Commit 90191749 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 3.14.0+dfsg

parent 89b1e879

.github/workflows/basic.yml

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name: SPAdes basic tests



on: [push]



jobs:

  build:

    runs-on: ${{ matrix.os }}

    

    strategy:

      matrix: 

        os: [ ubuntu-latest, macos-latest ]

    

    steps:

    - uses: actions/checkout@v1

      with:

        fetch-depth: 1

    

    - name: prepare

      run: cd assembler && mkdir build_spades



    - name: cmake

      run: cd assembler/build_spades && cmake - G "Unix Makefiles" ../src



    - name: compile include test

      run: make -C assembler/build_spades/test/include_test include_test



    - name: compile debruijn test

      run: make -C assembler/build_spades/test/debruijn debruijn_test



    - name: include check

      run: cd assembler && build_spades/bin/include_test

      

    - name: debruijn check

      run: cd assembler && build_spades/bin/debruijn_test

.github/workflows/spades-test.yml

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name: SPAdes 1k test



on: [push]



jobs:

  build:

    runs-on: ${{ matrix.os }}

    

    strategy:

      matrix: 

        os: [ ubuntu-latest, macos-latest ]

    

    steps:

    - uses: actions/checkout@v1

      with:

        fetch-depth: 1



    - name: compile

      run: assembler/spades_compile.sh -j3



    - name: multi-cell mode check

      run: bin/spades.py --test

    - name: single-cell mode check

      run: bin/spades.py --sc --test

    - name: plasmid mode check

      run: bin/plasmidspades.py --test

    - name: metagenomic mode check

      run: bin/metaspades.py --test

README.md

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File changed.

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assembler/.clang-format

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---

Language:        Cpp

# BasedOnStyle:  Google

AccessModifierOffset: -4

AlignAfterOpenBracket: Align

AlignConsecutiveAssignments: false

AlignConsecutiveDeclarations: false

AlignEscapedNewlines: Left

AlignOperands:   true

AlignTrailingComments: true

AllowAllParametersOfDeclarationOnNextLine: true

AllowShortBlocksOnASingleLine: false

AllowShortCaseLabelsOnASingleLine: false

AllowShortFunctionsOnASingleLine: All

AllowShortIfStatementsOnASingleLine: true

AllowShortLoopsOnASingleLine: true

AlwaysBreakAfterDefinitionReturnType: None

AlwaysBreakAfterReturnType: None

AlwaysBreakBeforeMultilineStrings: true

AlwaysBreakTemplateDeclarations: true

BinPackArguments: true

BinPackParameters: true

BraceWrapping:   

  AfterClass:      false

  AfterControlStatement: false

  AfterEnum:       false

  AfterFunction:   false

  AfterNamespace:  false

  AfterObjCDeclaration: false

  AfterStruct:     false

  AfterUnion:      false

  BeforeCatch:     false

  BeforeElse:      false

  IndentBraces:    false

  SplitEmptyFunction: true

  SplitEmptyRecord: true

  SplitEmptyNamespace: true

BreakBeforeBinaryOperators: None

BreakBeforeBraces: Attach

BreakBeforeInheritanceComma: false

BreakBeforeTernaryOperators: true

BreakConstructorInitializersBeforeComma: false

BreakConstructorInitializers: BeforeColon

BreakAfterJavaFieldAnnotations: false

BreakStringLiterals: true

ColumnLimit:     120

CommentPragmas:  '^ IWYU pragma:'

CompactNamespaces: false

ConstructorInitializerAllOnOneLineOrOnePerLine: true

ConstructorInitializerIndentWidth: 4

ContinuationIndentWidth: 4

Cpp11BracedListStyle: true

DerivePointerAlignment: true

DisableFormat:   false

ExperimentalAutoDetectBinPacking: false

FixNamespaceComments: true

ForEachMacros:   

  - foreach

  - Q_FOREACH

  - BOOST_FOREACH

IncludeCategories: 

  - Regex:           '^<.*\.h>'

    Priority:        1

  - Regex:           '^<.*'

    Priority:        2

  - Regex:           '.*'

    Priority:        3

IncludeIsMainRegex: '([-_](test|unittest))?$'

IndentCaseLabels: true

IndentWidth:     4

IndentWrappedFunctionNames: false

JavaScriptQuotes: Leave

JavaScriptWrapImports: true

KeepEmptyLinesAtTheStartOfBlocks: false

MacroBlockBegin: ''

MacroBlockEnd:   ''

MaxEmptyLinesToKeep: 1

NamespaceIndentation: None

ObjCBlockIndentWidth: 2

ObjCSpaceAfterProperty: false

ObjCSpaceBeforeProtocolList: false

PenaltyBreakAssignment: 2

PenaltyBreakBeforeFirstCallParameter: 1

PenaltyBreakComment: 300

PenaltyBreakFirstLessLess: 120

PenaltyBreakString: 1000

PenaltyExcessCharacter: 1000000

PenaltyReturnTypeOnItsOwnLine: 200

PointerAlignment: Left

ReflowComments:  true

SortIncludes:    true

SortUsingDeclarations: true

SpaceAfterCStyleCast: false

SpaceAfterTemplateKeyword: true

SpaceBeforeAssignmentOperators: true

SpaceBeforeParens: ControlStatements

SpaceInEmptyParentheses: false

SpacesBeforeTrailingComments: 2

SpacesInAngles:  false

SpacesInContainerLiterals: true

SpacesInCStyleCastParentheses: false

SpacesInParentheses: false

SpacesInSquareBrackets: false

Standard:        Auto

TabWidth:        8

UseTab:          Never

...

assembler/LICENSE

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@@ -28,8 +28,6 @@ Current SPAdes contributors: 


    Dmitry Antipov,

    Elena Bushmanova,

    Vasisliy Ershov,

    Yuriy Gorshkov,

    Alexey Gurevich,

    Anton Korobeynikov,

    Olga Kunyavskaya,
@@ -46,6 +44,8 @@ Also contributed: 
    Max Alekseyev,

    Anton Bankevich,

    Mikhail Dvorkin,

    Vasisliy Ershov,

    Yuriy Gorshkov,

    Alexander Kulikov,

    Valery Lesin,

    Sergey Nikolenko,