[med-svn] [scrm] 01/05: Imported Upstream version 1.7.2
Andreas Tille
tille at debian.org
Thu May 19 16:03:26 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository scrm.
commit ad9ebe701368814e641fc4e3b1521233a4c023b4
Author: Andreas Tille <tille at debian.org>
Date: Thu May 19 17:52:53 2016 +0200
Imported Upstream version 1.7.2
---
.travis.yml | 1 +
.travis/build_static_binaries.sh | 3 ++-
NEWS.md | 13 +++++++++++++
README.md | 11 ++++-------
configure.ac | 2 +-
doc/scrm.1 | 2 +-
src/contemporaries_container.h | 20 +++++++++++++-------
src/forest.cc | 4 +++-
src/summary_statistics/oriented_forest.h | 1 +
src/time_interval.cc | 4 ++--
tests/test_binaries.sh | 12 ++++++++----
11 files changed, 49 insertions(+), 24 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index 5da88cd..277f129 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,6 +31,7 @@ deploy:
secure: UrEhKzTdSr7NB4ptDYcWKN02XjfgJgN1fNFu8G2a52Jpk1Z3UeenbmKxIDLj11JUlU427br7t1oQyScYSYEGEM5VEI0aWf7D2i9cPfSRD9QYnHOPG2XZE/xgkwWAm0s4TjnTBmudGSxs9g2KRjDXLz1f191jVGIghnHlxw/C9Ok=
file:
- "scrm-src.tar.gz"
+ - "scrm-x64-static"
- "scrm-x64-static.tar.gz"
- "scrm-win32.zip"
- "scrm-win64.zip"
diff --git a/.travis/build_static_binaries.sh b/.travis/build_static_binaries.sh
index 4731b38..c220ad2 100755
--- a/.travis/build_static_binaries.sh
+++ b/.travis/build_static_binaries.sh
@@ -3,5 +3,6 @@
# Build statically linked binaries
CXXFLAGS="-O3" LDFLAGS='-static' ./configure || exit 1
make clean && make && \
- tar -zcvf "scrm-x64-static.tar.gz" scrm doc/manual.html
+ tar -zcvf "scrm-x64-static.tar.gz" scrm doc/manual.html &&
+ cp scrm scrm-x64-static
diff --git a/NEWS.md b/NEWS.md
index 73781d2..2e5b8d9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,18 @@
scrm Version History
========================
+scrm 1.7.2
+------------------------
+Released: 2016-04-10
+
+### Bug Fixes
++ Fixes a different bug that could occur when using the "-eI" option.
+ The contemporaries buffer was always cleared correctly between
+ repetitions, and could cause scrm to throw an error (#104).
+ Thanks again to @jackkamm for reporting this bug.
+
+
+
scrm 1.7.1
------------------------
Released: 2016-03-23
@@ -12,6 +24,7 @@ Released: 2016-03-23
and the time of the "-eI" event (if any), and neglect all events
during that time. We recommend to repeat all simulations which
used "-eI" with the updated version (#102).
+ Thanks to @jackkamm for reporting this bug.
diff --git a/README.md b/README.md
index 4d2ad57..43aa6cd 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,6 @@
+[](http://www.repostatus.org/#active)
+[](https://travis-ci.org/scrm/scrm)
+
scrm
====
@@ -14,12 +17,7 @@ You can download the latest stable release packaged for a variety of different
platform from [_scrm_'s homepage][1].
Instructions on building the binary from the source packages are available in the [wiki][3].
-### Stable/Development Version From GitHub
-
-Version | Branch | Build Status
-------------------- | ------ | -----------------
-Stable Version | stable | [](https://travis-ci.org/scrm/scrm)
-Development Version | master | [](https://travis-ci.org/scrm/scrm)
+### Development Version From GitHub
You can also install `scrm` directly from the git repository. Here, you need to install `autoconf` first:
@@ -39,7 +37,6 @@ Afterwards you can build the binary using
make
```
-
## Usage
We designed scrm to be compatible to the famous program `ms` from Richard R. Hudson.
You can use it as a drop in replacement for `ms` if you avoid the options `-c` and `-s`.
diff --git a/configure.ac b/configure.ac
index f348720..35ed415 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([scrm], [1.7.1],[https://github.com/paulstaab/scrm/issues])
+AC_INIT([scrm], [1.7.2],[https://github.com/paulstaab/scrm/issues])
AM_INIT_AUTOMAKE([subdir-objects -Wall -Werror foreign])
# Use -O3 as default optimization level
diff --git a/doc/scrm.1 b/doc/scrm.1
index 272c6d9..0adc252 100644
--- a/doc/scrm.1
+++ b/doc/scrm.1
@@ -1,4 +1,4 @@
-.TH SCRM 1 "Mar 2015" "Version 1.4.0"
+.TH SCRM 1 "April 2016" "Version 1.7.2"
.SH NAME
scrm \- An accurate coalescent simulator for genome-scale sequences
diff --git a/src/contemporaries_container.h b/src/contemporaries_container.h
index 75ff36c..ff84caa 100644
--- a/src/contemporaries_container.h
+++ b/src/contemporaries_container.h
@@ -111,7 +111,7 @@ class ContemporariesContainer {
void remove(Node *node);
void replaceChildren(Node *add_node);
void replace(Node *add_node, Node *del_node_1, Node *del_node_2 = NULL);
- void clear();
+ void clear(const bool clear_buffer = true);
void buffer(const double current_time);
Node* sample(const size_t pop) const;
@@ -261,18 +261,24 @@ inline void ContemporariesContainer::replace(Node *add_node, Node *del_node_1, N
if (!add_node->is_root()) add(add_node);
}
-inline void ContemporariesContainer::clear() {
+
+inline void ContemporariesContainer::clear(const bool clear_buffer) {
if (use_set_) {
- for (auto it = contemporaries_set().begin(); it != contemporaries_set().end(); ++it) {
- if ((*it).size() > 0) (*it).clear();
+ for (auto & pop_container : contemporaries_set()) pop_container.clear();
+ if (clear_buffer) {
+ for (auto & pop_container : buffer_set()) pop_container.clear();
}
} else {
- for (auto it = contemporaries_vector().begin(); it != contemporaries_vector().end(); ++it) {
- if ((*it).size() > 0) (*it).clear();
+ for (auto & pop_container : contemporaries_vector()) pop_container.clear();
+ if (clear_buffer) {
+ for (auto & pop_container : buffer_vector()) pop_container.clear();
}
}
+ if (clear_buffer) buffer_time_ = DBL_MAX;
+ assert(this->empty());
}
+
inline size_t ContemporariesContainer::size(const size_t pop) const {
if (use_set_) return contemporaries_set().at(pop).size();
else return contemporaries_vector().at(pop).size();
@@ -292,7 +298,7 @@ inline size_t ContemporariesContainer::size(const size_t pop) const {
inline void ContemporariesContainer::buffer(const double current_time) {
buffer_time_ = current_time;
use_first_ = 1 - use_first_;
- this->clear();
+ this->clear(false);
}
// Uniformly samples a random node from the current contemporaries.
diff --git a/src/forest.cc b/src/forest.cc
index 3f02869..9db3404 100644
--- a/src/forest.cc
+++ b/src/forest.cc
@@ -288,6 +288,7 @@ void Forest::buildInitialTree() {
assert(this->segment_count() == 0);
assert(this->rec_bases_.size() == 1);
assert(this->model().getCurrentSequencePosition() == 0.0);
+ assert(this->contemporaries()->empty());
this->set_next_base(0.0);
++current_rec_;
@@ -313,7 +314,7 @@ void Forest::buildInitialTree() {
if (new_leaf->height() == 0.0) last_added_node = new_leaf;
dout << "* starting coalescences" << std::endl;
- //Coalesces the separate tree into the main tree
+ // Coalesces the separate tree into the main tree
this->sampleCoalescences(new_leaf);
dout << "* * Tree:" << std::endl;
@@ -1260,6 +1261,7 @@ void Forest::clear() {
// Clear nodes
nodes()->clear();
+ contemporaries()->clear(true);
// Reset Position & Segment Counts
this->rec_bases_.clear();
diff --git a/src/summary_statistics/oriented_forest.h b/src/summary_statistics/oriented_forest.h
index c8b7bbf..ad382ef 100644
--- a/src/summary_statistics/oriented_forest.h
+++ b/src/summary_statistics/oriented_forest.h
@@ -43,6 +43,7 @@ class OrientedForest : public SummaryStatistic
void printSegmentOutput(std::ostream &output) const;
void clear() { }
+ double segment_length() const { return segment_length_; }
std::vector<int> parents() const { return parents_; }
std::vector<double> heights() const { return heights_; }
diff --git a/src/time_interval.cc b/src/time_interval.cc
index 61d9a57..012ad83 100644
--- a/src/time_interval.cc
+++ b/src/time_interval.cc
@@ -49,7 +49,7 @@ TimeIntervalIterator::TimeIntervalIterator(Forest *forest) {
// Used only for unit testing, and hence private.
this->forest_ = forest;
this->contemporaries_ = &(forest->contemporaries_);
- this->contemporaries_->clear();
+ this->contemporaries_->clear(false);
this->node_iterator_ = forest->nodes()->iterator();
this->good_ = false;
this->inside_node_ = NULL;
@@ -142,7 +142,7 @@ void TimeIntervalIterator::next() {
}
void TimeIntervalIterator::searchContemporariesBottomUp(Node* node, const bool use_buffer) {
- contemporaries()->clear();
+ contemporaries()->clear(false);
Node* start_node = NULL;
if ( use_buffer ) {
diff --git a/tests/test_binaries.sh b/tests/test_binaries.sh
index 807304b..88e8641 100755
--- a/tests/test_binaries.sh
+++ b/tests/test_binaries.sh
@@ -39,12 +39,15 @@ echo "Testing Initial Tree"
test_scrm 3 100 -t 5 -L -oSFS -transpose-segsites || exit 1
test_scrm 50 20 -O || exit 1
test_scrm 25 1 -T || exit 1
+ test_scrm 10 5 -I 1 5 -eI 1.0 5 -L || exit 1
+ test_scrm 10 5 -I 2 2 2 0.5 -eI 1.0 3 3 -L || exit 1
echo ""
echo "Testing Recombinations"
- test_scrm 4 10 -r 5 100 || exit 1
- test_scrm 6 10 -r 1 100 -t 5 -L -T -transpose-segsites || exit 1
- test_scrm 8 10 -r 1 100 -t 5 -oSFS -O || exit 1
+ test_scrm 4 10 -r 5 100 -l -1 || exit 1
+ test_scrm 6 10 -r 1 100 -t 5 -L -T -transpose-segsites -l -1 || exit 1
+ test_scrm 8 10 -r 1 100 -t 5 -oSFS -O -l -1 || exit 1
+ test_scrm 10 5 -r 5 100 -I 2 2 2 0.5 -eI 1.0 3 3 -L -l -1 || exit 1
echo ""
echo "Testing Pruning"
@@ -52,6 +55,7 @@ echo "Testing Pruning"
test_scrm 3 50 -r 10 500 -l 0 -t 1 -oSFS || exit 1
test_scrm 10 20 -r 10 500 -l 2r -L || exit 1
test_scrm 10 20 -r 1 500 -l -1 -T || exit 1
+ test_scrm 10 5 -r 5 100 -I 2 2 2 0.5 -eI 1.0 3 3 -L -l 2r || exit 1
echo ""
echo "Testing Migration"
@@ -88,6 +92,6 @@ echo ""
echo "Various Edge Cases"
test_scrm 6 1 -I 2 3 3 0.5 -r 1 100 -es 0 2 0.5 -ej 1 3 1 -t 1 || exit 1
test_scrm 10 1 -es 1.0 1 0.5 -ej 1.0 2 1 || exit 1
- test_scrm 4 1 -t 1.0 -I 2 2 0 -ej 1.0 1 2 -eI 3.5 0 2
+ test_scrm 4 1 -t 1.0 -I 2 2 0 -ej 1.0 1 2 -eI 3.5 0 2 || exit 1
echo ""
--
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