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added pvar, psam and pgen compression #1303

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Merged
gaow merged 2 commits into from
Mar 27, 2026
Merged

added pvar, psam and pgen compression #1303

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7a73f5f
Delete code/reference_data/rss_ld_sketch.ipynb
jaempawi Mar 27, 2026
70e282a
added compress pvar, psam and pgen outputs
jaempawi Mar 27, 2026
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13 changes: 11 additions & 2 deletions code/reference_data/rss_ld_sketch.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -698,7 +698,9 @@
"# Steps per chromosome:\n",
"# 1. For each block: plink2 --import-dosage → unsorted pgen, then --sort-vars → sorted pgen\n",
"# 2. plink2 --pmerge-list → one per-chrom pgen\n",
"# 3. Clean up all intermediates including -merge.* files\n",
"# 3. Concatenate .afreq\n",
"# 4. Clean up intermediates including -merge.* files and per-block dirs\n",
"# 5. zstd compress final pgen/pvar/psam/afreq\n",
"#\n",
"# Run after process_block completes (or run together: sos run ... process_block merge_chrom)\n",
"parameter: chrom = 0\n",
Expand All @@ -719,7 +721,7 @@
"_chroms = _chroms_to_process(output_dir, chrom)\n",
"\n",
"input: []\n",
"output: [f\"{output_dir}/{c}/{cohort_id}.{c}.pgen\" for c in _chroms]\n",
"output: [f\"{output_dir}/{c}/{cohort_id}.{c}.pgen.zst\" for c in _chroms]\n",
"\n",
"for _chrom in _chroms:\n",
" bash(f\"\"\"\n",
Expand Down Expand Up @@ -791,6 +793,13 @@
" for block_dir in \"${{chrom_dir}}\"/*/; do\n",
" rm -rf \"${{block_dir}}\"\n",
" done\n",
"\n",
" # ── Step 5: zstd compress final outputs ──\n",
" for ext in pgen pvar psam afreq; do\n",
" zstd --ultra -22 -T{numThreads} \"${{final_prefix}}.${{ext}}\" \\\n",
" -o \"${{final_prefix}}.${{ext}}.zst\" \\\n",
" && rm -f \"${{final_prefix}}.${{ext}}\"\n",
" done\n",
" \"\"\")"
]
}
Expand Down