bardin-lab / readtagger

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• testing_improvements
• add_support_for_files_with_missing_reads
• allow_multiple_readtagger_input_files
• blast_io
• blast_work
• bugfixes_multithreading
• cluster_refinement
• debug_0.3.25
• debug_highmem
• dep_update
• dovetailing_debug
• fix_add_mate
• fix_build
• fix_file_seeking
• fix_qual_to_string
• fix_source_path_annotate_path
• fix_viral_integration_finding
• genotyping
• genotyping_improvements
• improve_false_positives
• improve_filtering_pipeline
• long_read_detection
• master
• more_accurate_support_quantification
• multi_sample_comparisons
• nref_fix
• parallelize_readtagger
• plot_coverage
• pyup-update-bcbio-gff-0.6.4-to-0.6.6
• pyup-update-biopython-1.68-to-1.69
• pyup-update-biopython-1.69-to-1.70
• pyup-update-biopython-1.70-to-1.71
• pyup-update-biopython-1.70-to-1.72
• pyup-update-biopython-1.73-to-1.74
• pyup-update-biopython-1.74-to-1.75
• pyup-update-cached_property-1.3.0-to-1.3.1
• pyup-update-cached_property-1.3.1-to-1.4.0
• pyup-update-cached_property-1.4.0-to-1.4.2
• pyup-update-cached_property-1.4.0-to-1.4.3
• pyup-update-cached_property-1.4.0-to-1.5.1
• pyup-update-click-6.7-to-7.0
• pyup-update-click-7.0-to-7.1.1
• pyup-update-contextlib2-0.5.4-to-0.5.5
• pyup-update-contextlib2-0.5.5-to-0.6.0
• pyup-update-contextlib2-0.5.5-to-0.6.0.post1
• pyup-update-cookiecutter-1.5.1-to-1.6.0
• pyup-update-edlib-1.2.3-to-1.2.3.post1
• pyup-update-edlib-1.2.3.post1-to-1.2.4
• pyup-update-edlib-1.2.4-to-1.2.4.post1
• pyup-update-edlib-1.2.4.post1-to-1.3.4
• pyup-update-flake8-3.3.0-to-3.4.0
• pyup-update-flake8-3.3.0-to-3.4.1
• pyup-update-flake8-docstrings-1.0.3-to-1.1.0
• pyup-update-flake8_docstrings-1.0.3-to-1.1.0
• pyup-update-flake8_docstrings-1.1.0-to-1.3.0
• pyup-update-flake8_docstrings-1.3.0-to-1.3.1
• pyup-update-flake8_docstrings-1.3.0-to-1.4.0
• pyup-update-flake8_docstrings-1.4.0-to-1.5.0
• pyup-update-futures-3.0.5-to-3.1.0
• pyup-update-futures-3.0.5-to-3.1.1
• pyup-update-futures-3.1.1-to-3.2.0
• pyup-update-futures-3.2.0-to-3.3.0
• pyup-update-multiprocessing_logging-0.2.4-to-0.2.5
• pyup-update-multiprocessing_logging-0.2.4-to-0.2.6
• pyup-update-multiprocessing_logging-0.2.6-to-0.3.0
• pyup-update-pandas-0.23.0-to-0.23.1
• pyup-update-pandas-0.23.0-to-0.23.2
• pyup-update-pandas-0.23.0-to-0.23.3
• pyup-update-pandas-0.23.0-to-0.23.4
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• pyup-update-pandas-0.25.3-to-1.0.0
• pyup-update-pandas-0.25.3-to-1.0.1
• pyup-update-planemo-0.38.1-to-0.39.0
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• pyup-update-planemo-0.45.0-to-0.46.1
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• pyup-update-planemo-0.48.0-to-0.49.2
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• pyup-update-planemo-0.48.0-to-0.50.1
• pyup-update-planemo-0.48.0-to-0.51.0
• pyup-update-planemo-0.48.0-to-0.52.0
• pyup-update-planemo-0.48.0-to-0.53.0
• pyup-update-planemo-0.48.0-to-0.54.0
• pyup-update-planemo-0.48.0-to-0.55.0
• pyup-update-planemo-0.58.1-to-0.58.2
• pyup-update-planemo-0.58.2-to-0.59.0
• pyup-update-planemo-0.58.2-to-0.60.0
• pyup-update-planemo-0.58.2-to-0.61.0
• pyup-update-planemo-0.60.0-to-0.61.0
• pyup-update-planemo-0.61.0-to-0.62.0
• pyup-update-planemo-0.61.0-to-0.62.1
• pyup-update-pydocstyle-1.1.1-to-2.0.0
• pyup-update-pydocstyle-3.0.0-to-4.0.0
• pyup-update-pydocstyle-3.0.0-to-4.0.1
• pyup-update-pydocstyle-4.0.1-to-5.0.1
• pyup-update-pydocstyle-4.0.1-to-5.0.2
• pyup-update-pysam-0.10.0-to-0.11
• pyup-update-pysam-0.11-to-0.11.1
• pyup-update-pysam-0.11.1-to-0.11.2
• pyup-update-pysam-0.11.1-to-0.11.2.1
• pyup-update-pysam-0.11.1-to-0.11.2.2
• pyup-update-pysam-0.11.2.2-to-0.12
• pyup-update-pysam-0.11.2.2-to-0.12.0.1
• pyup-update-pysam-0.12.0.1-to-0.13
• pyup-update-pysam-0.13-to-0.14
• pyup-update-pysam-0.14-to-0.14.1
• pyup-update-pysam-0.14.1-to-0.15.0
• pyup-update-pysam-0.14.1-to-0.15.1
• pyup-update-pysam-0.15.1-to-0.15.2
• pyup-update-pysam-0.15.2-to-0.15.3
• pyup-update-pytest-3.0.6-to-3.0.7
• pyup-update-pytest-3.0.7-to-3.1.0
• pyup-update-pytest-3.0.7-to-3.1.1
• pyup-update-pytest-3.0.7-to-3.1.2
• pyup-update-pytest-3.1.2-to-3.1.3
• pyup-update-pytest-3.1.2-to-3.2.0
• pyup-update-pytest-3.2.0-to-3.2.1
• pyup-update-pytest-3.2.0-to-3.2.2
• pyup-update-pytest-3.2.2-to-3.2.3
• pyup-update-pytest-3.2.3-to-3.2.4
• pyup-update-pytest-3.2.4-to-3.2.5
• pyup-update-pytest-3.2.5-to-3.3.0
• pyup-update-pytest-3.2.5-to-3.3.1
• pyup-update-pytest-3.2.5-to-3.3.2
• pyup-update-pytest-3.2.5-to-3.4.0
• pyup-update-pytest-3.2.5-to-3.4.1
• pyup-update-pytest-3.4.1-to-3.4.2
• pyup-update-pytest-3.4.1-to-3.5.0
• pyup-update-pytest-3.4.1-to-3.5.1
• pyup-update-pytest-3.4.1-to-3.6.0
• pyup-update-pytest-3.4.1-to-3.6.1
• pyup-update-pytest-3.4.1-to-3.6.2
• pyup-update-pytest-3.4.1-to-3.6.3
• pyup-update-pytest-3.4.1-to-3.6.4
• pyup-update-pytest-3.4.1-to-3.7.0
• pyup-update-pytest-3.4.1-to-3.7.1
• pyup-update-pytest-3.4.1-to-3.7.2
• pyup-update-pytest-3.4.1-to-3.7.4
• pyup-update-pytest-3.4.1-to-3.8.0
• pyup-update-pytest-3.4.1-to-3.8.1
• pyup-update-pytest-3.4.1-to-3.8.2
• pyup-update-pytest-3.4.1-to-3.9.1
• pyup-update-pytest-3.9.1-to-3.9.2
• pyup-update-pytest-4.1.1-to-4.3.1
• pyup-update-pytest-4.3.1-to-4.4.0
• pyup-update-pytest-4.3.1-to-4.4.1
• pyup-update-pytest-4.3.1-to-4.4.2
• pyup-update-pytest-4.3.1-to-4.5.0
• pyup-update-pytest-4.3.1-to-4.6.0
• pyup-update-pytest-4.3.1-to-4.6.1
• pyup-update-pytest-4.3.1-to-4.6.2
• pyup-update-pytest-4.3.1-to-4.6.3
• pyup-update-pytest-4.3.1-to-5.0.0
• pyup-update-pytest-4.3.1-to-5.0.1
• pyup-update-pytest-4.3.1-to-5.1.1
• pyup-update-pytest-4.3.1-to-5.1.2
• pyup-update-pytest-4.3.1-to-5.1.3
• pyup-update-pytest-4.3.1-to-5.2.0
• pyup-update-pytest-4.3.1-to-5.2.1
• pyup-update-pytest-4.3.1-to-5.2.2
• pyup-update-pytest-5.2.2-to-5.2.3
• pyup-update-pytest-5.2.2-to-5.2.4
• pyup-update-pytest-5.2.2-to-5.3.0
• pyup-update-pytest-5.2.2-to-5.3.1
• pyup-update-pytest-5.2.2-to-5.3.3
• pyup-update-pytest-5.2.2-to-5.3.4
• pyup-update-pytest-5.2.2-to-5.3.5
• pyup-update-pytest-cov-2.4.0-to-2.5.0
• pyup-update-pytest-cov-2.4.0-to-2.5.1
• pyup-update-pytest-cov-2.5.1-to-2.6.0
• pyup-update-pytest-cov-2.6.1-to-2.7.1
• pyup-update-pytest-cov-2.7.1-to-2.8.1
• pyup-update-pytest-datadir-0.2.0-to-1.0.0
• pyup-update-pytest-datadir-0.2.0-to-1.0.1
• pyup-update-pytest-flake8-0.8.1-to-0.9.1
• pyup-update-pytest-flake8-0.9.1-to-1.0.0
• pyup-update-pytest-mock-1.10.0-to-1.10.2
• pyup-update-pytest-mock-1.10.2-to-1.10.3
• pyup-update-pytest-mock-1.10.2-to-1.10.4
• pyup-update-pytest-mock-1.10.4-to-1.11.0
• pyup-update-pytest-mock-1.10.4-to-1.11.1
• pyup-update-pytest-mock-1.10.4-to-1.11.2
• pyup-update-pytest-mock-1.11.2-to-1.12.0
• pyup-update-pytest-mock-1.11.2-to-1.12.1
• pyup-update-pytest-mock-1.11.2-to-1.13.0
• pyup-update-pytest-mock-1.11.2-to-2.0.0
• pyup-update-pytest-mock-1.11.2-to-3.0.0
• pyup-update-pytest-mock-1.5.0-to-1.6.0
• pyup-update-pytest-mock-1.6.0-to-1.6.1
• pyup-update-pytest-mock-1.6.0-to-1.6.2
• pyup-update-pytest-mock-1.6.2-to-1.6.3
• pyup-update-pytest-mock-1.6.3-to-1.7.0
• pyup-update-pytest-mock-1.6.3-to-1.7.1
• pyup-update-pytest-mock-1.7.1-to-1.10.0
• pyup-update-pytest-mock-1.7.1-to-1.8.0
• pyup-update-pytest-mock-1.7.1-to-1.9.0
• pyup-update-pytest-xdist-1.22.0-to-1.22.2
• pyup-update-pytest-xdist-1.22.2-to-1.22.4
• pyup-update-pytest-xdist-1.22.2-to-1.22.5
• pyup-update-pytest-xdist-1.22.2-to-1.23.0
• pyup-update-pytest-xdist-1.22.2-to-1.23.1
• pyup-update-pytest-xdist-1.22.2-to-1.23.2
• pyup-update-pytest-xdist-1.26.0-to-1.26.1
• pyup-update-pytest-xdist-1.26.0-to-1.27.0
• pyup-update-scipy-0.19.0-to-0.19.1
• pyup-update-scipy-0.19.1-to-1.0.0
• pyup-update-scipy-1.0.0-to-1.0.1
• pyup-update-scipy-1.0.1-to-1.1.0
• pyup-update-scipy-1.2.0-to-1.2.1
• pyup-update-scipy-1.2.1-to-1.3.0
• pyup-update-scipy-1.2.1-to-1.3.1
• pyup-update-scipy-1.3.1-to-1.3.2
• pyup-update-scipy-1.3.1-to-1.3.3
• pyup-update-six-1.10.0-to-1.11.0
• pyup-update-tox-2.6.0-to-2.7.0
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• pyup-update-tox-2.7.0-to-2.8.1
• pyup-update-tox-2.8.1-to-2.8.2
• pyup-update-tox-2.8.1-to-2.9.0
• pyup-update-tox-2.9.0-to-2.9.1
• pyup-update-tox-2.9.1-to-3.0.0
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• pyup-update-tox-2.9.1-to-3.1.3
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• pyup-update-tox-3.12.1-to-3.14.0
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• pyup-update-tox-3.8.3-to-3.8.6
• pyup-update-tox-3.8.3-to-3.9.0
• shm_dir
• simplify_readtagger
• softclip_cluster_fix
• sort_by_readname
• temp_files_cleanup
• test_fasta_out
• timeout
• tsd_and_assembly
• v0.1.10
• v0.1.11
• v0.1.12
• v0.1.13
• v0.1.8
• v0.1.9
• v0.2.0
• v0.3.0
• v0.3.1
• v0.3.10
• v0.3.11
• v0.3.12
• v0.3.13
• v0.3.14
• v0.3.15
• v0.3.16
• v0.3.17
• v0.3.18
• v0.3.19
• v0.3.2
• v0.3.20
• v0.3.21
• v0.3.22
• v0.3.23
• v0.3.24
• v0.3.25
• v0.3.3
• v0.3.4
• v0.3.5
• v0.3.6
• v0.3.7
• v0.3.9
• v0.4.0
• v0.4.1
• v0.4.10
• v0.4.11
• v0.4.12
• v0.4.13
• v0.4.14
• v0.4.15
• v0.4.16
• v0.4.17
• v0.4.18
• v0.4.19
• v0.4.2
• v0.4.20
• v0.4.3
• v0.4.4
• v0.4.5
• v0.4.6
• v0.4.7
• v0.4.8
• v0.4.9
• v0.5.0
• v0.5.1
• v0.5.10
• v0.5.11
• v0.5.12
• v0.5.13
• v0.5.14
• v0.5.15
• v0.5.16
• v0.5.17
• v0.5.19
• v0.5.2
• v0.5.20
• v0.5.21
• v0.5.22
• v0.5.23
• v0.5.3
• v0.5.4
• v0.5.5
• v0.5.6
• v0.5.7
• v0.5.8
• v0.5.9

Build # 252

Build Type

push

travis-ci

Committed by mvdbeek

Commit Message

Fix case where input files are already sorted

Run Details

1403 of 1434 relevant lines covered (97.84%)

1.95 hits per line