Commit bd7747be authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.1

parent e2ac24df

.circleci/config.yml

+1 −1
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@@ -2,7 +2,7 @@ version: 2 
jobs:

  build:

    docker:

      - image: ubuntu:xenial

      - image: ubuntu:bionic

    steps:

      - run: |

          apt-get update -qq

.github/ISSUE_TEMPLATE.rb

0 → 100644
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# Please report



- [ ] version of ABySS with `abyss-pe version`

- [ ] distribution of Linux with `lsb_release -d`



# Assembly error



- [ ] complete `abyss-pe` command line

- [ ] last 20 lines of the output of `abyss-pe`

- [ ] number of sequenced bases

- [ ] estimated genome size and ploidy

- [ ] estimated sequencing depth of coverage



# Build error



Consider installing ABySS using [Linuxbrew](https://linuxbrew.sh) on Linux or [Homebrew](https://brew.sh) on macOS with `brew install abyss`, or using [Bioconda](https://bioconda.github.io) with `conda install abyss`.



- [ ] Have you tried installing ABySS using Brew or Bioconda?

- [ ] version of GCC or compiler with `gcc --version`

- [ ] complete `./configure` command line

- [ ] last 20 lines of the output of `./configure`

- [ ] last 20 lines of the output of `make`

ABYSS/abyss.cc

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@@ -73,6 +73,15 @@ static void assemble(const string& pathIn, const string& pathOut) 
	AssemblyAlgorithms::setCoverageParameters(

			AssemblyAlgorithms::coverageHistogram(g));



	if (opt::kc > 0) {

		cout << "Minimum k-mer multiplicity kc is " << opt::kc << endl;

		cout << "Removing low-multiplicity k-mers" << endl;

		size_t removed = AssemblyAlgorithms::applyKmerCoverageThreshold(g, opt::kc);

		cout << "Removed " <<  removed

			<< " low-multiplicity k-mers, " << g.size()

			<< " k-mers remaining" << std::endl;

	}



	cout << "Generating adjacency" << endl;

	AssemblyAlgorithms::generateAdjacency(&g);

Assembly/BranchGroup.h

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@@ -2,6 +2,7 @@ 
#define BRANCHGROUP_H 1



#include "Common/Algorithms.h"

#include "Common/Exception.h"

#include <algorithm> // for swap

#include <map>

#include <utility>
@@ -211,7 +212,7 @@ isAmbiguous(const SequenceCollectionHash& g) const 


namespace std {

	template <>

	inline void swap(BranchGroup&, BranchGroup&) { assert(false); }

	inline void swap(BranchGroup&, BranchGroup&) NOEXCEPT { assert(false); }

}



#endif

Assembly/BranchRecordBase.h

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#ifndef ASSEMBLY_BRANCHRECORDBASE_H

#define ASSEMBLY_BRANCHRECORDBASE_H 1



#include "Common/Exception.h"



#include <algorithm>

#include <cassert>

#include <utility>
@@ -172,7 +174,7 @@ operator Sequence() const 


namespace std {

	template <>

	inline void swap(BranchRecord& a, BranchRecord& b)

	inline void swap(BranchRecord& a, BranchRecord& b) NOEXCEPT

	{

		a.swap(b);

	}