old_contents: import hail as hl
  
  from .utils import benchmark, resource, get_mt
  
  
  @benchmark
  def import_vcf_write():
      mt = hl.import_vcf(resource('profile.vcf.bgz'))
      out = hl.utils.new_temp_file(suffix='mt')
      mt.write(out)
  
  
  @benchmark
  def import_vcf_count_rows():
      mt = hl.import_vcf(resource('profile.vcf.bgz'))
      mt.count_rows()
  
  
  @benchmark
  def export_vcf():
      mt = hl.read_matrix_table(resource('profile.mt'))
      out = hl.utils.new_temp_file(suffix='vcf.bgz')
      hl.export_vcf(mt, out)
  
  
  @benchmark
  def sample_qc():
      hl.sample_qc(get_mt()).cols()._force_count()
  
  
  @benchmark
  def variant_qc():
      hl.variant_qc(get_mt()).rows()._force_count()
  
  
  @benchmark
  def variant_and_sample_qc():
      mt = get_mt()
      hl.sample_qc(hl.variant_qc(mt))._force_count_rows()
  
  
  @benchmark
  def hwe_normalized_pca():
      mt = get_mt()
      mt = mt.filter_rows(mt.info.AF[0] > 0.01)
      hl.hwe_normalized_pca(mt.GT)
  
  
  @benchmark
  def split_multi_hts():
      mt = hl.read_matrix_table(resource('profile.mt'))
      hl.split_multi_hts(mt)._force_count_rows()
  
  
  @benchmark
  def split_multi():
      mt = hl.read_matrix_table(resource('profile.mt'))
      hl.split_multi(mt)._force_count_rows()
  
  
  @benchmark
  def concordance():
      mt = get_mt()
      mt = mt.filter_rows(mt.alleles.length() == 2)
      _, r, c = hl.methods.qc.concordance(mt, mt, _localize_global_statistics=False)
      r._force_count()
      c._force_count()
  
new_contents: import hail as hl
  from .utils import benchmark, resource, get_mt
  
  
  @benchmark
  def import_vcf_write():
      mt = hl.import_vcf(resource('profile.vcf.bgz'))
      out = hl.utils.new_temp_file(suffix='mt')
      mt.write(out)
  
  
  @benchmark
  def import_vcf_count_rows():
      mt = hl.import_vcf(resource('profile.vcf.bgz'))
      mt.count_rows()
  
  
  @benchmark
  def export_vcf():
      mt = hl.read_matrix_table(resource('profile.mt'))
      out = hl.utils.new_temp_file(suffix='vcf.bgz')
      hl.export_vcf(mt, out)
  
  
  @benchmark
  def sample_qc():
      hl.sample_qc(get_mt()).cols()._force_count()
  
  
  @benchmark
  def variant_qc():
      hl.variant_qc(get_mt()).rows()._force_count()
  
  
  @benchmark
  def variant_and_sample_qc():
      mt = get_mt()
      hl.sample_qc(hl.variant_qc(mt))._force_count_rows()
  
  
  @benchmark
  def hwe_normalized_pca():
      mt = get_mt()
      mt = mt.filter_rows(mt.info.AF[0] > 0.01)
      hl.hwe_normalized_pca(mt.GT)
  
  
  @benchmark
  def split_multi_hts():
      mt = hl.read_matrix_table(resource('profile.mt'))
      hl.split_multi_hts(mt)._force_count_rows()
  
  
  @benchmark
  def split_multi():
      mt = hl.read_matrix_table(resource('profile.mt'))
      hl.split_multi(mt)._force_count_rows()
  
  
  @benchmark
  def concordance():
      mt = get_mt()
      mt = mt.filter_rows(mt.alleles.length() == 2)
      _, r, c = hl.methods.qc.concordance(mt, mt, _localize_global_statistics=False)
      r._force_count()
      c._force_count()
  
  
  @benchmark
  def genetics_pipeline():
      mt = get_mt()
      mt = mt.split_multi_hts(mt)
      mt = hl.variant_qc(mt)
      mt = hl.sample_qc(mt)
      mt = mt.filter_cols(mt.sample_qc.call_rate > 0.95)
      mt = mt.filter_rows(mt.variant_qc.AC[1] > 5)
      mt = mt.filter_entries(hl.case().when(hl.is_indel(mt.alleles[0], mt.alleles[1]), mt.GQ > 20).default(mt.GQ > 10))
      mt.write('/tmp/genetics_pipeline.mt', overwrite=True)
  
subject: Add an example genetics pipeline (#7095)