[med-svn] [bowtie2] 01/05: New upstream version 2.3.4.1
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Wed Feb 7 23:08:38 UTC 2018
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository bowtie2.
commit 2805c806421cebb0ffcb5a3b5c3ec17c524f26ac
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Wed Feb 7 22:11:46 2018 +0100
New upstream version 2.3.4.1
---
MANUAL | 29 ++++++++++++-----------------
MANUAL.markdown | 2 +-
Makefile | 8 ++++----
NEWS | 5 +++++
VERSION | 2 +-
bowtie2-inspect | 1 -
doc/manual.html | 6 +++---
doc/website/manual.ssi | 4 ++--
doc/website/recent_news.ssi | 5 +++++
doc/website/rhsidebar.ssi | 4 ++--
outq.h | 12 ++++++++----
11 files changed, 43 insertions(+), 35 deletions(-)
diff --git a/MANUAL b/MANUAL
index f8a528a..8544c70 100644
--- a/MANUAL
+++ b/MANUAL
@@ -128,10 +128,11 @@ Building from source
Building Bowtie 2 from source requires a GNU-like environment with GCC,
GNU Make and other basics. It should be possible to build Bowtie 2 on
most vanilla Linux installations or on a Mac installation with Xcode
-installed. Bowtie 2 can also be built on Windows using a 64-bit MinGW
-distribution and MSYS. In order to simplify the MinGW setup it might be
-worth investigating popular MinGW personal builds since these are coming
-already prepared with most of the toolchains needed.
+installed. (But see note about the TBB library below). Bowtie 2 can also
+be built on Windows using a 64-bit MinGW distribution and MSYS. In order
+to simplify the MinGW setup it might be worth investigating popular
+MinGW personal builds since these are coming already prepared with most
+of the toolchains needed.
First, download the source package from the sourceforge site. Make sure
you’re getting the source package; the file downloaded should end in
@@ -140,18 +141,12 @@ the Bowtie 2 tools by running GNU make (usually with the command make,
but sometimes with gmake) with no arguments. If building with MinGW, run
make from the MSYS environment.
-Bowtie 2 is using the multithreading software model in order to speed up
-execution times on SMP architectures where this is possible. The
-Threading Building Blocks library, TBB, is now the default threading
-library in Bowtie 2. On POSIX platforms (like Linux, Mac OS, etc.) if
-TBB is not available the pthread library will be used. Although it is
-possible to use pthread library on Windows, a non-POSIX platform, due to
-performance reasons Bowtie 2 will try to use Windows native
-multithreading if possible. We recommend that you first install the
-Threading Building Blocks library, but if unable to do so please specify
-make NO_TBB=1. TBB comes installed by default on many popular Linux
-distros. Please note, packages built without TBB will have _-legacy_
-appended to the name.
+Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the
+Threading Building Blocks library (TBB) for this. If TBB is not
+available on your system (e.g. make prints an error like
+tbb/mutex.h: No such file or directory), you can install it yourself
+(see Threading Building Blocks library) or build Bowtie 2 with
+make NO_TBB=1 to use pthreads or Windows native multithreading instead.
Adding to PATH
@@ -1458,7 +1453,7 @@ library (i.e. if BOWTIE_PTHREADS=0 is not specified at build time).
Guarantees that output SAM records are printed in an order corresponding
to the order of the reads in the original input file, even when -p is
set greater than 1. Specifying --reorder and setting -p greater than 1
-causes Bowtie 2 to run somewhat slower and use somewhat more memory then
+causes Bowtie 2 to run somewhat slower and use somewhat more memory than
if --reorder were not specified. Has no effect if -p is set to 1, since
output order will naturally correspond to input order in that case.
diff --git a/MANUAL.markdown b/MANUAL.markdown
index f23cfdc..2c3b40c 100644
--- a/MANUAL.markdown
+++ b/MANUAL.markdown
@@ -1841,7 +1841,7 @@ not specified at build time).
Guarantees that output SAM records are printed in an order corresponding to the
order of the reads in the original input file, even when [`-p`] is set greater
than 1. Specifying `--reorder` and setting [`-p`] greater than 1 causes Bowtie
-2 to run somewhat slower and use somewhat more memory then if `--reorder` were
+2 to run somewhat slower and use somewhat more memory than if `--reorder` were
not specified. Has no effect if [`-p`] is set to 1, since output order will
naturally correspond to input order in that case.
diff --git a/Makefile b/Makefile
index d4c8d63..69ce0e9 100644
--- a/Makefile
+++ b/Makefile
@@ -30,6 +30,7 @@ GCC_SUFFIX :=
CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX ?= $(CPP)
+CXXFLAGS += -std=c++98
HEADERS := $(wildcard *.h)
BOWTIE_MM := 1
@@ -47,9 +48,8 @@ ifneq (,$(findstring MINGW,$(shell uname)))
WINDOWS := 1
MINGW := 1
# POSIX memory-mapped files not currently supported on Windows
- BOWTIE_MM := 0
- BOWTIE_SHARED_MEM := 0
- CXXFLAGS += -ansi
+ BOWTIE_MM :=
+ BOWTIE_SHARED_MEM :=
endif
MACOS :=
@@ -546,7 +546,7 @@ test: simple-test random-test
.PHONY: clean
clean:
- rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN)\
+ rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) \
$(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) \
bowtie2-src.zip bowtie2-bin.zip
rm -f core.* .tmp.head
diff --git a/NEWS b/NEWS
index 10a1cac..b861fd6 100644
--- a/NEWS
+++ b/NEWS
@@ -19,6 +19,11 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu
Version Release History
=======================
+Version 2.3.4.1 - Feb 3, 2018
+
+ * Fixed an issue with `--reorder` that caused bowtie2 to crash
+ while reordering SAM output
+
Version 2.3.4 - Dec 29, 2017
* Fixed major issue causing corrupt SAM output when using many
diff --git a/VERSION b/VERSION
index 3f684d2..726b895 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.4
+2.3.4.1
diff --git a/bowtie2-inspect b/bowtie2-inspect
index dc89d1b..1424c6f 100755
--- a/bowtie2-inspect
+++ b/bowtie2-inspect
@@ -77,7 +77,6 @@ def main():
argv.appendleft('--wrapper')
argv.appendleft(inspect_bin_spec)
logging.info('Command: %s' % ' '.join(argv))
- print argv
subprocess.call(argv)
if __name__ == '__main__':
diff --git a/doc/manual.html b/doc/manual.html
index 7b4d1e4..e361b5f 100644
--- a/doc/manual.html
+++ b/doc/manual.html
@@ -133,9 +133,9 @@
<h1 id="obtaining-bowtie-2">Obtaining Bowtie 2</h1>
<p>Download Bowtie 2 sources and binaries from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">Download</a> section of the Sourceforge site. Binaries are available for the Intel <code>x86_64</code> architecture running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself, make sure to get the source package, i.e., the filename that ends in “-source.zip”.</p>
<h2 id="building-from-source">Building from source</h2>
-<p>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <a href="http://developer.apple.com/xcode/">Xcode</a> installed. Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepare [...]
+<p>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <a href="http://developer.apple.com/xcode/">Xcode</a> installed. (But see note about the TBB library below). Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal b [...]
<p>First, download the source package from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">sourceforge site</a>. Make sure you’re getting the source package; the file downloaded should end in <code>-source.zip</code>. Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with MinGW, run <code> [...]
-<p>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. The Threading Building Blocks library, TBB, is now the default threading library in Bowtie 2. On POSIX platforms (like Linux, Mac OS, etc.) if TBB is not available the pthread library will be used. Although it is possible to use pthread library on Windows, a non-POSIX platform, due to performance reasons Bowtie 2 will try to use Windows native multithre [...]
+<p>Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading Building Blocks library (TBB) for this. If TBB is not available on your system (e.g. <code>make</code> prints an error like <code>tbb/mutex.h: No such file or directory</code>), you can install it yourself (see <a href="https://www.threadingbuildingblocks.org">Threading Building Blocks library</a>) or build Bowtie 2 with <code>make NO_TBB=1</code> to use pthreads or Windows native multithreading instead.</p>
<h2 id="adding-to-path">Adding to PATH</h2>
<p>By adding your new Bowtie 2 directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH environment variable</a>, you ensure that whenever you run <code>bowtie2</code>, <code>bowtie2-build</code> or <code>bowtie2-inspect</code> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system’s instructions for adding the directory to your <a href= [...]
<p>If you would like to install Bowtie 2 by copying the Bowtie 2 executable files to an existing directory in your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>, make sure that you copy all the executables, including <code>bowtie2</code>, <code>bowtie2-align-s</code>, <code>bowtie2-align-l</code>, <code>bowtie2-build</code>, <code>bowtie2-build-s</code>, <code>bowtie2-build-l</code>, <code>bowtie2-inspect</code>, <code>bowtie2-inspect-s</code> and <code>bowtie2-inspect- [...]
@@ -1016,7 +1016,7 @@ Seed 4 rc: TTATGCATGA</code></pre>
<pre><code>--reorder</code></pre>
</td>
<td>
-<p>Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when <a href="#bowtie2-options-p"><code>-p</code></a> is set greater than 1. Specifying <code>--reorder</code> and setting <a href="#bowtie2-options-p"><code>-p</code></a> greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory then if <code>--reorder</code> were not specified. Has no effect if <a href="#bowtie2-options-p"><code [...]
+<p>Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when <a href="#bowtie2-options-p"><code>-p</code></a> is set greater than 1. Specifying <code>--reorder</code> and setting <a href="#bowtie2-options-p"><code>-p</code></a> greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory than if <code>--reorder</code> were not specified. Has no effect if <a href="#bowtie2-options-p"><code [...]
</td>
</tr>
<tr>
diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi
index 0afcb0a..cb636a0 100644
--- a/doc/website/manual.ssi
+++ b/doc/website/manual.ssi
@@ -1,5 +1,5 @@
<h1>Table of Contents</h1>
-<p> Version <b>2.3.3</b></p>
+<p> Version <b>2.3.4.1</b></p>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
@@ -1005,7 +1005,7 @@ Seed 4 rc: TTATGCATGA</code></pre>
<pre><code>--reorder</code></pre>
</td>
<td>
-<p>Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when <a href="#bowtie2-options-p"><code>-p</code></a> is set greater than 1. Specifying <code>--reorder</code> and setting <a href="#bowtie2-options-p"><code>-p</code></a> greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory then if <code>--reorder</code> were not specified. Has no effect if <a href="#bowtie2-options-p"><code [...]
+<p>Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when <a href="#bowtie2-options-p"><code>-p</code></a> is set greater than 1. Specifying <code>--reorder</code> and setting <a href="#bowtie2-options-p"><code>-p</code></a> greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory than if <code>--reorder</code> were not specified. Has no effect if <a href="#bowtie2-options-p"><code [...]
</td>
</tr>
<tr>
diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
index c51b343..187b3ab 100644
--- a/doc/website/recent_news.ssi
+++ b/doc/website/recent_news.ssi
@@ -1,3 +1,8 @@
+<h2>Version 2.3.4.1 - February 03, 2018</h2>
+<ul>
+ <li>Fixed an issue with <tt><a href="manual.shtml#bowtie2-options-reorder">--reorder</a></tt> that caused bowtie2 to crash while reordering SAM output</li>
+</ul>
+
<h2>Version 2.3.4 - December 29, 2017</h2>
<ul>
<li>Fixed major issue causing corrupt SAM output when using many threads (<tt><a href="manual.shtml#bowtie2-options-p">-p/--threads</a></tt>) on certain systems.</li>
diff --git a/doc/website/rhsidebar.ssi b/doc/website/rhsidebar.ssi
index e425c1b..0222e5e 100644
--- a/doc/website/rhsidebar.ssi
+++ b/doc/website/rhsidebar.ssi
@@ -18,10 +18,10 @@
</tr>
<tr>
<td>
- <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4">Bowtie2 2.3.4</a>
+ <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1">Bowtie2 2.3.4.1</a>
</td>
<td align="right">
- 12/29/17
+ 02/03/18
</td>
</tr>
<tr>
diff --git a/outq.h b/outq.h
index 537d5f8..da38388 100644
--- a/outq.h
+++ b/outq.h
@@ -59,6 +59,8 @@ public:
threadSafe_(threadSafe),
mutex_m(),
nthreads_(nthreads),
+ perThreadBuf(NULL),
+ perThreadCounter(NULL),
perThreadBufSize_(perThreadBufSize)
{
nstarted_=0;
@@ -77,11 +79,13 @@ public:
}
~OutputQueue() {
- for (size_t i = 0; i < nthreads_; i++) {
- delete[] perThreadBuf[i];
+ if(perThreadBuf != NULL) {
+ for (size_t i = 0; i < nthreads_; i++) {
+ delete[] perThreadBuf[i];
+ }
+ delete[] perThreadBuf;
+ delete[] perThreadCounter;
}
- delete[] perThreadBuf;
- delete[] perThreadCounter;
}
/**
--
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