Commit b538cfd6 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0.3

parent fe441e45

.circleci/config.yml

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version: 2

jobs:

  build:

    docker:

      - image: ubuntu:xenial

    steps:

      - run: |

          apt-get update -qq

          apt-get install -qq autoconf automake clang g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc gdb valgrind

      - checkout

      - run: |

          ./autogen.sh

          ./configure CC=clang CXX=clang++ --with-mpi=/usr/lib/openmpi

      - run: make -j

      - run: make -j check

      - run: make -j distcheck

.github/stale.yml

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# Configuration for probot-stale - https://github.com/probot/stale



# Number of days of inactivity before an Issue or Pull Request becomes stale

daysUntilStale: 21

# Number of days of inactivity before a stale Issue or Pull Request is closed

daysUntilClose: 7

# Issues or Pull Requests with these labels will never be considered stale

exemptLabels:

  - gsoc-outreachy

  - help wanted

  - in progress

# Label to use when marking as stale

staleLabel: stale

# Comment to post when marking as stale. Set to `false` to disable

markComment: >

  This issue has been automatically marked as stale because it has not had

  recent activity. It will be closed if no further activity occurs.

.travis.yml

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language: cpp

compiler:

  - gcc

  - clang

before_install:

  - sudo apt-get update -qq

  - sudo apt-get install -qq libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev

AdjList/AdjList.cpp

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@@ -56,8 +56,10 @@ static const char USAGE_MESSAGE[] = 
"      --adj             output the graph in ADJ format [default]\n"

"      --asqg            output the graph in ASQG format\n"

"      --dot             output the graph in GraphViz format\n"

"      --gfa             output the graph in GFA1 format\n"

"      --gfa1            output the graph in GFA1 format\n"

"      --gfa2            output the graph in GFA2 format\n"

"      --gv              output the graph in GraphViz format\n"

"      --gfa             output the graph in GFA format\n"

"      --sam             output the graph in SAM format\n"

"      --SS              expect contigs to be oriented correctly\n"

"      --no-SS           no assumption about contig orientation\n"
@@ -100,8 +102,10 @@ static const struct option longopts[] = { 
	{ "adj",     no_argument,       &opt::format, ADJ },

	{ "asqg",    no_argument,       &opt::format, ASQG },

	{ "dot",     no_argument,       &opt::format, DOT },

	{ "gfa",     no_argument,       &opt::format, GFA1 },

	{ "gfa1",    no_argument,       &opt::format, GFA1 },

	{ "gfa2",    no_argument,       &opt::format, GFA2 },

	{ "gv",      no_argument,       &opt::format, DOT },

	{ "gfa",     no_argument,       &opt::format, GFA },

	{ "sam",     no_argument,       &opt::format, SAM },

	{ "SS",      no_argument,       &opt::ss, 1 },

	{ "no-SS",   no_argument,       &opt::ss, 0 },

Assembly/BubbleAlgorithm.h

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@@ -237,7 +237,7 @@ void writeBubble(std::ostream& out, const BranchGroup& group, unsigned id) 
			<< currBranch.calculateBranchMultiplicity() << '\n'

			<< contig.c_str() << '\n';

	}

	assert(out.good());

	assert_good(out, opt::snpPath);

}



/** Collapse a bubble to a single path. */