Benchmarking
Latest benchmarking results:
------------------------------------------------------------------------------------------------------------------------ benchmark: 57 tests ------------------------------------------------------------------------------------------------------------------------
Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_set_binary_tag 93.8382 (1.0) 199.8786 (1.0) 96.1554 (1.0) 2.6241 (1.0) 95.7036 (1.0) 1.2442 (1.0) 276;303 10,399.8372 (1.0) 3170 1
test_fasta_iteration_long_sequences_without_persistence 145.3292 (1.55) 296.4940 (1.48) 176.5367 (1.84) 30.0896 (11.47) 167.2544 (1.75) 25.1532 (20.22) 840;579 5,664.5438 (0.54) 4972 1
test_fasta_iteration_long_sequences_as_file 149.0638 (1.59) 312.6319 (1.56) 177.2990 (1.84) 30.5218 (11.63) 168.6383 (1.76) 27.7516 (22.30) 669;510 5,640.1883 (0.54) 4493 1
test_fasta_iteration_long_sequences 150.3211 (1.60) 429.9153 (2.15) 176.7384 (1.84) 30.7021 (11.70) 167.5002 (1.75) 21.7482 (17.48) 682;647 5,658.0803 (0.54) 4845 1
test_fasta_iteration_short_sequences_as_file 190.6604 (2.03) 395.8736 (1.98) 216.6984 (2.25) 32.8710 (12.53) 208.9385 (2.18) 16.8057 (13.51) 291;326 4,614.7086 (0.44) 3205 1
test_read_python_uncompressed 214.1297 (2.28) 450.2051 (2.25) 234.6956 (2.44) 33.3642 (12.71) 223.4913 (2.34) 15.0129 (12.07) 140;221 4,260.8375 (0.41) 2043 1
test_fastq_iteration_short_sequences_as_file 217.5961 (2.32) 420.1643 (2.10) 238.0264 (2.48) 30.4469 (11.60) 228.8874 (2.39) 15.5573 (12.50) 209;235 4,201.2146 (0.40) 2877 1
test_iterate_file_uncompressed 225.5719 (2.40) 481.0989 (2.41) 249.7603 (2.60) 40.7266 (15.52) 239.5548 (2.50) 15.9908 (12.85) 209;327 4,003.8387 (0.38) 3627 1
test_iterate_file_compressed 257.5517 (2.74) 576.6843 (2.89) 287.2536 (2.99) 49.8803 (19.01) 277.4149 (2.90) 14.3824 (11.56) 126;248 3,481.2446 (0.33) 3023 1
test_iterate_generic_uncompressed 344.8855 (3.68) 712.5959 (3.57) 370.9369 (3.86) 46.2477 (17.62) 365.0384 (3.81) 15.7915 (12.69) 54;83 2,695.8763 (0.26) 2240 1
test_iterate_parsed_uncompressed 349.3819 (3.72) 765.3460 (3.83) 378.1446 (3.93) 54.2199 (20.66) 369.5488 (3.86) 15.4320 (12.40) 48;69 2,644.4910 (0.25) 1638 1
test_read_python_compressed 462.0645 (4.92) 836.2234 (4.18) 493.6158 (5.13) 51.2946 (19.55) 485.5469 (5.07) 11.4385 (9.19) 28;46 2,025.8670 (0.19) 906 1
test_iterate_parsed_compressed 586.5730 (6.25) 1,050.1631 (5.25) 632.5464 (6.58) 82.6438 (31.49) 608.1080 (6.35) 20.1799 (16.22) 115;143 1,580.9117 (0.15) 1474 1
test_iterate_generic_compressed 587.7707 (6.26) 1,093.4286 (5.47) 639.6830 (6.65) 85.2593 (32.49) 612.6408 (6.40) 19.9433 (16.03) 105;144 1,563.2743 (0.15) 1260 1
test_fasta_iteration_short_sequences_without_persistence 725.2563 (7.73) 1,091.6069 (5.46) 774.6549 (8.06) 53.0901 (20.23) 751.8455 (7.86) 45.0788 (36.23) 172;110 1,290.8974 (0.12) 1276 1
test_read_binary_tag 817.2598 (8.71) 1,232.0559 (6.16) 902.7002 (9.39) 87.7807 (33.45) 871.5261 (9.11) 17.4227 (14.00) 39;55 1,107.7875 (0.11) 331 1
test_fastq_iteration_short_sequences_without_persistence 840.3640 (8.96) 1,201.5756 (6.01) 870.9679 (9.06) 35.8709 (13.67) 866.1682 (9.05) 15.9768 (12.84) 53;85 1,148.1480 (0.11) 1124 1
test_count_number_lines_from_sam_with_pysam 2,755.6140 (29.37) 9,656.9806 (48.31) 2,963.2206 (30.82) 729.0077 (277.81) 2,814.3115 (29.41) 106.2388 (85.38) 8;14 337.4707 (0.03) 281 1
test_fasta_iteration_short_sequences 2,905.5942 (30.96) 3,674.1439 (18.38) 2,982.3892 (31.02) 90.9585 (34.66) 2,941.2108 (30.73) 96.1348 (77.26) 27;7 335.3016 (0.03) 302 1
test_fastq_iteration_short_sequences 3,601.3145 (38.38) 4,065.5769 (20.34) 3,671.8361 (38.19) 71.5348 (27.26) 3,635.1625 (37.98) 81.5415 (65.53) 43;10 272.3433 (0.03) 243 1
test_count_number_lines_from_bam_with_pysam 4,178.8872 (44.53) 12,063.5536 (60.35) 4,395.9713 (45.72) 794.3991 (302.73) 4,240.1757 (44.31) 67.0198 (53.86) 6;19 227.4810 (0.02) 205 1
test_build_depth_from_bam_with_pysam 6,290.2980 (67.03) 6,788.0806 (33.96) 6,420.3862 (66.77) 126.5447 (48.22) 6,357.6270 (66.43) 94.3104 (75.80) 35;29 155.7539 (0.01) 145 1
test_build_depth_with_filter_from_bam_with_pysam 6,935.8926 (73.91) 8,309.5767 (41.57) 7,085.6801 (73.69) 221.5069 (84.41) 7,005.6170 (73.20) 74.4388 (59.83) 14;27 141.1297 (0.01) 139 1
test_build_query_positions_from_bam_with_pysam 8,729.2437 (93.02) 16,836.6525 (84.23) 9,173.2902 (95.40) 1,057.4321 (402.97) 8,885.4395 (92.84) 264.7634 (212.79) 3;9 109.0121 (0.01) 103 1
test_build_mapping_qualities_from_bam_with_pysam 8,805.0570 (93.83) 15,829.8910 (79.20) 9,274.7475 (96.46) 964.6925 (367.63) 9,004.7438 (94.09) 354.9103 (285.24) 4;9 107.8196 (0.01) 106 1
test_build_query_qualities_from_bam_with_pysam 8,947.6798 (95.35) 16,756.8158 (83.83) 9,272.9117 (96.44) 1,008.7759 (384.43) 9,017.0493 (94.22) 217.2068 (174.57) 3;5 107.8410 (0.01) 94 1
test_build_query_bases_from_bam_with_samtoolspysam 9,149.0448 (97.50) 9,776.0092 (48.91) 9,208.3405 (95.77) 86.1889 (32.85) 9,190.2809 (96.03) 34.1963 (27.48) 5;7 108.5972 (0.01) 84 1
test_count_number_lines_from_bam_with_samtoolspipe 10,431.4052 (111.16) 13,431.7447 (67.20) 11,052.2360 (114.94) 445.8241 (169.90) 11,014.8042 (115.09) 492.6044 (395.91) 17;3 90.4794 (0.01) 90 1
test_count_number_lines_from_bam_with_samtools 12,057.8520 (128.50) 13,537.5429 (67.73) 12,595.0708 (130.99) 381.1799 (145.26) 12,499.5783 (130.61) 457.8107 (367.94) 25;1 79.3961 (0.01) 73 1
test_count_number_lines_from_sam_with_samtoolspipe 12,434.8756 (132.51) 14,234.1983 (71.21) 13,034.1032 (135.55) 371.0373 (141.40) 13,049.9089 (136.36) 464.8147 (373.57) 21;3 76.7218 (0.01) 72 1
test_build_query_bases_from_bam_with_pysam 12,811.6887 (136.53) 19,972.7099 (99.92) 13,268.7908 (137.99) 1,103.9459 (420.70) 13,023.1632 (136.08) 202.3596 (162.64) 4;6 75.3648 (0.01) 76 1
test_build_pileup_from_bam_with_samtoolspipe 13,480.7490 (143.66) 15,413.4836 (77.11) 13,968.3817 (145.27) 362.1282 (138.00) 13,917.4843 (145.42) 447.9736 (360.04) 12;3 71.5903 (0.01) 66 1
test_count_number_lines_from_sam_with_samtools 13,963.2300 (148.80) 15,936.2238 (79.73) 14,442.5627 (150.20) 340.4846 (129.75) 14,395.4996 (150.42) 339.3036 (272.70) 12;2 69.2398 (0.01) 59 1
test_build_pileup_from_bam_with_samtoolsshell 15,140.2969 (161.34) 16,469.8567 (82.40) 15,525.9034 (161.47) 256.0741 (97.59) 15,526.7641 (162.24) 318.5044 (255.98) 13;2 64.4085 (0.01) 51 1
test_build_depth_from_bam_with_samtoolsshell 15,291.4841 (162.96) 16,387.9916 (81.99) 15,656.5365 (162.83) 217.2420 (82.79) 15,609.9945 (163.11) 258.9412 (208.11) 16;2 63.8711 (0.01) 57 1
test_build_query_bases_from_bam_with_samtoolspipe 15,478.0652 (164.94) 17,068.8462 (85.40) 16,072.5749 (167.15) 327.6668 (124.87) 16,040.5049 (167.61) 428.1597 (344.11) 18;2 62.2178 (0.01) 60 1
test_build_query_bases_from_bam_with_samtoolsshell 15,765.5794 (168.01) 17,102.8059 (85.57) 16,305.4955 (169.57) 367.6865 (140.12) 16,256.2486 (169.86) 593.9230 (477.34) 20;0 61.3290 (0.01) 57 1
test_build_depth_from_bam_with_samtoolspipe 16,024.7944 (170.77) 25,804.2309 (129.10) 17,041.3497 (177.23) 1,522.0046 (580.01) 16,726.8887 (174.78) 767.1015 (616.52) 1;1 58.6808 (0.01) 40 1
test_build_query_qualities_from_bam_with_samtoolspipe 16,275.7467 (173.44) 18,501.0433 (92.56) 17,262.6517 (179.53) 642.2656 (244.76) 17,255.3696 (180.30) 1,060.3429 (852.20) 20;0 57.9285 (0.01) 51 1
test_build_pileup_from_bam_with_pysam 16,632.5681 (177.25) 19,306.6560 (96.59) 17,037.7162 (177.19) 531.0751 (202.38) 16,870.8330 (176.28) 279.1677 (224.37) 3;4 58.6933 (0.01) 32 1
test_build_mapping_qualities_from_bam_with_samtoolspipe 17,398.3518 (185.41) 18,481.6569 (92.46) 17,832.1261 (185.45) 294.9103 (112.39) 17,837.8206 (186.39) 511.8400 (411.37) 21;0 56.0786 (0.01) 52 1
test_build_query_names_from_bam_with_pysam 31,534.0199 (336.05) 38,316.2647 (191.70) 32,677.2804 (339.84) 1,371.6101 (522.70) 32,179.0325 (336.24) 1,392.1391 (>1000.0) 3;1 30.6023 (0.00) 30 1
test_fetch_plain 43,747.1233 (466.20) 48,690.7829 (243.60) 44,573.8085 (463.56) 1,170.8588 (446.20) 44,067.5411 (460.46) 1,436.5837 (>1000.0) 3;1 22.4347 (0.00) 22 1
test_build_query_positions_from_bam_with_samtoolspipe 46,316.5548 (493.58) 53,700.3577 (268.66) 48,235.6640 (501.64) 1,861.0317 (709.21) 47,625.2194 (497.63) 2,603.7074 (>1000.0) 6;1 20.7315 (0.00) 21 1
test_build_query_bases_with_reference_from_bam_with_samtoolspysam 51,565.1479 (549.51) 53,523.1121 (267.78) 51,778.6650 (538.49) 424.4621 (161.76) 51,656.8925 (539.76) 110.5051 (88.81) 1;4 19.3130 (0.00) 20 1
test_build_query_bases_with_reference_from_bam_with_pysam 58,850.6740 (627.15) 62,164.5451 (311.01) 60,161.6779 (625.67) 1,120.6101 (427.05) 59,595.2785 (622.71) 1,995.0196 (>1000.0) 7;0 16.6219 (0.00) 16 1
test_iterate_file_large_uncompressed 59,419.9076 (633.22) 69,053.0874 (345.48) 62,825.7126 (653.38) 3,805.1150 (>1000.0) 60,805.1391 (635.35) 6,407.6949 (>1000.0) 3;0 15.9170 (0.00) 14 1
test_iterate_file_large_compressed 63,986.9571 (681.89) 74,156.9120 (371.01) 68,370.8835 (711.05) 3,254.6200 (>1000.0) 67,221.2075 (702.39) 4,770.3525 (>1000.0) 5;0 14.6261 (0.00) 16 1
test_read_python_large_uncompressed 67,611.8080 (720.51) 89,112.1533 (445.83) 73,631.8916 (765.76) 5,978.7052 (>1000.0) 71,702.4822 (749.21) 7,856.0165 (>1000.0) 2;1 13.5811 (0.00) 13 1
test_fetch_parsed 72,237.5344 (769.81) 81,976.9856 (410.13) 74,540.4099 (775.21) 2,326.3668 (886.54) 74,016.3419 (773.39) 1,579.0667 (>1000.0) 1;1 13.4155 (0.00) 14 1
test_build_query_bases_from_bam_with_pysam_pileups 75,841.3766 (808.21) 87,975.1425 (440.14) 79,393.9784 (825.68) 3,516.2458 (>1000.0) 79,346.7313 (829.09) 5,217.5033 (>1000.0) 2;0 12.5954 (0.00) 13 1
test_build_query_bases_with_reference_from_bam_with_samtoolspipe 131,162.9396 (>1000.0) 132,858.8147 (664.70) 131,838.0199 (>1000.0) 595.6090 (226.98) 131,801.5633 (>1000.0) 956.9665 (769.11) 2;0 7.5851 (0.00) 8 1
test_iterate_parsed_large_uncompressed 132,991.8914 (>1000.0) 140,153.4099 (701.19) 134,101.5892 (>1000.0) 2,452.3161 (934.54) 133,218.1590 (>1000.0) 396.3616 (318.56) 1;1 7.4570 (0.00) 8 1
test_iterate_generic_large_uncompressed 134,743.7277 (>1000.0) 142,329.4526 (712.08) 138,167.4954 (>1000.0) 3,346.7773 (>1000.0) 136,839.1849 (>1000.0) 6,541.1879 (>1000.0) 4;0 7.2376 (0.00) 8 1
test_read_python_large_compressed 175,127.6311 (>1000.0) 190,855.1529 (954.86) 181,702.9339 (>1000.0) 5,756.2207 (>1000.0) 181,221.0185 (>1000.0) 8,577.6616 (>1000.0) 2;0 5.5035 (0.00) 6 1
test_iterate_parsed_large_compressed 231,405.7611 (>1000.0) 243,728.8519 (>1000.0) 239,037.8296 (>1000.0) 5,212.7778 (>1000.0) 241,544.3324 (>1000.0) 8,062.6113 (>1000.0) 1;0 4.1834 (0.00) 5 1
test_iterate_generic_large_compressed 235,042.3876 (>1000.0) 256,518.8371 (>1000.0) 242,535.5468 (>1000.0) 8,272.5197 (>1000.0) 240,163.0748 (>1000.0) 8,360.1568 (>1000.0) 1;0 4.1231 (0.00) 5 1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------