Commit f9cdfa4a authored by Shayan Doust's avatar Shayan Doust
Browse files

New upstream version 1.2.9

parent 65d48896

.travis.yml

+1 −14
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@@ -13,17 +13,4 @@ script: 
  - sudo make install

  - megahit --test

  - megahit --test --kmin-1pass

  - megahit --test --no-hw-accel

after_success:

  # Create lcov report

  - wget http://downloads.sourceforge.net/ltp/lcov-1.14.tar.gz

  - tar zvxf lcov-1.14.tar.gz

  - export PATH=lcov-1.14/bin/:${PATH}

  - lcov --capture --directory . --output-file coverage.info

  - lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter system-files

  - lcov --remove coverage.info '*xxhash/*' --output-file coverage.info # filter xxhash-files

  - lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info # filter parallel-hashmap-files

  - lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info # filter pprintpp files

  - lcov --list coverage.info # debug info

  # Uploading report to CodeCov

  - bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports"
 
 No newline at end of file
 
  - megahit --test --no-hw-accelo || echo "Codecov did not collect coverage reports"

CHANGELOG.md

+6 −0
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### 1.2.9 / 2019-10-13

-   Fix segfault triggered by length-zero sequences

-   Fix memory detection problem for some outdated MacOS versions

-   Fix an incorrect assertion in unitig graph refreshing

-   Added `--verbose` to output full log to the screen



### 1.2.8 / 2019-08-10

-   Add intermediate `megahit_core_popcnt` for CPUs that have ABM but not BMI2

-   Allow new assembly task with `--continue`

CMakeLists.txt

+4 −2
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@@ -101,9 +101,11 @@ add_custom_target( 
        simple_test

        COMMAND ./megahit --test -t 2

        COMMAND MEGAHIT_NUM_MERCY_FACTOR=1.5 ./megahit --test -t 4 --mem-flag 0 --no-hw-accel

        COMMAND ./megahit --test -t 2 --kmin-1pass

        COMMAND rm -rf test-random && python3 ../test_data/generate_random_fasta.py > random.fa && ./megahit -r random.fa --k-list 255 --min-count 1 -o test-random

        COMMAND ./megahit --test -t 2 --kmin-1pass --prune-level 3 --prune-depth 0

        COMMAND rm -rf test-random && python3 ${TEST_DATA}/generate_random_fasta.py > random.fa && ./megahit -r random.fa --k-list 255 --min-count 1 -o test-random

        COMMAND rm -rf test-fastg && ./megahit --test -t 2 --mem-flag 2 --keep-tmp-files -o test-fastg

        COMMAND rm -rf test-empty && ./megahit -r ${TEST_DATA}/empty.fa -o test-empty

        COMMAND rm -rf test-no-contig && ./megahit -r ${TEST_DATA}/r4.fa -o test-no-contig

        COMMAND ./megahit_toolkit contig2fastg 59 test-fastg/intermediate_contigs/k59.contigs.fa > 59.fastg

        COMMAND ./megahit_toolkit readstat < test-fastg/intermediate_contigs/k59.contigs.fa

)

README.md

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@@ -19,9 +19,9 @@ conda install -c bioconda megahit 
### Pre-built binaries for x86_64 Linux



```sh

wget https://github.com/voutcn/megahit/releases/download/v1.2.8/MEGAHIT-1.2.8-Linux-x86_64-static.tar.gz

tar zvxf MEGAHIT-1.2.8-Linux-x86_64-static.tar.gz

cd MEGAHIT-1.2.8-Linux-x86_64-static/bin/

wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz

tar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz

cd MEGAHIT-1.2.9-Linux-x86_64-static/bin/

./megahit --test  # run on a toy dataset

./megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR

```

azure-pipelines.yml

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jobs:

  - job: ubuntu_1604

    pool:

      vmImage: 'Ubuntu-16.04'

    strategy:

      matrix:

        python36:

          python.version: '3.6'

          build.type: 'Debug'

          sanitizer: 'ON'

          static: 'OFF'

        Python27:

          python.version: '2.7'

          build.type: 'Release'

          sanitizer: 'OFF'

          static: 'ON'

    steps:

      - task: UsePythonVersion@0

        inputs:

          versionSpec: '$(python.version)'

          addToPath: true

      - script: |

          mkdir build

          cd build

          cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DSTATIC_BUILD=$(static) ..

          make simple_test -j `nproc`

        displayName: 'build and test'



  - job: macos

    strategy:

      matrix:

        1013:

          image: macos-10.13

        latest:

          image: macos-latest

    pool:

      vmImage: $(image)

    steps:

      - script: |

          brew install cmake gcc@9 zlib bzip2

        displayName: 'install dependencies'

      - script: |

          mkdir build

          cd build

          CC=gcc-9 CXX=g++-9 cmake ..

          make simple_test -j `sysctl -n hw.physicalcpu`

        displayName: 'build and test'



  - job: assembly

    timeoutInMinutes: 0

    strategy:

      matrix:

        codecov:

          build.type: 'Release'

          sanitizer: 'OFF'

          coverage: 'ON'

        sanitize:

          build.type: 'Debug'

          sanitizer: 'ON'

          coverage: 'OFF'

    pool:

      vmImage: 'Ubuntu-16.04'

    steps:

      - script: |

          mkdir build

          cd build

          cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DCOVERAGE=$(coverage) ..

          make -j `nproc`

          make simple_test

          sudo make install

        displayName: 'build and test'

      - script: |

          curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_1.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 1.fq.gz

          curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_2.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 2.fq.gz

          megahit --presets meta-large -1 1.fq.gz -2 2.fq.gz -m5e9 --verbose

        displayName: 'assemble'

      - script: |

          if [ $(coverage) = 'ON' ]; then

            wget http://downloads.sourceforge.net/ltp/lcov-1.14.tar.gz

            tar zvxf lcov-1.14.tar.gz

            export PATH=lcov-1.14/bin/:${PATH}

            lcov --capture --directory . --output-file coverage.info

            lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter system-files

            lcov --remove coverage.info '*xxhash/*' --output-file coverage.info # filter xxhash-files

            lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info # filter parallel-hashmap-files

            lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info # filter pprintpp files

            lcov --list coverage.info # debug info

            bash <(curl -s https://codecov.io/bash) -f coverage.info -t $(CODECOV_TOKEN) || echo "Codecov did not collect coverage reports"

          fi

        displayName: 'codecov'