generated from ydeng/python-program
Basic filtering system and tests completed
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17
.vscode/settings.json
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17
.vscode/settings.json
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@ -0,0 +1,17 @@
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{
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"python.testing.pytestArgs": [],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true,
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"python.linting.pylintArgs": [
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"--rcfile=setup.cfg"
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],
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"python.analysis.autoSearchPaths": true,
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"python.analysis.extraPaths": [
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"src"
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],
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"cSpell.words": [
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"pytest",
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"pyvcf",
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"vcfs"
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],
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}
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5
Jenkinsfile
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5
Jenkinsfile
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@ -9,7 +9,6 @@ pipeline {
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}
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stage("unit tests") {
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steps {
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// TODO Update the
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sh returnStatus: true, script: "python -m pytest --junitxml=unit_tests.xml --cov-report xml:test_coverage.xml --cov=program"
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xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
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cobertura autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'test_coverage.xml', failUnhealthy: false, failUnstable: false, maxNumberOfBuilds: 64, lineCoverageTargets: '50, 0, 0', methodCoverageTargets: '50, 0, 0', onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false
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@ -18,7 +17,7 @@ pipeline {
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stage("build") {
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steps {
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sh "python -m build"
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// Additional build steps go here
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// TODO Additional build steps go here
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}
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}
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stage("test installation") {
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@ -30,7 +29,7 @@ pipeline {
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stage("archive") {
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steps {
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archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
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// Additional archival or documentation steps go here
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// TODO Additional archival or documentation steps go here
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}
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}
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stage("publish") {
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@ -8,3 +8,4 @@ dependencies:
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- pytest
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- twine
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- sphinx
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- pyvcf
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14
setup.cfg
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setup.cfg
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[metadata]
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name = sample
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name = modvcfsamples
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version = 0.0.1
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[options]
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package_dir =
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= src
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# install_requires =
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# cachier ==2.1
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= ./src
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install_requires =
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pyvcf ==0.6.8
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# [options.entry_points]
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# console_scripts =
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# avariantas = program.program:entry_function
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[options.entry_points]
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console_scripts =
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modvcfsamples = modvcfsamples.cli:main
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[tool:pytest]
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pythonpath = src
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39
src/modvcfsamples/cli.py
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src/modvcfsamples/cli.py
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import argparse
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import os
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from modvcfsamples import sample
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def run(vcfs: list[str], only: list[str], output_dir: str):
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for vcf in vcfs:
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vcf_records = sample.get_records_from_vcf(vcf)
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sample.filter_all_sample_datatypes(vcf_records, *only)
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sample.write_records_to_vcf(vcf_records, os.path.join(output_dir, os.path.basename(vcf)))
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def main():
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"vcfs",
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help="The VCFs to run filtering on",
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nargs="+",
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metavar="I",
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type=str
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)
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parser.add_argument(
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"output_dir",
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help="The output directory",
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metavar="O",
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type=str
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)
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parser.add_argument(
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"--only",
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"-n",
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help="Remove everything but the sample datatype",
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action="append",
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type=str
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)
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args = parser.parse_args()
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run(args.vcfs, args.only, args.output_dir)
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if __name__ == "__main__":
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main()
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34
src/modvcfsamples/sample.py
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src/modvcfsamples/sample.py
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import vcf
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from collections import namedtuple
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from copy import deepcopy
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def get_records_from_vcf(path: str):
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vcf_records = []
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with open(path, "r") as vcf_stream:
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reader = vcf.Reader(vcf_stream)
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for record in reader:
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vcf_records.append(record)
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return vcf_records
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def filter_sample_datatype(record, *datatypes: str):
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call_data = namedtuple("Data", *datatypes)
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filtered_calls = []
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modified_record = deepcopy(record)
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for call in record.samples:
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kept_data = {}
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for datatype in datatypes:
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kept_data[datatype] = call[datatype]
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filtered_calls.append(call_data(**kept_data))
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modified_record.samples = filtered_calls
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return modified_record
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def filter_all_sample_datatypes(records: list, *datatypes: str):
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for record in records:
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yield filter_sample_datatype(record, *datatypes)
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def write_records_to_vcf(records: list, path: str):
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with open(path, "w") as vcf_stream:
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writer = vcf.Writer(vcf_stream, records[0])
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for record in records:
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writer.write_record(record)
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# TODO Do stuff!
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38
tests/modvcfsamples/test_sample.py
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tests/modvcfsamples/test_sample.py
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from modvcfsamples.sample import filter_sample_datatype, filter_all_sample_datatypes, get_records_from_vcf
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import os
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def test_get_records_from_vcf_not_none():
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records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
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assert len(records) > 0
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def test_filter_sample_datatype_not_none():
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records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
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filter_for = ["GT"]
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modified_record = filter_sample_datatype(records[0], *filter_for)
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assert modified_record is not None
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def test_filter_sample_datatype_only_filtered():
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records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
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filter_for = ["GT"]
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modified_record = filter_sample_datatype(records[0], *filter_for)
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for sample in modified_record.samples:
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assert len(sample) <= len(filter_for)
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for key, _ in sample._asdict().items():
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assert key in filter_for
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def test_filter_all_sample_datatypes_not_empty():
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records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
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filter_for = ["GT"]
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modified_records = list(filter_all_sample_datatypes(records, *filter_for))
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assert len(modified_records) == 11
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def test_filter_all_sample_datatypes_filtered():
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records = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf"))
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filter_for = ["GT"]
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modified_records = list(filter_all_sample_datatypes(records, *filter_for))
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for modified_record in modified_records:
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for sample in modified_record.samples:
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assert len(sample) <= len(filter_for)
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for key, _ in sample._asdict().items():
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assert key in filter_for
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# TODO Test program!
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17
tests/resources/test_files_shortened.vcf
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tests/resources/test_files_shortened.vcf
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##fileformat=VCFv4.1
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##fileDate=10122015_22h01m13s
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##source=SHAPEIT2.v837
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##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Gambian Chinese French Brazilian Nigerian Pakistani English Colombian Indian Japanese
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1 846808 rs4475691 C T 100 . AC=1276;AN=5008;DP=20368 GT:GQ:DP 1|1:70:60 0|0:30:10 0|0:20:40 ./.:0:0 0|0:70:60 0|0:90:30 0|0:80:70 0|0:50:80 ./.:0:0 0|0:100:80
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1 846854 rs111957712 G A 100 . AC=114;AN=5008;DP=20538 GT:GQ:DP ./.:0:0 0|0:40:30 0|0:80:30 0|0:0:20 0|0:40:80 0|0:10:30 ./.:0:0 ./.:0:0 0|0:70:0 0|0:90:30
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1 846864 rs950122 G C 100 . AC=1116;AN=5008;DP=20582 GT:GQ:DP 1|1:60:0 0|0:20:0 0|0:90:70 0|0:80:50 0|0:80:30 0|0:10:80 0|0:100:20 0|0:30:40 ./.:0:0 0|0:30:90
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1 847228 rs3905286 C T 100 . AC=1215;AN=5008;DP=20731 GT:GQ:DP 1|1:70:80 0|0:90:80 0|0:60:50 0|0:60:90 0|0:30:40 0|0:70:10 0|0:100:80 0|0:100:50 0|1:70:100 0|0:40:40
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1 847297 rs11507768 G A 100 . AC=359;AN=5008;DP=20809 GT:GQ:DP 1|0:0:60 0|0:10:30 0|0:80:60 ./.:0:0 0|0:10:100 0|0:10:100 ./.:0:0 0|0:100:40 0|0:20:20 0|0:10:0
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1 847491 rs28407778 G A 100 . AC=1262;AN=5008;DP=16939 GT:GQ:DP 1|1:0:100 0|0:70:40 0|0:0:60 0|0:90:90 0|0:90:90 ./.:0:0 0|0:70:60 0|0:70:0 0|1:90:100 0|0:60:60
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1 848023 rs144407116 C A 100 . AC=52;AN=5008;DP=22562 GT:GQ:DP 0|1:10:60 0|0:20:80 0|0:20:50 0|0:20:90 0|0:90:10 0|0:70:60 0|0:40:30 0|0:60:0 0|0:40:40 0|0:10:10
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1 848090 rs4246505 G A 100 . AC=857;AN=5008;DP=19301 GT:GQ:DP 0|0:70:70 0|0:90:30 0|0:40:10 0|0:80:20 0|0:50:50 0|0:10:30 ./.:0:0 0|0:20:60 ./.:0:0 0|0:90:0
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1 848445 rs4626817 G A 100 . AC=1255;AN=5008;DP=18444 GT:GQ:DP 1|1:100:40 0|0:80:90 0|0:30:100 0|0:100:60 0|0:40:90 0|0:20:30 0|0:70:100 ./.:0:0 ./.:0:0 0|0:80:30
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1 848456 rs11507767 A G 100 . AC=1266;AN=5008;DP=18137 GT:GQ:DP 1|1:40:30 ./.:0:0 0|0:60:90 0|0:60:40 0|0:100:80 0|0:50:50 0|0:0:10 0|0:60:0 0|1:100:100 ./.:0:0
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1 848738 rs3829741 C T 100 . AC=855;AN=5008;DP=16663 GT:GQ:DP 0|0:50:90 0|0:50:50 0|0:50:30 0|0:60:60 0|0:80:40 0|0:50:80 0|0:0:80 0|0:0:30 0|1:10:0 0|0:70:30
|
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