yat/omic/config_bam.h"
 #include <htslib/sam.h>
 #else // if sam.h is not available #define CIGAR
+#include <cstdint> // needed for int8_t
 /// describe how CIGAR operation/length is packed into a 32-bit
 #define BAM_CIGAR_SHIFT 4
@@ -85 +85 @@
 #endif // end of backport
 
+namespace theplu {
+namespace yat {
+namespace utility {
+
+  /**
+     The inverse of BAM_CIGAR_STR[x], where BAM_CIGAR_STR is
+     "MIDNSHP=XB".
+
+     \throws if input is not one of "MIDNSHP=XB".
+
+     \since New in yat 0.19
+  */
+  int8_t cigar_table(unsigned char c);
+
+}}} // end of namespace utility, yat and theplu
+
 #endif // end of file

branches/kendall-score/yat/utility/Deleter.h

@@ -23 +23 @@
 */
 
+#include <new> // for delete operator
+
 namespace theplu {
 namespace yat {
@@ -31 +33 @@
 
      The class is typically used as second argument to a
-     boost::shared_ptr, which enables to decide at runtime whether the
+     std::shared_ptr, which enables to decide at runtime whether the
      shared_ptr should own the pointee, i.e., should the pointee be
      destructed at destruction of last shared_ptr pointing to the

branches/kendall-score/yat/utility/Exception.cc

@@ -35 +35 @@
 namespace utility {
 
+  invalid_argument::invalid_argument(const std::string& message)
+    : std::invalid_argument(message)
+  {}
+
+
   runtime_error::runtime_error(std::string message)
     : std::runtime_error(message) 

branches/kendall-score/yat/utility/Exception.h

@@ -31 +31 @@
 namespace utility {
 
-  
+  /**
+     \brief Class used for all invalid arguments detected within yat library.
+
+     \since New in yat 0.19
+   */
+  class invalid_argument : public std::invalid_argument
+  {
+  public:
+    /**
+       \brief Constructor
+
+       \param message message to be displayed using function what().
+     */
+    invalid_argument(const std::string& message);
+  };
+
 
   /**

branches/kendall-score/yat/utility/Makefile.am

@@ -23 +23 @@
   yat/utility/Alignment.cc \
   yat/utility/BasicMatrix.cc \
+  yat/utility/Cigar.cc \
   yat/utility/ColumnStream.cc \
   yat/utility/CommandLine.cc \

branches/kendall-score/yat/utility/Segment.h

@@ -66 +66 @@
     Segment(const T& begin, const T& end)
       : begin_(begin), end_(end) {}
+
+    /**
+       \brief Constructor
+
+       Creates a segment [begin, end)
+
+       \since New in yat 0.19
+     */
+    Segment(T&& begin, T&& end)
+      : begin_(std::move(begin)), end_(std::move(end)) {}
 
     /**

branches/kendall-score/yat/utility/SegmentSet.h

@@ -7 +7 @@
   Copyright (C) 2010 Peter Johansson
   Copyright (C) 2012 Jari Häkkinen
-  Copyright (C) 2014, 2016 Peter Johansson
+  Copyright (C) 2014, 2016, 2021 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -45 +45 @@
    */
   template<typename T, class Compare = std::less<T> >
-  class SegmentSet 
-    : public SegmentTree<std::set<Segment<T, Compare>, 
+  class SegmentSet
+    : public SegmentTree<std::set<Segment<T, Compare>,
                                   SegmentCompare<T, Compare> >,
                          Compare,
@@ -67 +67 @@
       std::pair<typename me::iterator, typename me::iterator> p =
         this->overlap_range(segment);
-      return insert_merge(p, segment);
+      Segment<T> tmp(segment);
+      return move_insert_merge(p, std::move(tmp));
+    }
+
+    /**
+       insert \a segment into set. If there is no gap between \a
+       segment and neighboring segments the segments are merged.
+
+       \since New in yat 0.19
+     */
+    typename me::const_iterator
+    insert_merge(typename me::value_type&& segment)
+    {
+      std::pair<typename me::iterator, typename me::iterator> p =
+        this->overlap_range(segment);
+      return move_insert_merge(p, std::move(segment));
     }
 
@@ -83 +98 @@
                                        const typename me::value_type& segment)
     {
+      typename me::value_type tmp(segment);
+      return insert_merge(hint, std::move(tmp));
+    }
+
+
+    /**
+       \since New in yat 0.19
+     */
+    typename me::iterator
+    insert_merge(typename me::iterator hint,
+                 typename me::value_type&& segment)
+    {
       std::pair<typename me::iterator, typename me::iterator> p(hint, hint);
       if (this->container_.empty())
-        return insert_merge(p, segment);
+        return move_insert_merge(p, std::move(segment));
 
       // If hint points to an element that is less than segment, hint
       // is no good and we ignore the hint.
       if (hint!=this->end() && compare(*hint, segment))
-        return insert_merge(segment);
+        return insert_merge(std::move(segment));
 
       if (p.first!=this->begin()) {
@@ -97 +124 @@
         // no good.
         if (compare(segment, *p.first))
-          return insert_merge(segment);
+          return insert_merge(std::move(segment));
         // find first element that is smaller than segment
         while (p.first!=this->begin() && !compare(*p.first, segment))
@@ -111 +138 @@
         ++p.second;
 
-      return insert_merge(p, segment);
-    }
+      return move_insert_merge(p, std::move(segment));
+    }
+
 
     /**
@@ -132 +160 @@
     }
   private:
-    // used by public functions insert_merge.
+    // used by functions merge_basic. This function does the actual
+    // work. Note that it takes an rvalue; functions that only have
+    // access to an lvalue const& need to create a (temporary) copy
+    // that can be moved in.
     //
     // p.first points to the first segment that overlaps with \a segment or
@@ -138 +169 @@
     // p.second points to the first segment that is greater than \a segment
     typename me::const_iterator
-    insert_merge(const std::pair<typename me::iterator,
-                                 typename me::iterator>& p,
-                 const typename me::value_type& segment)
+    move_insert_merge(const std::pair<typename me::iterator,
+                                      typename me::iterator>& p,
+                      typename me::value_type&& segment)
     {
       YAT_ASSERT(p.first==this->end() || !compare(*p.first, segment));
       YAT_ASSERT(p.second==this->end() || compare(segment, *p.second));
       if (p.first==p.second) { // no overlap between set and segment
-        return this->container_.insert(p.first, segment);
+        return this->container_.insert(p.first, std::move(segment));
       }
       /*
@@ -166 +197 @@
 
       this->container_.erase(p.first, p.second);
-      return this->container_.insert(p.second, segment2);
+      return this->container_.insert(p.second, std::move(segment2));
     }
 

branches/kendall-score/yat/utility/SegmentTree.h

@@ -5 +5 @@
 
 /*
-  Copyright (C) 2010, 2011, 2012, 2013 Peter Johansson
+  Copyright (C) 2010, 2011, 2012, 2013, 2021 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -29 +29 @@
 #include <algorithm>
 #include <functional>
+#include <utility>
 
 namespace theplu {
@@ -180 +181 @@
 
     /**
+       Same as insert(const&) but move \a value rather than copy.
+
+       \since New in yat 0.19
+     */
+    std::pair<iterator, bool> insert(value_type&& value);
+
+    /**
        \return Comparison functor to compare two keys (Segment)
      */
     key_compare key_comp(void) const
     {
-      return key_compare(compare);
+      return container_.key_comp();
     }
 
@@ -226 +234 @@
        \c values
      */
-    value_compare value_comp(void) const { return key_comp(); }
+    value_compare value_comp(void) const { return container_.value_comp(); }
 
   protected:
@@ -301 +309 @@
 
   template<typename T, class Compare, class Value2Key>
+  std::pair<typename SegmentTree<T, Compare, Value2Key>::iterator, bool>
+  SegmentTree<T, Compare,Value2Key>::insert(value_type&& segment)
+  {
+    return container_.insert(std::move(segment));
+  }
+
+
+  template<typename T, class Compare, class Value2Key>
   typename SegmentTree<T, Compare, Value2Key>::iterator
   SegmentTree<T, Compare,Value2Key>::lower_bound(const element_type& element)