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Fix conflicts and merge
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alexpreynolds committed Jan 24, 2017
2 parents 7f28320 + 298f4b6 commit d4aa2fc
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34 changes: 12 additions & 22 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,29 +1,19 @@
language: cpp
os:
- linux
- osx
compiler:
- gcc
# - clang
# Change this to your needs
- clang
before_install:
# g++ 4.8.3
- if [ "$CXX" == "g++" ]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi
# clang 3.4
- if [ "$CXX" == "clang++" ]; then sudo add-apt-repository -y ppa:h-rayflood/llvm; fi
- sudo apt-get update -qq
- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi; fi
- if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qq; fi
install:
# g++ 4.8.3
- if [ "$CXX" == "g++" ]; then sudo apt-get install -qq g++-4.8; fi
- if [ "$CXX" == "g++" ]; then sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50; fi
# clang 3.4
- if [ "$CXX" == "clang++" ]; then sudo apt-get install --allow-unauthenticated -qq clang-3.4; fi
- if [ "$CXX" == "clang++" ]; then export CXXFLAGS="-std=c++0x -stdlib=libc++"; fi
- if [ "$CXX" == "clang++" ]; then svn co --quiet http://llvm.org/svn/llvm-project/libcxx/trunk libcxx; fi
- if [ "$CXX" == "clang++" ]; then cd libcxx/lib && bash buildit; fi
- if [ "$CXX" == "clang++" ]; then sudo cp ./libc++.so.1.0 /usr/lib/; fi
- if [ "$CXX" == "clang++" ]; then sudo mkdir /usr/include/c++/v1; fi
- if [ "$CXX" == "clang++" ]; then cd .. && sudo cp -r include/* /usr/include/c++/v1/; fi
- if [ "$CXX" == "clang++" ]; then cd /usr/lib && sudo ln -sf libc++.so.1.0 libc++.so; fi
- if [ "$CXX" == "clang++" ]; then sudo ln -sf libc++.so.1.0 libc++.so.1 && cd $cwd; fi
#- if [ "$CXX" == "clang++" ]; then export CXX="clang++-3.4"; fi
script: make -j4
- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq gcc-4.8; fi; fi
- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 50; fi; fi
- if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq g++-4.8; fi; fi
- if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50; fi; fi
script:
- if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make -j4; fi; fi
- if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make -j4; fi; fi
6 changes: 6 additions & 0 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ install_gprof: prep_c install_conversion_scripts install_starchcluster_scripts
install_starchcluster_scripts: prep_c
-cp ${APPDIR}/starch/bin/starchcluster_sge ${BINDIR}/
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel ${BINDIR}/
-cp ${APPDIR}/starch/bin/starchcluster_slurm ${BINDIR}/

install_conversion_scripts: prep_c
-cp ${APPDIR}/conversion/src/wrappers/bam2bed ${BINDIR}/bam2bed
Expand All @@ -88,8 +89,10 @@ install_conversion_scripts: prep_c
-cp ${APPDIR}/conversion/src/wrappers/vcf2starch ${BINDIR}/vcf2starch
-cp ${APPDIR}/conversion/src/wrappers/wig2starch ${BINDIR}/wig2starch
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_sge ${BINDIR}/bam2bed_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_slurm ${BINDIR}/bam2bed_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_gnuParallel ${BINDIR}/bam2bed_gnuParallel
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_sge ${BINDIR}/bam2starch_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_slurm ${BINDIR}/bam2starch_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_gnuParallel ${BINDIR}/bam2starch_gnuParallel

install_osx_packaging_bins: prep_c
Expand All @@ -104,6 +107,7 @@ install_osx_packaging_bins: prep_c
-cp ${APPDIR}/starch/bin/starchcat ${OSXPKGDIR}/
-cp ${APPDIR}/starch/bin/starchcluster_sge ${OSXPKGDIR}/starchcluster_sge
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel ${OSXPKGDIR}/starchcluster_gnuParallel
-cp ${APPDIR}/starch/bin/starchcluster_slurm ${OSXPKGDIR}/starchcluster_slurm
-cp ${APPDIR}/conversion/bin/convert2bed ${OSXPKGDIR}/
-cp ${APPDIR}/conversion/src/wrappers/bam2bed ${OSXPKGDIR}/bam2bed
-cp ${APPDIR}/conversion/src/wrappers/gff2bed ${OSXPKGDIR}/gff2bed
Expand All @@ -124,8 +128,10 @@ install_osx_packaging_bins: prep_c
-cp ${APPDIR}/conversion/src/wrappers/vcf2starch ${OSXPKGDIR}/vcf2starch
-cp ${APPDIR}/conversion/src/wrappers/wig2starch ${OSXPKGDIR}/wig2starch
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_sge ${OSXPKGDIR}/bam2bed_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_slurm ${OSXPKGDIR}/bam2bed_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_gnuParallel ${OSXPKGDIR}/bam2bed_gnuParallel
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_sge ${OSXPKGDIR}/bam2starch_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_slurm ${OSXPKGDIR}/bam2starch_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_gnuParallel ${OSXPKGDIR}/bam2starch_gnuParallel
mkdir -p ${OSXLIBDIR}

Expand Down
22 changes: 11 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
## BEDOPS v2.4.20: high-performance genomic feature operations ##
## BEDOPS v2.4.21: high-performance genomic feature operations ##

[![Build Status](https://travis-ci.org/bedops/bedops.svg?branch=master)](https://travis-ci.org/bedops/bedops) [![GitHub stars](https://img.shields.io/github/stars/bedops/bedops.svg)](https://github.com/bedops/bedops/stargazers) [![Project license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://github.com/bedops/bedops/blob/master/LICENSE) [![Documentation Status](https://readthedocs.org/projects/bedops/badge/?version=latest)](https://readthedocs.org/projects/bedops/?badge=latest)

<!-- <img src="http://bedops.readthedocs.io/en/latest/_static/logo_with_label_v2.png" align="right" style="max-width:33%" /> -->

### About ###

**BEDOPS v2.4.20** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
**BEDOPS v2.4.21** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.20** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.21** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.


### Downloads ###
Expand All @@ -28,21 +28,21 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
<tr>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.20/bedops_linux_x86_64-v2.4.20.v2.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.20/bedops_linux_i386-v2.4.20.tar.bz2">i386 (32-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.21/bedops_linux_x86_64-v2.4.21.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.21/bedops_linux_i386-v2.4.21.tar.bz2">i386 (32-bit)</a> binaries</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.20/BEDOPS.2.4.20.pkg.zip">Intel (32-/64-bit, 10.7-10.11)</a> installer package</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.21/BEDOPS.2.4.21.pkg.zip">Intel (32-/64-bit, 10.7-10.11)</a> installer package</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/archive/v2.4.20.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.20.zip">Source code</a> (zip)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.21.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.21.zip">Source code</a> (zip)</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#installation-via-source-code">Compilation instructions</a></li>
</ul>
</td>
Expand All @@ -51,19 +51,19 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv

### Documentation ###

Complete documentation for **BEDOPS v2.4.20** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
Complete documentation for **BEDOPS v2.4.21** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>

### Citation ###

If you use **BEDOPS v2.4.20** in your research, please cite the following manuscript:
If you use **BEDOPS v2.4.21** in your research, please cite the following manuscript:

> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
> [**BEDOPS: high-performance genomic feature operations**
> *Bioinformatics* (2012) 28 (14): 1919-1920.] (http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract)
### Copyright ###

> Copyright (C) 2011-2016 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
> Copyright (C) 2011-2017 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
>
> Source code, documentation and media assets released under <a href="https://github.com/bedops/bedops/blob/master/LICENSE">GNU Public License Version 2</a> (GPL v2).
2 changes: 1 addition & 1 deletion applications/bed/bedextract/src/ExtractRows.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2016 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
Expand Down
38 changes: 26 additions & 12 deletions applications/bed/bedmap/src/Bedmap.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2016 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -383,11 +383,15 @@ namespace BedMap {
typedef typename PT::PType PType;
rtn = new typename VTypes::EchoMapAll(PT(PType(), multivalColSep));
}
else if ( nm == visName<typename VTypes::EchoMapLength>() )
rtn = new typename VTypes::EchoMapLength;
else if ( nm == visName<typename VTypes::EchoMapIntersectLength>() )
rtn = new typename VTypes::EchoMapIntersectLength;
else if ( nm == visName<typename VTypes::EchoMapRange>() )
else if ( nm == visName<typename VTypes::EchoMapLength>() ) {
typedef typename VTypes::EchoMapLength::ProcessType PT;
typedef typename PT::PType PType;
rtn = new typename VTypes::EchoMapLength(PT(PType(), multivalColSep));
} else if ( nm == visName<typename VTypes::EchoMapIntersectLength>() ) {
typedef typename VTypes::EchoMapIntersectLength::ProcessType PT;
typedef typename PT::PType PType;
rtn = new typename VTypes::EchoMapIntersectLength(PT(PType(), multivalColSep));
} else if ( nm == visName<typename VTypes::EchoMapRange>() )
rtn = new typename VTypes::EchoMapRange;
else if ( nm == visName<typename VTypes::EchoRefAll>() )
rtn = new typename VTypes::EchoRefAll;
Expand Down Expand Up @@ -497,9 +501,13 @@ namespace BedMap {
}
else if ( nm == visName<typename VTypes::Max>() )
rtn = new typename VTypes::Max(pt);
else if ( nm == visName<typename VTypes::MaxElement>() ) {
typedef typename VTypes::MaxElement::ProcessType MPT;
rtn = new typename VTypes::MaxElement(MPT(precision, useScientific));
else if ( nm == visName<typename VTypes::MaxElementStable>() ) {
typedef typename VTypes::MaxElementStable::ProcessType MPT;
rtn = new typename VTypes::MaxElementStable(MPT(precision, useScientific));
}
else if ( nm == visName<typename VTypes::MaxElementRand>() ) {
typedef typename VTypes::MaxElementRand::ProcessType MPT;
rtn = new typename VTypes::MaxElementRand(MPT(precision, useScientific));
}
else if ( nm == visName<typename VTypes::Median>() )
rtn = new typename VTypes::Median(pt);
Expand All @@ -516,9 +524,13 @@ namespace BedMap {
}
else if ( nm == visName<typename VTypes::Min>() )
rtn = new typename VTypes::Min(pt);
else if ( nm == visName<typename VTypes::MinElement>() ) {
typedef typename VTypes::MinElement::ProcessType MPT;
rtn = new typename VTypes::MinElement(MPT(precision, useScientific));
else if ( nm == visName<typename VTypes::MinElementRand>() ) {
typedef typename VTypes::MinElementRand::ProcessType MPT;
rtn = new typename VTypes::MinElementRand(MPT(precision, useScientific));
}
else if ( nm == visName<typename VTypes::MinElementStable>() ) {
typedef typename VTypes::MinElementStable::ProcessType MPT;
rtn = new typename VTypes::MinElementStable(MPT(precision, useScientific));
}
else if ( nm == visName<typename VTypes::StdDev>() )
rtn = new typename VTypes::StdDev(pt);
Expand All @@ -534,6 +546,8 @@ namespace BedMap {
}
else if ( nm == visName<typename VTypes::Variance>() )
rtn = new typename VTypes::Variance(pt);
else if ( nm == visName<typename VTypes::WMean>() )
rtn = new typename VTypes::WMean(pt);

return(rtn);
}
Expand Down

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