Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

MinGW version of pysam #1274

Open
wants to merge 19 commits into
base: master
Choose a base branch
from
Open

MinGW version of pysam #1274

wants to merge 19 commits into from

Conversation

teepean
Copy link

@teepean teepean commented Mar 28, 2024 •
edited
Loading

Build tested on MSYS2 ucrt64 environment.

Test results:

$ pytest tests
====================================================================================== 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
rootdir: C:/msys64/home/Teemu/pysam-mingw
configfile: setup.cfg
collected 958 items

tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_rod04bcq
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_v6vkedcm
[E::cram_index_load] Could not retrieve index file for 'C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_v6vkedcm'
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_f0bjsq3v
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_vr5dipo7
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write__iz2satn
[W::sanitise_SQ_lines] Header https://github.com/sq length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for 'C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write__iz2satn'
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM C:/msys64/home/Teemu/pysam-mingw/tests/tmp/pysamtests_tmp_check_read_write_mzq5hk5x
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED (exercises invalid accesses, which crashes with Python 3.11)
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex FAILED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 FAILED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 FAILED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 FAILED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: C:/msys64/home/Teemu/pysam-mingw/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED (fails on linux - https issue?)
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED (test contains bug)
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing

@teepean
MinGW support
8e84369
@teepean
Update setup.py
fba8d95 
Pysam seems to be working at least under MSYS2 shell.
@teepean
Remove extra comments from setup.py
a35d6ba
@teepean
Copy link
Author

teepean commented Mar 28, 2024

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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
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) ======================================================================

@teepean
Update setup.py
a97e545 
Couple of fixes to get pysam compiling on Linux
@teepean
Update setup.py
1dcff07 
Couple more fixes for Linux
@jmarshall
Copy link
Member

Please add a Windows build to the job matrix in .github/workflows/ci.yaml so that we can see this build in operation.

@teepean
Copy link
Author

teepean commented Apr 21, 2024

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@teepean @jmarshall