debug ld clump

Zilong-Li · Sep 27, 2024 · fd934bf · fd934bf
1 parent cf2d0a2
commit fd934bf
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diff --git a/Makefile b/Makefile
@@ -189,8 +189,8 @@ ld_prune:
 	diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
 
 ld_clump:
-	./PCAone -B adj.residuals --ld-bim adj.kept.bim --clump example/plink.pheno0.assoc --clump-p1 0.01 --clump-p2 0.05 --clump-r2 0.1 --clump-bp 10000000 -m 1 -o adj_clump_m1
 	./PCAone -B adj.residuals --ld-bim adj.kept.bim --clump example/plink.pheno0.assoc --clump-p1 0.01 --clump-p2 0.05 --clump-r2 0.1 --clump-bp 10000000 -m 0 -o adj_clump_m0 
+	./PCAone -B adj.residuals --ld-bim adj.kept.bim --clump example/plink.pheno0.assoc --clump-p1 0.01 --clump-p2 0.05 --clump-r2 0.1 --clump-bp 10000000 -m 1 -o adj_clump_m1
 	diff adj_clump_m0.p0.clump adj_clump_m1.p0.clump > /dev/null
 
 ld_tests:

diff --git a/src/LD.cpp b/src/LD.cpp
@@ -504,6 +504,7 @@ void run_ld_stuff(const Param& params, Data* data) {
             G, idx_per_chr, bp_per_chr, pvals_per_chr);
 
       } else {
+        cao.print("size of G", data->G.rows(), data->G.cols());
         ld_clump_single_pheno(
             params.fileout + ".p" + std::to_string(i) + ".clump", head,
             params.clump_bp, params.clump_r2, params.clump_p1, params.clump_p2,