Split callset into chunks for processing and add additional cli args#72
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nalinigans merged 5 commits intodevelopfrom Jan 15, 2025
Merged
Split callset into chunks for processing and add additional cli args#72nalinigans merged 5 commits intodevelopfrom
nalinigans merged 5 commits intodevelopfrom
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nalinigans
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mlathara
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Jan 14, 2025
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one question: otherwise lgtm
examples/genomicsdb_query
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| # Check if there is room for row_tuples to be parallelized | ||
| chunk_size = int(args.chunk_size) | ||
| if len(configs) < args.nproc and chunk_size > 1: | ||
| if row_tuples is None: |
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Should we consider only doing the splitting by row tuples if all samples are being queried? I'm worried about the case where only a few random (but disjoint) samples are queried and that could lead to us creating a whole bunch of configs where each config is only querying a single sample
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Sure, you have a point and we could do the splitting only if all samples are being queried.
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Mainly allow for multiprocessing of samples in callset based on
chunk sizeif no samples were specified togenomicsdb_query.Additionally add cli support to specify
chunk size, addbypass-intersecting-intervals-phaseand allow adryrunto see what may be processed without actually executing the query.