Commit 49833fae authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.4.37+dfsg

parent 0a6ce561

.gitignore

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@@ -69,3 +69,5 @@ applications/bed/closestfeats/bin/ 
applications/bed/conversion/bin/

applications/bed/sort-bed/bin/

applications/bed/starch/bin/



.vscode
 
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.readthedocs.yml

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# .readthedocs.yml

# Read the Docs configuration file

# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details



# Required

version: 2



# Build documentation in the docs/ directory with Sphinx

sphinx:

  configuration: docs/conf.py



# Build documentation with MkDocs

#mkdocs:

#  configuration: mkdocs.yml



# Optionally build your docs in additional formats such as PDF and ePub

formats: all



# Optionally set the version of Python and requirements required to build your docs

python:

  version: 3.6

  install:

    - requirements: docs/requirements.txt
 
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README.md

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## BEDOPS v2.4.36: high-performance genomic feature operations ##

## BEDOPS v2.4.37: 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)
@@ -6,9 +6,9 @@ 


### About ###



**BEDOPS v2.4.36** 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 v2.4.37** 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 v2.4.36** 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 v2.4.37** 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 ###
@@ -16,32 +16,32 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv 
<table width="100%">

<tr>

<th width="33%" align="left">

<img src="https://bedops.readthedocs.io/en/latest/_images/linux_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">

Linux

</th>

<th width="33%" align="left">

<img src="https://bedops.readthedocs.io/en/latest/_images/macosx_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">

Mac OS X

</th>

<th width="34%" align="left">

<img src="https://bedops.readthedocs.io/en/latest/_images/source_v2.png" height="26px" style="height:26px !important; width: auto !important; margin-bottom:10px;">

Source code

</th>

</tr>

<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/v2.4.36/bedops_linux_x86_64-v2.4.36.tar.bz2">x86-64 (64-bit)</a> binaries</li>

<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.37/bedops_linux_x86_64-v2.4.37.tar.bz2">x86-64 (64-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/v2.4.36/BEDOPS.2.4.36.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>

<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.37/BEDOPS.2.4.37.pkg.zip">Intel (64-bit, 10.10-10.14)</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/v2.4.36.tar.gz">Source code</a> (tar.gz)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.36.zip">Source code</a> (zip)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.37.tar.gz">Source code</a> (tar.gz)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.37.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>
@@ -50,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv 


### Documentation ###



Complete documentation for **BEDOPS v2.4.36** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>

Complete documentation for **BEDOPS v2.4.37** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>



### Citation ###



If you use **BEDOPS v2.4.36** in your research, please cite the following manuscript:

If you use **BEDOPS v2.4.37** in your research, please cite the following manuscript:



> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.  

> [**BEDOPS: high-performance genomic feature operations**

applications/bed/bedmap/src/Bedmap.cpp

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@@ -187,6 +187,7 @@ int main(int argc, char **argv) { 
    std::cout << "  citation: " << BedMap::citation << std::endl;

    std::cout << "  version:  " << BedMap::version << std::endl;

    std::cout << "  authors:  " << BedMap::authors << std::endl;

    return EXIT_SUCCESS;

  } catch(const BedMap::NoInput& ni) { // show usage and exit failure

    std::cerr << BedMap::prognm << std::endl;

    std::cerr << "  citation: " << BedMap::citation << std::endl;

applications/bed/conversion/src/convert2bed.h

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@@ -53,7 +53,7 @@ 


#include "suite/BEDOPS.Constants.hpp"



#define C2B_VERSION "2.4.36"

#define C2B_VERSION "2.4.37"



typedef int boolean;

extern const boolean kTrue;