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Row fields: | |
'locus': locus<GRCh37> | |
'alleles': array<str> | |
'freq': array<struct { | |
AC: int32, | |
AF: float64, | |
AN: int32, | |
homozygote_count: int32 | |
}> | |
'age_hist_het': array<struct { |
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Table._same: rows differ: | |
1L Struct(vep=Struct(assembly_name='GRCh37', allele_string='A/T', ancestral=None, colocated_variants=None, context=None, end=55523002, id='1_55523002_A/T', input='1\t55523002\t.\tA\tT\t.\t.\tGT', intergenic_consequences=None, most_severe_consequence='splice_acceptor_variant', motif_feature_consequences=None, regulatory_feature_consequences=None, seq_region_name='1', start=55523002, strand=1, transcript_consequences=[Struct(allele_num=1, amino_acids=None, biotype='protein_coding', canonical=1, ccds='CCDS603.1', cdna_start=None, cdna_end=None, cds_end=None, cds_start=None, codons=None, consequence_terms=['splice_acceptor_variant'], distance=None, domains=None, exon=None, gene_id='ENSG00000169174', gene_pheno=1, gene_symbol='PCSK9', gene_symbol_source='HGNC', hgnc_id='20001', hgvsc='ENST00000302118.5:c.997-2A>T', hgvsp=None, hgvs_offset=None, impact='HIGH', intron='6/11', lof='LC', lof_flags=None, lof_filter='ANC_ALLELE', minimised=1, polyphen_prediction=None, polyphen_score=None, pr |
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Found non-overlapping benchmarks: | |
matrix_table_scan_count_cols | |
matrix_table_scan_count_rows | |
Failed benchmarks in run 1: | |
group_by_collect_per_row | |
read_with_index_p1000 | |
matrix_table_show | |
gnomad_coverage_stats_optimized | |
group_by_take_rekey | |
export_range_matrix_table_entry_field_p100 |
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$ hail-bench compare 0.2.33-v33-release.json 0.2.33-4a663d2893e7-v34-release-candidate.json | |
Failed benchmarks in run 1: | |
table_big_aggregate_compile_and_execute | |
block_matrix_nested_multiply | |
pc_relate_big | |
table_range_array_range_force_count | |
compile_2k_merge | |
table_big_aggregate_compilation | |
Failed benchmarks in run 2: | |
block_matrix_nested_multiply |
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Failed benchmarks in run 1: | |
block_matrix_nested_multiply | |
pc_relate_big | |
Failed benchmarks in run 2: | |
pc_relate_big | |
large_range_matrix_table_sum | |
Benchmark Name Ratio Time 1 Time 2 | |
-------------- ----- ------ ------ | |
ndarray_matmul_float64_benchmark 286.0% 3.273 9.361 | |
read_force_count_p100 127.8% 2.037 2.603 |
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$ hail-bench compare 0.2.36-release.json 0.2.37-df59d9ba6a79-release-candidate.json | |
Failed benchmarks in run 1: | |
block_matrix_nested_multiply | |
pc_relate_big | |
Failed benchmarks in run 2: | |
block_matrix_nested_multiply | |
pc_relate_big | |
Benchmark Name Ratio Time 1 Time 2 | |
-------------- ----- ------ ------ | |
union_p100_p100 168.5% 14.295 24.086 |
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Failed benchmarks in run 1: | |
pc_relate_big | |
Failed benchmarks in run 2: | |
pc_relate_big | |
Benchmark Name Ratio Time 1 Time 2 | |
-------------- ----- ------ ------ | |
matrix_table_call_stats_star_star 130.0% 7.493 9.743 | |
table_aggregate_downsample_dense 121.0% 54.725 66.242 | |
variant_and_sample_qc_nested_with_filters_4 118.2% 39.312 46.450 | |
group_by_collect_per_row 116.4% 3.221 3.748 |
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import hail as hl | |
import pytest | |
mt = hl.read_matrix_table('joined.mt') | |
rs = mt.rows() | |
cs = mt.cols() | |
es = mt.entries() | |
""" | |
Schema of `mt`: |
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import hail as hl | |
import pytest | |
mt = hl.read_matrix_table('joined.mt') | |
rs = mt.rows() | |
cs = mt.cols() | |
es = mt.entries() | |
""" | |
Schema of `mt`: |
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#!/opt/conda/default/bin/python3 | |
import json | |
import os | |
import subprocess as sp | |
import sys | |
import errno | |
from subprocess import check_output | |
assert sys.version_info > (3, 0), sys.version_info |
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