From 53c9feb2f0912a164d9ba2d33f68599d19e20280 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Wed, 21 Jun 2023 14:21:05 +0200
Subject: [PATCH] update cli

---
 workflow/rules/quilt.smk     | 6 ++++++
 workflow/rules/refpanels.smk | 3 +--
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/quilt.smk b/workflow/rules/quilt.smk
index 5c43dd7..80eb2aa 100644
--- a/workflow/rules/quilt.smk
+++ b/workflow/rules/quilt.smk
@@ -242,6 +242,7 @@ rule quilt_run_regular:
         nGibbsSamples=config["quilt1"]["nGibbsSamples"],
         lowram=config["quilt1"]["lowram"],
         impute_rare_common=config["quilt1"]["impute_rare_common"],
+        rare_af_threshold=config["quilt1"]["rare_af_threshold"],
         n_seek_its=config["quilt1"]["n_seek_its"],
         n_burnin_its=config["quilt1"]["n_burn_in_seek_its"],
         block_gibbs=config["quilt1"]["small_ref_panel_block_gibbs_iterations"],
@@ -274,6 +275,7 @@ rule quilt_run_regular:
             --nGibbsSamples={params.nGibbsSamples} \
             --use_hapMatcherR={params.lowram} \
             --impute_rare_common={params.impute_rare_common} \
+            --rare_af_threshold={params.rare_af_threshold} \
             --n_seek_its={params.n_seek_its} \
             --n_burn_in_seek_its={params.n_burnin_its} \
             --small_ref_panel_block_gibbs_iterations='{params.block_gibbs}' \
@@ -345,6 +347,7 @@ rule quilt_run_mspbwt:
         n_seek_its=config["quilt2"]["n_seek_its"],
         n_burnin_its=config["quilt2"]["n_burn_in_seek_its"],
         lowram=config["quilt2"]["lowram"],
+        rare_af_threshold=config["quilt2"]["rare_af_threshold"],
         impute_rare_common=config["quilt2"]["impute_rare_common"],
         block_gibbs=config["quilt2"]["small_ref_panel_block_gibbs_iterations"],
         gibbs_iters=config["quilt2"]["small_ref_panel_gibbs_iterations"],
@@ -378,6 +381,7 @@ rule quilt_run_mspbwt:
             --nGibbsSamples={params.nGibbsSamples} \
             --n_seek_its={params.n_seek_its} \
             --n_burn_in_seek_its={params.n_burnin_its} \
+            --rare_af_threshold={params.rare_af_threshold} \
             --small_ref_panel_block_gibbs_iterations='{params.block_gibbs}' \
             --small_ref_panel_gibbs_iterations={params.gibbs_iters} \
             --output_filename={output} &> {log}
@@ -449,6 +453,7 @@ rule quilt_run_zilong:
         n_seek_its=config["quilt2"]["n_seek_its"],
         lowram=config["quilt2"]["lowram"],
         impute_rare_common=config["quilt2"]["impute_rare_common"],
+        rare_af_threshold=config["quilt2"]["rare_af_threshold"],
         n_burnin_its=config["quilt2"]["n_burn_in_seek_its"],
         block_gibbs=config["quilt2"]["small_ref_panel_block_gibbs_iterations"],
         gibbs_iters=config["quilt2"]["small_ref_panel_gibbs_iterations"],
@@ -484,6 +489,7 @@ rule quilt_run_zilong:
             --nGibbsSamples={params.nGibbsSamples} \
             --n_seek_its={params.n_seek_its} \
             --n_burn_in_seek_its={params.n_burnin_its} \
+            --rare_af_threshold={params.rare_af_threshold} \
             --small_ref_panel_block_gibbs_iterations='{params.block_gibbs}' \
             --small_ref_panel_gibbs_iterations={params.gibbs_iters} \
             --output_filename={output} &> {log}
diff --git a/workflow/rules/refpanels.smk b/workflow/rules/refpanels.smk
index 16f43ec..3b8bd1a 100644
--- a/workflow/rules/refpanels.smk
+++ b/workflow/rules/refpanels.smk
@@ -39,7 +39,6 @@ rule subset_refpanel:
             bcftools view -v snps -m2 -M2 --samples-file {input} --threads 4 {params.vcf}| bcftools norm - -d snps -Ob -o {output.vcf} --threads 4 && bcftools index -f {output.vcf} && \
             touch -m {output.vcf}.csi && \
             bcftools view -G {output.vcf} -Oz -o {output.sites} --threads 4 && tabix -f {output.sites} && \
-            bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' {output.sites} | bgzip -c > {output.tsv} && tabix -s1 -b2 -e2 {output.tsv} \
-            # bcftools convert --haplegendsample {params.prefix} {output.vcf} && \
+            bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' {output.sites} | bgzip -c > {output.tsv} && tabix -s1 -b2 -e2 {output.tsv}
         )  &> {log}
         """