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More explode refactoring #91

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merged 5 commits into from
Mar 25, 2024
Merged

More explode refactoring #91

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52ad9c0
Breaking changes to ICF metadata
jeromekelleher Mar 25, 2024
555ac94
Rename VcfMetadata to IcfMetadata
jeromekelleher Mar 25, 2024
a5c277a
Rename more pcvcf -> icf
jeromekelleher Mar 25, 2024
2c846f9
Rename icf tests
jeromekelleher Mar 25, 2024
1cb8bd6
Switch to LZ4 as the default compressor
jeromekelleher Mar 25, 2024
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8 changes: 4 additions & 4 deletions bio2zarr/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ def setup_logging(verbosity):
@column_chunk_size
def explode(vcfs, zarr_path, verbose, worker_processes, column_chunk_size):
"""
Convert VCF(s) to columnar intermediate format
Convert VCF(s) to intermediate columnar format
"""
setup_logging(verbose)
vcf.explode(
Expand All @@ -92,7 +92,7 @@ def explode(vcfs, zarr_path, verbose, worker_processes, column_chunk_size):
@worker_processes
def dexplode_init(vcfs, icf_path, num_partitions, verbose, worker_processes):
"""
Initial step for parallel conversion of VCF(s) to columnar intermediate format
Initial step for parallel conversion of VCF(s) to intermediate columnar format
over the requested number of paritions.
"""
setup_logging(verbose)
Expand All @@ -115,7 +115,7 @@ def dexplode_init(vcfs, icf_path, num_partitions, verbose, worker_processes):
@column_chunk_size
def dexplode_slice(path, start, end, verbose, worker_processes, column_chunk_size):
"""
Convert VCF(s) to columnar intermediate format
Convert VCF(s) to intermediate columnar format
"""
setup_logging(verbose)
vcf.explode_slice(
Expand All @@ -133,7 +133,7 @@ def dexplode_slice(path, start, end, verbose, worker_processes, column_chunk_siz
@verbose
def dexplode_finalise(path, verbose):
"""
Final step for parallel conversion of VCF(s) to columnar intermediate format
Final step for parallel conversion of VCF(s) to intermediate columnar format
"""
setup_logging(verbose)
vcf.explode_finalise(path)
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