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Remove redundant prodedures and columns #1308

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Merged
gaow merged 2 commits into from
Mar 31, 2026
Merged

Remove redundant prodedures and columns #1308

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6da44f3
remove redundant steps
Mar 31, 2026
96d5995
Merge branch 'StatFunGen:main' into main
SamuelSun2000 Mar 31, 2026
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12 changes: 8 additions & 4 deletions code/reference_data/rss_ld_sketch.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -768,7 +768,7 @@
" # Step 2: Merge all per-block pgens -> one per-chrom pgen\n",
" $[plink2_bin] \\\n",
" --pmerge-list \"${merge_list}\" pfile \\\n",
" --make-pgen vzs \\\n",
" --make-pgen \\\n",
" --sort-vars \\\n",
" --out \"${final_prefix}\"\n",
"\n",
Expand All @@ -787,16 +787,20 @@
" # Extract ID, MIN, and MAX from the concatenated .afreq (columns 2, 7, 8)\n",
" awk 'NR > 1 {print $2, $7, $8}' \"${final_prefix}.afreq\" > \"${final_prefix}.recovery_params\"\n",
"\n",
" # Decompress the .pvar.zst \n",
" $[plink2_bin] --zst-decompress \"${final_prefix}.pvar.zst\" > \"${final_prefix}.pvar.tmp\"\n",
" cp \"${final_prefix}.pvar\" \"${final_prefix}.pvar.tmp\"\n",
"\n",
" awk 'NR==FNR {min[$1]=$2; max[$1]=$3; next} \n",
" /^#/ {print $0 \"\\tU_MIN\\tU_MAX\"; next} \n",
" {if ($3 in min) print $0 \"\\t\" min[$3] \"\\t\" max[$3]; else print $0 \"\\tNA\\tNA\"}' \\\n",
" \"${final_prefix}.recovery_params\" \"${final_prefix}.pvar.tmp\" > \"${final_prefix}.pvar\"\n",
"\n",
" # Replace the compressed file with the updated text file\n",
" rm \"${final_prefix}.pvar.tmp\" \"${final_prefix}.pvar.zst\" \"${final_prefix}.recovery_params\"\n",
" rm \"${final_prefix}.pvar.tmp\" \"${final_prefix}.recovery_params\"\n",
"\n",
" awk '{print $1,$2,$3,$4,$5,$6}' OFS=\"\\t\" \\\n",
" \"${final_prefix}.afreq\" > \"${final_prefix}.afreq.tmp\"\n",
" \n",
" mv \"${final_prefix}.afreq.tmp\" \"${final_prefix}.afreq\"\n",
"\n",
"\n",
"R: expand = \"$[ ]\"\n",
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