Open teepean opened 5 months ago
Benchmark had some errors.
$ pytest tests/*_bench.py
====================================================================================== test session starts =======================================================================================
platform win32 -- Python 3.11.8, pytest-8.0.1, pluggy-1.4.0 -- C:/msys64/ucrt64/bin/python.exe
cachedir: .pytest_cache
benchmark: 4.0.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: C:/msys64/home/Teemu/pysam-mingw
configfile: setup.cfg
plugins: benchmark-4.0.0
collected 75 items
tests/AlignedSegment_bench.py::test_set_binary_tag PASSED
tests/AlignedSegment_bench.py::test_read_binary_tag PASSED
tests/AlignmentFileFetch_bench.py::test_build_fetch_from_bam_with_samtoolsshell The system cannot find the path specified.
FAILED
tests/AlignmentFileFetch_bench.py::test_build_fetch_from_bam_with_samtoolspipe PASSED
tests/AlignmentFileFetch_bench.py::test_build_fetch_from_bam_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_with_samtoolsshell The system cannot find the path specified.
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FAILED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_with_samtoolspipe PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_qualities_from_bam_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell The system cannot find the path specified.
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FAILED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_flagfilter_with_samtoolspipe PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_flagfilter_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_directflagfilter_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_aligned_pairs_default_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_aligned_pairs_matchesonly_with_pysam PASSED
tests/AlignmentFileFetch_bench.py::test_build_aligned_pairs_withseq_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_pileup_from_bam_with_samtoolsshell The system cannot find the path specified.
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PASSED
tests/AlignmentFilePileup_bench.py::test_build_pileup_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_pileup_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_depth_from_bam_with_samtoolsshell The system cannot find the path specified.
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PASSED
tests/AlignmentFilePileup_bench.py::test_build_depth_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_depth_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_depth_with_filter_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_from_bam_with_samtoolsshell The system cannot find the path specified.
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PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_from_bam_with_samtoolspysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_from_bam_with_pysam_pileups PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_with_reference_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_with_reference_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_bases_with_reference_from_bam_with_samtoolspysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_qualities_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_qualities_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_names_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_mapping_qualities_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_mapping_qualities_from_bam_with_pysam PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_positions_from_bam_with_samtoolspipe PASSED
tests/AlignmentFilePileup_bench.py::test_build_query_positions_from_bam_with_pysam PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_sam_with_samtools The system cannot find the path specified.
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PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_sam_with_samtoolspipe PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_sam_with_pysam PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_bam_with_samtools The system cannot find the path specified.
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PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_bam_with_samtoolspipe PASSED
tests/AlignmentFile_bench.py::test_count_number_lines_from_bam_with_pysam PASSED
tests/VariantFile_bench.py::test_build_filter_from_vcf_with_bcftoolsshell ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
--2024-03-28 17:34:32-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’.
--2024-03-28 17:34:33-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’.
[E::hts_open_format] Failed to open file "ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" : No such file or directory
Failed to read from ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz: No such file or directory
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
Failed to read from small.vcf.gz: unknown file type
FAILED
tests/VariantFile_bench.py::test_build_filter_from_vcf_with_bcftoolpipe ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
--2024-03-28 17:34:35-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’.
--2024-03-28 17:34:36-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’.
FAILED
tests/VariantFile_bench.py::test_build_filter_from_vcf_with_cyvcf2 ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
--2024-03-28 17:34:38-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’.
--2024-03-28 17:34:38-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’.
FAILED
tests/VariantFile_bench.py::test_build_filter_from_vcf_with_pysam ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
--2024-03-28 17:34:40-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz’.
--2024-03-28 17:34:41-- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
=> ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’
Resolving ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)... 193.62.193.167
Connecting to ftp.1000genomes.ebi.ac.uk (ftp.1000genomes.ebi.ac.uk)|193.62.193.167|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /vol1/ftp/release/20130502 ... done.
==> SIZE ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ... done.
==> PASV ... done. ==> RETR ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ...
No such file ‘ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi’.
FAILED
tests/faidx_bench.py::test_fasta_iteration_short_sequences PASSED
tests/faidx_bench.py::test_fasta_iteration_long_sequences PASSED
tests/faidx_bench.py::test_fasta_iteration_short_sequences_without_persistence PASSED
tests/faidx_bench.py::test_fasta_iteration_long_sequences_without_persistence PASSED
tests/faidx_bench.py::test_fasta_iteration_short_sequences_as_file PASSED
tests/faidx_bench.py::test_fasta_iteration_long_sequences_as_file PASSED
tests/faidx_bench.py::test_fastq_iteration_short_sequences PASSED
tests/faidx_bench.py::test_fastq_iteration_short_sequences_without_persistence PASSED
tests/faidx_bench.py::test_fastq_iteration_short_sequences_as_file PASSED
tests/tabix_bench.py::test_read_python_compressed FAILED
tests/tabix_bench.py::test_read_python_uncompressed PASSED
tests/tabix_bench.py::test_fetch_plain FAILED
tests/tabix_bench.py::test_fetch_parsed FAILED
tests/tabix_bench.py::test_iterate_generic_compressed FAILED
tests/tabix_bench.py::test_iterate_generic_uncompressed PASSED
tests/tabix_bench.py::test_iterate_parsed_compressed FAILED
tests/tabix_bench.py::test_iterate_parsed_uncompressed PASSED
tests/tabix_bench.py::test_iterate_file_compressed FAILED
tests/tabix_bench.py::test_iterate_file_uncompressed PASSED
tests/tabix_bench.py::test_read_python_large_compressed PASSED
tests/tabix_bench.py::test_read_python_large_uncompressed PASSED
tests/tabix_bench.py::test_iterate_generic_large_compressed PASSED
tests/tabix_bench.py::test_iterate_generic_large_uncompressed PASSED
tests/tabix_bench.py::test_iterate_parsed_large_compressed PASSED
tests/tabix_bench.py::test_iterate_parsed_large_uncompressed PASSED
tests/tabix_bench.py::test_iterate_file_large_compressed PASSED
tests/tabix_bench.py::test_iterate_file_large_uncompressed PASSED
============================================================================================ FAILURES ============================================================================================
__________________________________________________________________________ test_build_fetch_from_bam_with_samtoolsshell __________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf14bf650>
def test_build_fetch_from_bam_with_samtoolsshell(benchmark):
> result = benchmark(build_fetch_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
tests/AlignmentFileFetch_bench.py:10:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
fn = 'C:/msys64/home/Teemu/pysam-mingw/tests/pysam_data/ex2.bam'
def build_fetch_with_samtoolsshell(fn):
retval = os.popen("samtools view {} 2> /dev/null | wc -l".format(fn)).read()
> return int(retval.strip())
E ValueError: invalid literal for int() with base 10: ''
tests/AlignmentFileFetchTestUtils.py:10: ValueError
_____________________________________________________________________ test_build_query_sequences_from_bam_with_samtoolsshell _____________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf15684d0>
def test_build_query_sequences_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_query_sequences_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
> assert len(result) == 3270
E assert 0 == 3270
E + where 0 = len([])
tests/AlignmentFileFetch_bench.py:30: AssertionError
_______________________________________________________________ test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell ________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf156a010>
def test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell(benchmark):
result = benchmark(build_query_sequences_flagfilter_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
> assert len(result) == 3124
E assert 0 == 3124
E + where 0 = len([])
tests/AlignmentFileFetch_bench.py:54: AssertionError
_________________________________________________________________________ test_build_filter_from_vcf_with_bcftoolsshell __________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf15197d0>, genomes_data = 'small.vcf.gz'
@pytest.mark.benchmark(min_rounds=1)
def test_build_filter_from_vcf_with_bcftoolsshell(benchmark, genomes_data):
result = benchmark(build_filter_from_vcf_with_samtoolsshell, genomes_data)
> assert result == 9120
E assert 0 == 9120
tests/VariantFile_bench.py:34: AssertionError
__________________________________________________________________________ test_build_filter_from_vcf_with_bcftoolpipe ___________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf151ab50>, genomes_data = 'small.vcf.gz'
@pytest.mark.benchmark(min_rounds=1)
def test_build_filter_from_vcf_with_bcftoolpipe(benchmark, genomes_data):
result = benchmark(build_filter_from_vcf_with_bcftoolspipe, genomes_data)
> assert result == 9120
E assert 0 == 9120
tests/VariantFile_bench.py:40: AssertionError
_____________________________________________________________________________ test_build_filter_from_vcf_with_cyvcf2 _____________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf14d4ad0>, genomes_data = 'small.vcf.gz'
@pytest.mark.benchmark(min_rounds=1)
def test_build_filter_from_vcf_with_cyvcf2(benchmark, genomes_data):
result = benchmark(build_filter_from_vcf_with_cyvcf2, genomes_data)
# note: inconsistent with bcftools
> assert result == 9114
E assert 9120 == 9114
tests/VariantFile_bench.py:47: AssertionError
_____________________________________________________________________________ test_build_filter_from_vcf_with_pysam ______________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf1519b90>, genomes_data = 'small.vcf.gz'
@pytest.mark.benchmark(min_rounds=1)
def test_build_filter_from_vcf_with_pysam(benchmark, genomes_data):
> result = benchmark(build_filter_from_vcf_with_pysam, genomes_data)
tests/VariantFile_bench.py:52:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/VariantFileFetchTestUtils.py:50: in build_filter_from_vcf_with_pysam
with pysam.VariantFile(fn) as vcf:
pysam/libcbcf.pyx:4117: in pysam.libcbcf.VariantFile.__init__
self.open(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> raise ValueError('invalid file `{}` (mode=`{}`) - is it VCF/BCF format?'.format(filename, mode))
E ValueError: invalid file `b'small.vcf.gz'` (mode=`b'r'`) - is it VCF/BCF format?
pysam/libcbcf.pyx:4347: ValueError
__________________________________________________________________________________ test_read_python_compressed ___________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf14cb050>
def test_read_python_compressed(benchmark):
> result = benchmark(read_python_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
tests/tabix_bench.py:65:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:15: in read_python_compressed
with gzip.open(fn, mode="r") as f:
../../../ucrt64/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'GzipFile' object has no attribute 'fileobj'") raised in repr()] GzipFile object at 0x1acf1550370>
filename = 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz', mode = 'rb', compresslevel = 9, fileobj = None, mtime = None
def __init__(self, filename=None, mode=None,
compresslevel=_COMPRESS_LEVEL_BEST, fileobj=None, mtime=None):
"""Constructor for the GzipFile class.
At least one of fileobj and filename must be given a
non-trivial value.
The new class instance is based on fileobj, which can be a regular
file, an io.BytesIO object, or any other object which simulates a file.
It defaults to None, in which case filename is opened to provide
a file object.
When fileobj is not None, the filename argument is only used to be
included in the gzip file header, which may include the original
filename of the uncompressed file. It defaults to the filename of
fileobj, if discernible; otherwise, it defaults to the empty string,
and in this case the original filename is not included in the header.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
'xb' depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
'wb', 'a' and 'ab', and 'x' and 'xb'.
The compresslevel argument is an integer from 0 to 9 controlling the
level of compression; 1 is fastest and produces the least compression,
and 9 is slowest and produces the most compression. 0 is no compression
at all. The default is 9.
The mtime argument is an optional numeric timestamp to be written
to the last modification time field in the stream when compressing.
If omitted or None, the current time is used.
"""
if mode and ('t' in mode or 'U' in mode):
raise ValueError("Invalid mode: {!r}".format(mode))
if mode and 'b' not in mode:
mode += 'b'
if fileobj is None:
> fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
../../../ucrt64/lib/python3.11/gzip.py:174: FileNotFoundError
________________________________________________________________________________________ test_fetch_plain ________________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf1a51190>
def test_fetch_plain(benchmark):
> result = benchmark(fetch_plain, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
tests/tabix_bench.py:136:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:25: in fetch_plain
with pysam.Tabixfile(fn) as f:
pysam/libctabix.pyx:349: in pysam.libctabix.TabixFile.__cinit__
self._open(filename, mode, index, *args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> raise IOError("index `%s` not found" % filename_index)
E OSError: index `C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example_large.bed.gz.tbi` not found
pysam/libctabix.pyx:381: OSError
_______________________________________________________________________________________ test_fetch_parsed ________________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf1a5dad0>
def test_fetch_parsed(benchmark):
> result = benchmark(fetch_parsed, os.path.join(
TABIX_DATADIR, FN_LARGE_COMPRESSED))
tests/tabix_bench.py:142:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:30: in fetch_parsed
with pysam.Tabixfile(fn) as f:
pysam/libctabix.pyx:349: in pysam.libctabix.TabixFile.__cinit__
self._open(filename, mode, index, *args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> raise IOError("index `%s` not found" % filename_index)
E OSError: index `C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example_large.bed.gz.tbi` not found
pysam/libctabix.pyx:381: OSError
________________________________________________________________________________ test_iterate_generic_compressed _________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acef28f9d0>
def test_iterate_generic_compressed(benchmark):
> result = benchmark(iterate_generic_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
tests/tabix_bench.py:88:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:35: in iterate_generic_compressed
with gzip.open(fn) as f:
../../../ucrt64/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'GzipFile' object has no attribute 'fileobj'") raised in repr()] GzipFile object at 0x1acf156ff40>
filename = 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz', mode = 'rb', compresslevel = 9, fileobj = None, mtime = None
def __init__(self, filename=None, mode=None,
compresslevel=_COMPRESS_LEVEL_BEST, fileobj=None, mtime=None):
"""Constructor for the GzipFile class.
At least one of fileobj and filename must be given a
non-trivial value.
The new class instance is based on fileobj, which can be a regular
file, an io.BytesIO object, or any other object which simulates a file.
It defaults to None, in which case filename is opened to provide
a file object.
When fileobj is not None, the filename argument is only used to be
included in the gzip file header, which may include the original
filename of the uncompressed file. It defaults to the filename of
fileobj, if discernible; otherwise, it defaults to the empty string,
and in this case the original filename is not included in the header.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
'xb' depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
'wb', 'a' and 'ab', and 'x' and 'xb'.
The compresslevel argument is an integer from 0 to 9 controlling the
level of compression; 1 is fastest and produces the least compression,
and 9 is slowest and produces the most compression. 0 is no compression
at all. The default is 9.
The mtime argument is an optional numeric timestamp to be written
to the last modification time field in the stream when compressing.
If omitted or None, the current time is used.
"""
if mode and ('t' in mode or 'U' in mode):
raise ValueError("Invalid mode: {!r}".format(mode))
if mode and 'b' not in mode:
mode += 'b'
if fileobj is None:
> fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
../../../ucrt64/lib/python3.11/gzip.py:174: FileNotFoundError
_________________________________________________________________________________ test_iterate_parsed_compressed _________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acf1569d50>
def test_iterate_parsed_compressed(benchmark):
> result = benchmark(iterate_parsed_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
tests/tabix_bench.py:100:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:45: in iterate_parsed_compressed
with gzip.open(fn) as f:
../../../ucrt64/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'GzipFile' object has no attribute 'fileobj'") raised in repr()] GzipFile object at 0x1acf0b6f640>
filename = 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz', mode = 'rb', compresslevel = 9, fileobj = None, mtime = None
def __init__(self, filename=None, mode=None,
compresslevel=_COMPRESS_LEVEL_BEST, fileobj=None, mtime=None):
"""Constructor for the GzipFile class.
At least one of fileobj and filename must be given a
non-trivial value.
The new class instance is based on fileobj, which can be a regular
file, an io.BytesIO object, or any other object which simulates a file.
It defaults to None, in which case filename is opened to provide
a file object.
When fileobj is not None, the filename argument is only used to be
included in the gzip file header, which may include the original
filename of the uncompressed file. It defaults to the filename of
fileobj, if discernible; otherwise, it defaults to the empty string,
and in this case the original filename is not included in the header.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
'xb' depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
'wb', 'a' and 'ab', and 'x' and 'xb'.
The compresslevel argument is an integer from 0 to 9 controlling the
level of compression; 1 is fastest and produces the least compression,
and 9 is slowest and produces the most compression. 0 is no compression
at all. The default is 9.
The mtime argument is an optional numeric timestamp to be written
to the last modification time field in the stream when compressing.
If omitted or None, the current time is used.
"""
if mode and ('t' in mode or 'U' in mode):
raise ValueError("Invalid mode: {!r}".format(mode))
if mode and 'b' not in mode:
mode += 'b'
if fileobj is None:
> fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
../../../ucrt64/lib/python3.11/gzip.py:174: FileNotFoundError
__________________________________________________________________________________ test_iterate_file_compressed __________________________________________________________________________________
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0x000001acef21ebd0>
def test_iterate_file_compressed(benchmark):
> result = benchmark(iterate_file_compressed,
os.path.join(TABIX_DATADIR, FN_COMPRESSED))
tests/tabix_bench.py:112:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:125: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:147: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:275: in _calibrate_timer
duration = runner(loops_range)
../../../ucrt64/lib/python3.11/site-packages/pytest_benchmark/fixture.py:90: in runner
function_to_benchmark(*args, **kwargs)
tests/tabix_bench.py:55: in iterate_file_compressed
with gzip.open(fn) as f:
../../../ucrt64/lib/python3.11/gzip.py:58: in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'GzipFile' object has no attribute 'fileobj'") raised in repr()] GzipFile object at 0x1acf156e650>
filename = 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz', mode = 'rb', compresslevel = 9, fileobj = None, mtime = None
def __init__(self, filename=None, mode=None,
compresslevel=_COMPRESS_LEVEL_BEST, fileobj=None, mtime=None):
"""Constructor for the GzipFile class.
At least one of fileobj and filename must be given a
non-trivial value.
The new class instance is based on fileobj, which can be a regular
file, an io.BytesIO object, or any other object which simulates a file.
It defaults to None, in which case filename is opened to provide
a file object.
When fileobj is not None, the filename argument is only used to be
included in the gzip file header, which may include the original
filename of the uncompressed file. It defaults to the filename of
fileobj, if discernible; otherwise, it defaults to the empty string,
and in this case the original filename is not included in the header.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
'xb' depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
'wb', 'a' and 'ab', and 'x' and 'xb'.
The compresslevel argument is an integer from 0 to 9 controlling the
level of compression; 1 is fastest and produces the least compression,
and 9 is slowest and produces the most compression. 0 is no compression
at all. The default is 9.
The mtime argument is an optional numeric timestamp to be written
to the last modification time field in the stream when compressing.
If omitted or None, the current time is used.
"""
if mode and ('t' in mode or 'U' in mode):
raise ValueError("Invalid mode: {!r}".format(mode))
if mode and 'b' not in mode:
mode += 'b'
if fileobj is None:
> fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
E FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
../../../ucrt64/lib/python3.11/gzip.py:174: FileNotFoundError
======================================================================================== warnings summary ========================================================================================
tests/AlignmentFileFetch_bench.py:75
C:/msys64/home/Teemu/pysam-mingw/tests/AlignmentFileFetch_bench.py:75: PytestUnknownMarkWarning: Unknown pytest.mark.aligned_pairs - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.aligned_pairs
tests/AlignmentFileFetch_bench.py:82
C:/msys64/home/Teemu/pysam-mingw/tests/AlignmentFileFetch_bench.py:82: PytestUnknownMarkWarning: Unknown pytest.mark.aligned_pairs - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.aligned_pairs
tests/AlignmentFileFetch_bench.py:90
C:/msys64/home/Teemu/pysam-mingw/tests/AlignmentFileFetch_bench.py:90: PytestUnknownMarkWarning: Unknown pytest.mark.aligned_pairs - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.aligned_pairs
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-------------------------------------------------------------------------------------------------------------------------------------- benchmark: 67 tests ---------------------------------------------------------------------------------------------------------------------------------------
Name (time in ns) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_build_filter_from_vcf_with_cyvcf2 234.9989 (1.0) 9,270.0007 (1.0) 281.9915 (1.0) 87.1346 (1.0) 254.9990 (1.0) 5.0000 (1.0) 20153;25546 3,546,206.0962 (1.0) 156251 20
test_set_binary_tag 27,200.0034 (115.75) 50,300.0047 (5.43) 28,156.9209 (99.85) 1,246.8344 (14.31) 28,000.0095 (109.80) 499.9747 (99.99) 170;195 35,515.2470 (0.01) 6177 1
test_fasta_iteration_long_sequences_as_file 32,100.0116 (136.60) 285,099.9881 (30.76) 47,470.9381 (168.34) 16,274.0071 (186.77) 42,749.9908 (167.65) 21,399.9883 (>1000.0) 1938;123 21,065.5201 (0.01) 10894 1
test_fasta_iteration_long_sequences_without_persistence 37,099.9915 (157.87) 313,399.9999 (33.81) 59,054.9820 (209.42) 21,308.7008 (244.55) 52,699.9938 (206.67) 34,300.0283 (>1000.0) 1161;26 16,933.3724 (0.00) 6162 1
test_fasta_iteration_long_sequences 38,999.9768 (165.96) 390,000.0011 (42.07) 60,880.0462 (215.89) 22,927.5498 (263.13) 50,300.0047 (197.26) 39,300.0082 (>1000.0) 552;6 16,425.7431 (0.00) 3022 1
test_read_python_uncompressed 45,599.9980 (194.04) 325,999.9794 (35.17) 64,565.7668 (228.96) 19,145.1811 (219.72) 59,400.0012 (232.94) 28,949.9876 (>1000.0) 453;8 15,488.0837 (0.00) 2372 1
test_iterate_file_uncompressed 66,799.9848 (284.26) 176,600.0059 (19.05) 88,588.0193 (314.15) 21,806.9794 (250.27) 78,999.9904 (309.81) 35,800.0034 (>1000.0) 427;8 11,288.2081 (0.00) 2287 1
test_fasta_iteration_short_sequences_as_file 108,100.0082 (460.00) 471,699.9829 (50.88) 139,277.3996 (493.91) 28,424.7787 (326.22) 130,600.0049 (512.16) 41,200.0009 (>1000.0) 818;26 7,179.9158 (0.00) 3553 1
test_iterate_generic_uncompressed 113,099.9881 (481.28) 530,400.0224 (57.22) 154,412.0771 (547.58) 33,826.5269 (388.21) 144,499.9943 (566.67) 55,100.0121 (>1000.0) 1380;20 6,476.1774 (0.00) 4074 1
test_iterate_parsed_uncompressed 113,500.0202 (482.98) 526,899.9957 (56.84) 154,078.3389 (546.39) 33,893.7560 (388.98) 145,750.0039 (571.57) 56,499.9937 (>1000.0) 1498;17 6,490.2050 (0.00) 4238 1
test_fastq_iteration_short_sequences_as_file 157,000.0022 (668.09) 388,299.9881 (41.89) 208,545.3764 (739.54) 38,766.0967 (444.90) 196,850.0001 (771.96) 63,449.9738 (>1000.0) 1042;6 4,795.1195 (0.00) 2660 1
test_read_binary_tag 163,799.9958 (697.02) 345,500.0115 (37.27) 170,774.4563 (605.60) 9,951.3243 (114.21) 167,699.9964 (657.65) 5,199.9814 (>1000.0) 116;134 5,855.6767 (0.00) 1609 1
test_fasta_iteration_short_sequences_without_persistence 668,799.9994 (>1000.0) 1,360,800.0008 (146.80) 891,881.0566 (>1000.0) 135,028.9874 (>1000.0) 874,799.9964 (>1000.0) 177,775.0149 (>1000.0) 400;3 1,121.2257 (0.00) 1003 1
test_fastq_iteration_short_sequences_without_persistence 757,100.0024 (>1000.0) 1,274,600.0139 (137.50) 937,613.6094 (>1000.0) 84,310.4031 (967.59) 925,499.9750 (>1000.0) 116,249.9902 (>1000.0) 211;20 1,066.5374 (0.00) 823 1
test_count_number_lines_from_sam_with_pysam 893,999.9971 (>1000.0) 6,902,399.9968 (744.60) 1,184,081.5399 (>1000.0) 661,619.0719 (>1000.0) 1,060,699.9858 (>1000.0) 206,099.9686 (>1000.0) 24;29 844.5364 (0.00) 818 1
test_build_fetch_from_bam_with_pysam 1,007,000.0135 (>1000.0) 7,538,200.0068 (813.18) 1,229,967.0543 (>1000.0) 765,759.2127 (>1000.0) 1,055,400.0037 (>1000.0) 84,525.0252 (>1000.0) 19;123 813.0299 (0.00) 689 1
test_count_number_lines_from_bam_with_pysam 1,020,499.9999 (>1000.0) 7,063,900.0041 (762.02) 1,309,804.6900 (>1000.0) 809,672.7197 (>1000.0) 1,113,400.0088 (>1000.0) 172,850.0065 (>1000.0) 3;18 763.4726 (0.00) 128 1
test_build_query_sequences_from_bam_with_pysam 1,395,400.0024 (>1000.0) 1,611,999.9927 (173.89) 1,423,520.7210 (>1000.0) 21,277.3720 (244.19) 1,416,999.9922 (>1000.0) 19,724.9828 (>1000.0) 103;32 702.4836 (0.00) 637 1
test_fasta_iteration_short_sequences 1,420,500.0189 (>1000.0) 3,037,299.9900 (327.65) 1,622,402.1141 (>1000.0) 228,979.5344 (>1000.0) 1,532,200.0108 (>1000.0) 206,199.9839 (>1000.0) 53;33 616.3700 (0.00) 568 1
test_build_query_sequences_from_bam_directflagfilter_with_pysam 1,428,099.9894 (>1000.0) 2,301,900.0073 (248.32) 1,456,622.8826 (>1000.0) 39,512.3540 (453.46) 1,448,800.0015 (>1000.0) 21,274.9947 (>1000.0) 30;30 686.5195 (0.00) 673 1
test_build_pileup_from_bam_with_pysam 1,435,299.9860 (>1000.0) 9,367,499.9953 (>1000.0) 1,647,167.0629 (>1000.0) 867,040.9269 (>1000.0) 1,488,500.0128 (>1000.0) 60,250.0004 (>1000.0) 17;30 607.1030 (0.00) 589 1
test_build_query_sequences_from_bam_flagfilter_with_pysam 1,436,299.9937 (>1000.0) 1,975,899.9988 (213.15) 1,476,302.8303 (>1000.0) 30,285.2771 (347.57) 1,471,449.9994 (>1000.0) 24,049.9940 (>1000.0) 103;20 677.3678 (0.00) 636 1
test_build_query_qualities_from_bam_with_pysam 1,474,699.9950 (>1000.0) 8,511,399.9958 (918.17) 1,635,494.4997 (>1000.0) 740,416.4448 (>1000.0) 1,507,649.9840 (>1000.0) 32,800.0024 (>1000.0) 17;28 611.4359 (0.00) 600 1
test_build_depth_from_bam_with_pysam 1,498,300.0001 (>1000.0) 2,472,699.9982 (266.74) 1,674,343.0019 (>1000.0) 159,948.8043 (>1000.0) 1,620,199.9970 (>1000.0) 167,949.9910 (>1000.0) 79;34 597.2492 (0.00) 493 1
test_build_depth_with_filter_from_bam_with_pysam 1,677,299.9952 (>1000.0) 2,652,299.9979 (286.12) 2,095,937.0747 (>1000.0) 162,623.5560 (>1000.0) 2,130,100.0088 (>1000.0) 57,649.9806 (>1000.0) 128;140 477.1136 (0.00) 499 1
test_fastq_iteration_short_sequences 1,873,100.0018 (>1000.0) 3,159,900.0213 (340.87) 2,101,004.4391 (>1000.0) 135,590.6467 (>1000.0) 2,069,499.9839 (>1000.0) 123,800.0114 (>1000.0) 67;16 475.9628 (0.00) 383 1
test_build_query_positions_from_bam_with_pysam 2,551,499.9870 (>1000.0) 12,752,899.9874 (>1000.0) 3,372,312.6989 (>1000.0) 1,301,937.5990 (>1000.0) 3,216,699.9881 (>1000.0) 398,625.0231 (>1000.0) 9;11 296.5324 (0.00) 315 1
test_build_mapping_qualities_from_bam_with_pysam 2,559,899.9928 (>1000.0) 10,477,600.0080 (>1000.0) 2,867,538.9410 (>1000.0) 1,171,711.0988 (>1000.0) 2,635,700.0170 (>1000.0) 89,999.9723 (>1000.0) 10;30 348.7311 (0.00) 321 1
test_build_query_qualities_from_bam_with_pysam 2,578,899.9919 (>1000.0) 17,065,399.9958 (>1000.0) 3,068,287.6438 (>1000.0) 1,493,335.6875 (>1000.0) 2,717,650.0007 (>1000.0) 213,649.9970 (>1000.0) 13;37 325.9147 (0.00) 348 1
test_build_query_bases_from_bam_with_pysam 5,075,699.9990 (>1000.0) 13,051,799.9933 (>1000.0) 5,441,726.3471 (>1000.0) 1,204,891.4449 (>1000.0) 5,194,900.0044 (>1000.0) 151,799.9772 (>1000.0) 5;10 183.7652 (0.00) 167 1
test_build_aligned_pairs_matchesonly_with_pysam 7,868,399.9891 (>1000.0) 17,594,699.9807 (>1000.0) 10,718,511.3211 (>1000.0) 3,266,189.1533 (>1000.0) 8,664,900.0004 (>1000.0) 6,267,300.0211 (>1000.0) 31;0 93.2965 (0.00) 106 1
test_build_query_bases_from_bam_with_samtoolspysam 8,302,700.0073 (>1000.0) 13,263,300.0030 (>1000.0) 10,459,941.1223 (>1000.0) 936,433.3967 (>1000.0) 10,276,600.0200 (>1000.0) 907,850.0079 (>1000.0) 23;8 95.6028 (0.00) 107 1
test_build_aligned_pairs_default_with_pysam 8,516,200.0032 (>1000.0) 18,596,499.9837 (>1000.0) 11,266,838.9817 (>1000.0) 3,202,134.6506 (>1000.0) 9,358,600.0148 (>1000.0) 5,698,474.9899 (>1000.0) 19;0 88.7560 (0.00) 59 1
test_build_query_names_from_bam_with_pysam 9,859,899.9903 (>1000.0) 19,424,700.0036 (>1000.0) 10,782,062.3643 (>1000.0) 1,279,975.4977 (>1000.0) 10,579,299.9966 (>1000.0) 680,624.9949 (>1000.0) 3;3 92.7466 (0.00) 93 1
test_build_aligned_pairs_withseq_with_pysam 10,215,599.9921 (>1000.0) 20,063,399.9775 (>1000.0) 13,115,633.3337 (>1000.0) 3,623,710.0953 (>1000.0) 10,832,400.0030 (>1000.0) 7,068,724.9972 (>1000.0) 18;0 76.2449 (0.00) 57 1
test_build_query_bases_with_reference_from_bam_with_samtoolspysam 17,902,700.0268 (>1000.0) 19,565,099.9958 (>1000.0) 18,436,998.1467 (>1000.0) 380,059.4963 (>1000.0) 18,340,299.9974 (>1000.0) 424,900.0049 (>1000.0) 15;3 54.2388 (0.00) 54 1
test_build_fetch_from_bam_with_samtoolspipe 17,925,600.0265 (>1000.0) 32,562,999.9861 (>1000.0) 26,890,187.0952 (>1000.0) 2,938,550.3718 (>1000.0) 26,583,600.0035 (>1000.0) 4,439,149.9978 (>1000.0) 10;1 37.1883 (0.00) 31 1
test_build_query_bases_with_reference_from_bam_with_pysam 18,065,700.0165 (>1000.0) 26,554,299.9841 (>1000.0) 18,960,139.9982 (>1000.0) 1,586,828.9196 (>1000.0) 18,368,949.9972 (>1000.0) 1,165,099.9950 (>1000.0) 2;2 52.7422 (0.00) 50 1
test_build_filter_from_vcf_with_bcftoolpipe 21,057,600.0100 (>1000.0) 44,354,699.9886 (>1000.0) 28,830,790.0007 (>1000.0) 5,397,321.5003 (>1000.0) 30,052,599.9919 (>1000.0) 8,103,000.0292 (>1000.0) 10;1 34.6851 (0.00) 30 1
test_build_depth_from_bam_with_samtoolspipe 22,208,100.0102 (>1000.0) 52,789,800.0146 (>1000.0) 34,287,091.1760 (>1000.0) 5,695,304.8282 (>1000.0) 34,171,699.9974 (>1000.0) 7,442,899.9797 (>1000.0) 8;1 29.1655 (0.00) 34 1
test_build_query_sequences_from_bam_flagfilter_with_samtoolspipe 23,096,199.9914 (>1000.0) 31,184,999.9998 (>1000.0) 26,487,561.5360 (>1000.0) 2,223,362.0569 (>1000.0) 26,047,099.9929 (>1000.0) 3,870,574.9976 (>1000.0) 14;0 37.7536 (0.00) 39 1
test_build_query_sequences_from_bam_with_samtoolspipe 24,093,899.9923 (>1000.0) 32,868,999.9878 (>1000.0) 27,264,050.0017 (>1000.0) 2,199,266.4099 (>1000.0) 26,998,750.0069 (>1000.0) 3,050,999.9779 (>1000.0) 10;0 36.6783 (0.00) 34 1
test_build_pileup_from_bam_with_samtoolspipe 28,340,499.9936 (>1000.0) 39,801,299.9794 (>1000.0) 32,838,073.3282 (>1000.0) 3,691,400.7971 (>1000.0) 31,557,649.9852 (>1000.0) 5,777,600.0176 (>1000.0) 11;0 30.4525 (0.00) 30 1
test_build_query_qualities_from_bam_with_samtoolspipe 30,321,699.9746 (>1000.0) 42,218,199.9893 (>1000.0) 35,953,734.6141 (>1000.0) 3,363,327.3927 (>1000.0) 37,080,699.9999 (>1000.0) 5,354,599.9981 (>1000.0) 8;0 27.8135 (0.00) 26 1
test_count_number_lines_from_sam_with_samtoolspipe 30,481,499.9981 (>1000.0) 36,148,200.0153 (>1000.0) 33,052,353.8466 (>1000.0) 1,530,787.1007 (>1000.0) 32,769,700.0030 (>1000.0) 1,952,500.0243 (>1000.0) 9;0 30.2550 (0.00) 26 1
test_count_number_lines_from_bam_with_samtoolspipe 31,201,700.0106 (>1000.0) 60,523,399.9959 (>1000.0) 37,429,782.7567 (>1000.0) 6,888,758.1864 (>1000.0) 35,953,499.9880 (>1000.0) 3,904,925.0263 (>1000.0) 2;2 26.7167 (0.00) 29 1
test_build_query_bases_from_bam_with_pysam_pileups 31,219,600.0014 (>1000.0) 49,089,200.0089 (>1000.0) 33,694,890.3221 (>1000.0) 3,697,087.4778 (>1000.0) 32,597,300.0145 (>1000.0) 1,604,074.9761 (>1000.0) 3;3 29.6781 (0.00) 31 1
test_build_mapping_qualities_from_bam_with_samtoolspipe 31,409,699.9937 (>1000.0) 54,760,800.0052 (>1000.0) 39,955,563.9981 (>1000.0) 4,749,972.8155 (>1000.0) 40,248,600.0094 (>1000.0) 2,831,675.0104 (>1000.0) 6;5 25.0278 (0.00) 25 1
test_build_query_bases_from_bam_with_samtoolspipe 32,201,099.9953 (>1000.0) 59,084,499.9824 (>1000.0) 41,614,010.0002 (>1000.0) 7,472,416.4425 (>1000.0) 41,248,600.0132 (>1000.0) 9,232,999.9752 (>1000.0) 6;0 24.0304 (0.00) 20 1
test_read_python_large_uncompressed 34,723,399.9928 (>1000.0) 57,651,899.9878 (>1000.0) 43,147,045.8328 (>1000.0) 5,957,577.5450 (>1000.0) 42,149,200.0023 (>1000.0) 8,887,700.0089 (>1000.0) 6;0 23.1766 (0.00) 24 1
test_iterate_file_large_uncompressed 36,710,399.9888 (>1000.0) 49,854,799.9887 (>1000.0) 39,529,920.0004 (>1000.0) 2,715,245.1352 (>1000.0) 38,890,900.0030 (>1000.0) 2,858,949.9998 (>1000.0) 3;1 25.2973 (0.00) 25 1
test_iterate_file_large_compressed 37,686,400.0282 (>1000.0) 50,584,300.0137 (>1000.0) 40,704,485.7150 (>1000.0) 2,718,523.1209 (>1000.0) 40,414,799.9943 (>1000.0) 2,824,349.9983 (>1000.0) 2;1 24.5673 (0.00) 21 1
test_build_query_positions_from_bam_with_samtoolspipe 41,435,099.9927 (>1000.0) 52,128,899.9880 (>1000.0) 46,688,900.0035 (>1000.0) 2,782,449.5981 (>1000.0) 46,746,000.0073 (>1000.0) 3,762,800.0136 (>1000.0) 7;0 21.4184 (0.00) 21 1
test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell 44,425,300.0023 (>1000.0) 74,653,399.9918 (>1000.0) 56,770,488.2346 (>1000.0) 6,005,238.4373 (>1000.0) 55,965,100.0076 (>1000.0) 4,166,649.9965 (>1000.0) 3;2 17.6148 (0.00) 17 1
test_build_query_bases_with_reference_from_bam_with_samtoolspipe 45,414,600.0266 (>1000.0) 81,187,399.9774 (>1000.0) 54,510,676.1911 (>1000.0) 8,152,670.8921 (>1000.0) 51,939,400.0003 (>1000.0) 9,332,000.0087 (>1000.0) 3;1 18.3450 (0.00) 21 1
test_build_query_sequences_from_bam_with_samtoolsshell 47,061,599.9948 (>1000.0) 69,342,100.0033 (>1000.0) 56,769,733.3347 (>1000.0) 5,375,193.6037 (>1000.0) 57,136,099.9893 (>1000.0) 5,613,275.0033 (>1000.0) 4;1 17.6150 (0.00) 15 1
test_build_query_bases_from_bam_with_samtoolsshell 47,931,600.0128 (>1000.0) 64,687,300.0078 (>1000.0) 55,898,153.3356 (>1000.0) 4,999,540.3194 (>1000.0) 54,370,300.0003 (>1000.0) 8,034,350.0085 (>1000.0) 5;0 17.8897 (0.00) 15 1
test_build_depth_from_bam_with_samtoolsshell 50,572,000.0074 (>1000.0) 82,632,600.0097 (>1000.0) 59,711,956.2481 (>1000.0) 7,956,301.9163 (>1000.0) 57,036,899.9906 (>1000.0) 9,966,350.0005 (>1000.0) 2;1 16.7471 (0.00) 16 1
test_read_python_large_compressed 54,489,399.9759 (>1000.0) 68,944,600.0033 (>1000.0) 58,177,073.3367 (>1000.0) 3,672,376.5464 (>1000.0) 57,153,400.0046 (>1000.0) 3,878,250.0123 (>1000.0) 2;1 17.1889 (0.00) 15 1
test_build_pileup_from_bam_with_samtoolsshell 55,411,500.0123 (>1000.0) 87,900,899.9909 (>1000.0) 64,487,323.0754 (>1000.0) 8,052,759.7542 (>1000.0) 63,553,299.9877 (>1000.0) 4,444,300.0079 (>1000.0) 2;1 15.5069 (0.00) 13 1
test_count_number_lines_from_sam_with_samtools 68,104,100.0062 (>1000.0) 98,438,700.0208 (>1000.0) 78,105,060.0024 (>1000.0) 10,733,553.8225 (>1000.0) 74,213,950.0071 (>1000.0) 18,759,200.0002 (>1000.0) 2;0 12.8033 (0.00) 10 1
test_iterate_parsed_large_uncompressed 73,321,300.0058 (>1000.0) 87,116,100.0105 (>1000.0) 78,688,483.3384 (>1000.0) 4,534,815.8635 (>1000.0) 76,847,699.9947 (>1000.0) 7,713,600.0036 (>1000.0) 3;0 12.7083 (0.00) 12 1
test_count_number_lines_from_bam_with_samtools 76,733,299.9967 (>1000.0) 107,683,699.9855 (>1000.0) 90,769,072.7274 (>1000.0) 9,100,658.2539 (>1000.0) 92,548,100.0158 (>1000.0) 13,538,449.9881 (>1000.0) 3;0 11.0170 (0.00) 11 1
test_iterate_generic_large_uncompressed 79,285,200.0159 (>1000.0) 92,278,700.0018 (>1000.0) 85,596,436.3674 (>1000.0) 4,138,535.6379 (>1000.0) 85,302,799.9983 (>1000.0) 7,069,700.0046 (>1000.0) 3;0 11.6827 (0.00) 11 1
test_iterate_generic_large_compressed 93,231,799.9832 (>1000.0) 107,851,500.0117 (>1000.0) 101,728,144.4446 (>1000.0) 5,095,815.6129 (>1000.0) 102,224,200.0035 (>1000.0) 9,177,250.0018 (>1000.0) 3;0 9.8301 (0.00) 9 1
test_iterate_parsed_large_compressed 94,691,399.9796 (>1000.0) 106,865,400.0119 (>1000.0) 100,605,079.9973 (>1000.0) 4,345,635.9223 (>1000.0) 100,568,449.9978 (>1000.0) 7,006,200.0304 (>1000.0) 4;0 9.9399 (0.00) 10 1
test_build_filter_from_vcf_with_bcftoolsshell 124,731,799.9951 (>1000.0) 142,237,899.9996 (>1000.0) 135,295,062.5005 (>1000.0) 8,221,723.3810 (>1000.0) 140,171,349.9945 (>1000.0) 15,958,349.9917 (>1000.0) 3;0 7.3913 (0.00) 8 1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Legend:
Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile.
OPS: Operations Per Second, computed as 1 / Mean
==================================================================================== short test summary info =====================================================================================
FAILED tests/AlignmentFileFetch_bench.py::test_build_fetch_from_bam_with_samtoolsshell - ValueError: invalid literal for int() with base 10: ''
FAILED tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_with_samtoolsshell - assert 0 == 3270
FAILED tests/AlignmentFileFetch_bench.py::test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell - assert 0 == 3124
FAILED tests/VariantFile_bench.py::test_build_filter_from_vcf_with_bcftoolsshell - assert 0 == 9120
FAILED tests/VariantFile_bench.py::test_build_filter_from_vcf_with_bcftoolpipe - assert 0 == 9120
FAILED tests/VariantFile_bench.py::test_build_filter_from_vcf_with_cyvcf2 - assert 9120 == 9114
FAILED tests/VariantFile_bench.py::test_build_filter_from_vcf_with_pysam - ValueError: invalid file `b'small.vcf.gz'` (mode=`b'r'`) - is it VCF/BCF format?
FAILED tests/tabix_bench.py::test_read_python_compressed - FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
FAILED tests/tabix_bench.py::test_fetch_plain - OSError: index `C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example_large.bed.gz.tbi` not found
FAILED tests/tabix_bench.py::test_fetch_parsed - OSError: index `C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example_large.bed.gz.tbi` not found
FAILED tests/tabix_bench.py::test_iterate_generic_compressed - FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
FAILED tests/tabix_bench.py::test_iterate_parsed_compressed - FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
FAILED tests/tabix_bench.py::test_iterate_file_compressed - FileNotFoundError: [Errno 2] No such file or directory: 'C:/msys64/home/Teemu/pysam-mingw/tests/tabix_data/example.bed.gz'
======================================================================
13 failed, 62 passed, 3 warnings in 68.58s (0:01:08) ======================================================================
Please add a Windows build to the job matrix in .github/workflows/ci.yaml so that we can see this build in operation.
Please add a Windows build to the job matrix in .github/workflows/ci.yaml so that we can see this build in operation.
Looks like I have no idea how to get the build job working nor do I have the time to learn to do so at the moment.
Build tested on MSYS2 ucrt64 environment.
Test results: