@@ -58,6 +58,13 @@ def list_commands(self, ctx):
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help = "Force overwriting of existing directories" ,
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)
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+ progress = click .option (
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+ "-P /-Q" ,
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+ "--progress/--no-progress" ,
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+ default = True ,
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+ help = "Show progress bars (default: show)" ,
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+ )
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+
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one_based = click .option (
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"--one-based" ,
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is_flag = True ,
@@ -190,9 +197,17 @@ def show_work_summary(work_summary, json):
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@verbose
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@column_chunk_size
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@compressor
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+ @progress
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@worker_processes
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def explode (
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- vcfs , icf_path , force , verbose , column_chunk_size , compressor , worker_processes
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+ vcfs ,
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+ icf_path ,
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+ force ,
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+ verbose ,
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+ column_chunk_size ,
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+ compressor ,
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+ progress ,
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+ worker_processes ,
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):
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"""
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Convert VCF(s) to intermediate columnar format
@@ -205,7 +220,7 @@ def explode(
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worker_processes = worker_processes ,
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column_chunk_size = column_chunk_size ,
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compressor = get_compressor (compressor ),
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- show_progress = True ,
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+ show_progress = progress ,
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)
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@@ -218,6 +233,7 @@ def explode(
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@compressor
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@json
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@verbose
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+ @progress
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@worker_processes
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def dexplode_init (
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vcfs ,
@@ -228,6 +244,7 @@ def dexplode_init(
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compressor ,
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json ,
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verbose ,
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+ progress ,
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worker_processes ,
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):
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"""
@@ -243,7 +260,7 @@ def dexplode_init(
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column_chunk_size = column_chunk_size ,
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worker_processes = worker_processes ,
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compressor = get_compressor (compressor ),
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- show_progress = True ,
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+ show_progress = progress ,
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)
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show_work_summary (work_summary , json )
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@@ -310,6 +327,7 @@ def mkschema(icf_path):
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@samples_chunk_size
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@max_variant_chunks
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@max_memory
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+ @progress
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@worker_processes
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def encode (
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icf_path ,
@@ -321,6 +339,7 @@ def encode(
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samples_chunk_size ,
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max_variant_chunks ,
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max_memory ,
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+ progress ,
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worker_processes ,
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):
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"""
@@ -337,7 +356,7 @@ def encode(
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max_variant_chunks = max_variant_chunks ,
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worker_processes = worker_processes ,
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max_memory = max_memory ,
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- show_progress = True ,
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+ show_progress = progress ,
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)
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@@ -351,6 +370,7 @@ def encode(
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@samples_chunk_size
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@max_variant_chunks
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@json
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+ @progress
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@verbose
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def dencode_init (
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icf_path ,
@@ -362,6 +382,7 @@ def dencode_init(
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samples_chunk_size ,
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max_variant_chunks ,
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json ,
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+ progress ,
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verbose ,
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):
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"""
@@ -387,7 +408,7 @@ def dencode_init(
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variants_chunk_size = variants_chunk_size ,
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samples_chunk_size = samples_chunk_size ,
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max_variant_chunks = max_variant_chunks ,
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- show_progress = True ,
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+ show_progress = progress ,
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)
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show_work_summary (work_summary , json )
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@@ -413,12 +434,13 @@ def dencode_partition(zarr_path, partition, verbose, one_based):
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@click .command
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@zarr_path
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@verbose
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- def dencode_finalise (zarr_path , verbose ):
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+ @progress
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+ def dencode_finalise (zarr_path , verbose , progress ):
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"""
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Final step for distributed conversion of ICF to VCF Zarr.
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"""
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setup_logging (verbose )
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- vcf2zarr .encode_finalise (zarr_path , show_progress = True )
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+ vcf2zarr .encode_finalise (zarr_path , show_progress = progress )
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@click .command (name = "convert" )
@@ -428,6 +450,7 @@ def dencode_finalise(zarr_path, verbose):
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@variants_chunk_size
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@samples_chunk_size
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@verbose
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+ @progress
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@worker_processes
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def convert_vcf (
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vcfs ,
@@ -436,6 +459,7 @@ def convert_vcf(
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variants_chunk_size ,
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samples_chunk_size ,
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verbose ,
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+ progress ,
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worker_processes ,
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):
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"""
@@ -448,7 +472,7 @@ def convert_vcf(
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zarr_path ,
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variants_chunk_size = variants_chunk_size ,
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samples_chunk_size = samples_chunk_size ,
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- show_progress = True ,
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+ show_progress = progress ,
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worker_processes = worker_processes ,
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)
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@@ -481,6 +505,7 @@ def vcf2zarr_main():
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@click .argument ("in_path" , type = click .Path ())
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@click .argument ("zarr_path" , type = click .Path ())
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@worker_processes
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+ @progress
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@verbose
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@variants_chunk_size
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@samples_chunk_size
@@ -489,6 +514,7 @@ def convert_plink(
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zarr_path ,
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verbose ,
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worker_processes ,
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+ progress ,
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variants_chunk_size ,
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samples_chunk_size ,
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):
@@ -499,7 +525,7 @@ def convert_plink(
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plink .convert (
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in_path ,
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zarr_path ,
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- show_progress = True ,
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+ show_progress = progress ,
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worker_processes = worker_processes ,
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samples_chunk_size = samples_chunk_size ,
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variants_chunk_size = variants_chunk_size ,
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