Commit fe8d9e15 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.4.32+dfsg

parent eabeaa5b

.gitignore

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@@ -61,3 +61,11 @@ tramp 
# OS X stuff

.DS_Store

__MACOSX



applications/bed/bedextract/bin/

applications/bed/bedmap/bin/

applications/bed/bedops/bin/

applications/bed/closestfeats/bin/

applications/bed/conversion/bin/

applications/bed/sort-bed/bin/

applications/bed/starch/bin/
 
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.travis.yml

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@@ -15,5 +15,5 @@ install: 
  - 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
 
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  - if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make all; fi; fi

  - if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make all; fi; fi
 
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Makefile

+292 −98

File changed.

Preview size limit exceeded, changes collapsed.

README.md

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Original line number Diff line number Diff line 
## BEDOPS v2.4.26: high-performance genomic feature operations ##

## BEDOPS v2.4.32: 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 v2.4.26** 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 v2.4.32** 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 v2.4.26** 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 v2.4.32** 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 ###
@@ -28,21 +28,20 @@ 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/v2.4.26/bedops_linux_x86_64-v2.4.26.tar.bz2">x86-64 (64-bit)</a> binaries</li>

<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.26/bedops_linux_i386-v2.4.26.tar.bz2">i386 (32-bit)</a> binaries</li>

<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/bedops_linux_x86_64-v2.4.32.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/v2.4.26/BEDOPS.2.4.26.pkg.zip">Intel (32-/64-bit, 10.7-10.12)</a> installer package</li>

<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/BEDOPS.2.4.32.pkg.zip">Intel (64-bit, 10.10-10.13)</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/v2.4.26.tar.gz">Source code</a> (tar.gz)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.26.zip">Source code</a> (zip)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.tar.gz">Source code</a> (tar.gz)</li>

<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.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>
@@ -51,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv 


### Documentation ###



Complete documentation for **BEDOPS v2.4.26** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>

Complete documentation for **BEDOPS v2.4.32** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>



### Citation ###



If you use **BEDOPS v2.4.26** in your research, please cite the following manuscript:

If you use **BEDOPS v2.4.32** in your research, please cite the following manuscript:



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

> [**BEDOPS: high-performance genomic feature operations**
@@ -63,7 +62,7 @@ If you use **BEDOPS v2.4.26** in your research, please cite the following manusc 


### Copyright ###



> Copyright (C) 2011-2017 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds

> Copyright (C) 2011-2018 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).

applications/bed/bedextract/src/ExtractRows.cpp

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@@ -4,7 +4,7 @@ 
*/

//

//    BEDOPS

//    Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds

//    Copyright (C) 2011-2018 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
@@ -33,12 +33,13 @@ 
#include <map>

#include <numeric>

#include <string>

#include <type_traits>

#include <utility>

#include <vector>



#include "algorithm/bed/FindBedRange.hpp"

#include "algorithm/visitors/helpers/ProcessBedVisitorRow.hpp"

#include "data/bed/BedTypes.hpp"

//#include "data/bed/BedTypes.hpp"

#include "data/bed/BedCheckIterator.hpp"

#include "suite/BEDOPS.Constants.hpp"

#include "suite/BEDOPS.Version.hpp"
@@ -48,8 +49,9 @@ namespace { 


  const std::string prognm = "bedextract";

  const std::string citation = BEDOPS::citation();

  const std::string version = BEDOPS::revision();

  const std::string version = BEDOPS::version();

  const std::string authors = "Shane Neph & Alex Reynolds";

  constexpr std::size_t PoolSz = 2*8;



  //======

  // Help
@@ -66,12 +68,11 @@ namespace { 
  //=======

  template <typename ValueType>

  struct Cache {

    Cache() : empty_(true), value_()

    Cache() : empty_(true)

      { }



    template <typename T>

    void operator()(const T* t) {

      value_ = static_cast<ValueType>(*t);

      empty_ = false;

    }
@@ -80,7 +81,6 @@ namespace { 


  private:

    bool empty_;

    ValueType value_;

  };



  using Bed::extract_details::TargetBedType;
@@ -156,8 +156,8 @@ namespace { 
    }



    OpMode Mode() const { return m_; }

    FILE* File1() { return f1_; }

    FILE* File2() { return f2_; }

    FILE* File1() const { return f1_; }

    FILE* File2() const { return f2_; }

    std::string File2Name() const { return f2Name_; }

    std::string Chrome() const { return(chrom_); }
@@ -238,10 +238,20 @@ namespace { 
    return(c == EOF);

  }



  //=============

  // get_pool()

  //============

  template <typename BedTypePtr>

  Ext::PooledMemory<typename std::remove_pointer<BedTypePtr>::type, PoolSz>&

  get_pool() {

    static Ext::PooledMemory<typename std::remove_pointer<BedTypePtr>::type, PoolSz> pool;

    return pool;

  }



  //==========

  // doWork()

  //==========

  void doWork(Input& input) {

  void doWork(const Input& input) {

    // execute the mode requested by the user

    Input::OpMode mode = input.Mode();

    FILE* f = input.File1();
@@ -253,11 +263,13 @@ namespace { 
    if ( mode == Input::TWOFILE ) { // find elements of file1 that overlap specified ranges of file2

      Visitors::BedHelpers::Println printer;

      if ( input.File2Name() == "stdin" ) {

        Bed::bed_check_iterator<TargetBedType*> titer(std::cin, input.File2Name()), teof;

        auto& mem = get_pool<TargetBedType*>();

        Bed::bed_check_iterator<TargetBedType*, PoolSz> titer(std::cin, input.File2Name(), mem), teof;

        find_bed_range(f, titer, teof, printer);

      } else {

        std::ifstream* infile = new std::ifstream(input.File2Name().c_str());

        Bed::bed_check_iterator<TargetBedType*> titer(*infile, input.File2Name()), teof;

        auto& mem = get_pool<TargetBedType*>();

        Bed::bed_check_iterator<TargetBedType*, PoolSz> titer(*infile, input.File2Name(), mem), teof;

        find_bed_range(f, titer, teof, printer);

        delete infile;

      }
@@ -289,8 +301,9 @@ namespace { 
        if ( lbound.first && lbound.second != at_end ) {

          std::fseek(f, lbound.second, SEEK_SET);

          ByteOffset b = std::ftell(f);

          QueryBedType q(f);

          printf("%s\n", q.chrom());

          auto q = new QueryBedType(f);

          printf("%s\n", q->chrom());

          delete q;

          std::fseek(f, b, SEEK_SET);

        }

        else