def __init__(self, vcf_shards_output_dir, number_of_variants_per_shard): # type: (str, int) -> None """Initializes `_WriteVariantsToVCFShards` object. Args: vcf_shards_output_dir: The location for all VCF shards. number_of_variants_per_shard: The maximum number of variants that is written into one VCF shard. """ self._vcf_shards_output_dir = vcf_shards_output_dir self._number_of_variants_per_shard = number_of_variants_per_shard self._coder = vcfio._ToVcfRecordCoder() self._sample_names = [] self._variant_lines = [] self._counter = 0
def __init__(self, vcf_shards_output_dir, number_of_variants_per_shard): # type: (str, int) -> None """Initializes `_WriteVariantsToVCFShards` object. Args: vcf_shards_output_dir: The location for all VCF shards. number_of_variants_per_shard: The maximum number of variants that is written into one VCF shard. """ self._vcf_shards_output_dir = vcf_shards_output_dir self._number_of_variants_per_shard = number_of_variants_per_shard # Write shards as is. # This piece of code is triggered from vcf_to_bq._shard_variants() which # reads variants with the --use_1_based_coordinate=False option, regardless # if the flag was passed with that value or not. Therefore, write the shards # into BQ with 0-based coordinate assumption. self._coder = vcfio._ToVcfRecordCoder(bq_uses_1_based_coordinate=False) self._sample_names = [] self._variant_lines = [] self._counter = 0
def _get_coder(self): return vcfio._ToVcfRecordCoder()
def _get_coder(self, bq_uses_1_based_coordinate=False): return vcfio._ToVcfRecordCoder(bq_uses_1_based_coordinate)