From 21027b8bbeaa7caedda1fd294397b3cfef0df77d Mon Sep 17 00:00:00 2001 From: Susanna Morin Date: Wed, 31 Mar 2021 22:48:40 -0700 Subject: [PATCH] Use vg sim command instead of vg-toil sim --- scripts/mcmc_Makefile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/mcmc_Makefile b/scripts/mcmc_Makefile index 1693987d7f6..055d4da52de 100644 --- a/scripts/mcmc_Makefile +++ b/scripts/mcmc_Makefile @@ -52,8 +52,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg: $(TOIL_OS)/$(BASENAME)_$(HA $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg -$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg - toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_0) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(READS) $(TOIL_OS) +$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt + vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg: $(TOIL_OS)/$(BASENAME).vg $(TOIL_OS)/$(BASENAME).gbwt $(TOIL_OS)/$(BASENAME).xg vg paths -d -v $(TOIL_OS)/$(BASENAME).vg > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg @@ -65,8 +65,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg: $(TOIL_OS)/$(BASENAME)_$(HA $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg -$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg - toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_1) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(READS) $(TOIL_OS) +$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt + vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam $(TOIL_OS)/$(BASENAME)_merged.gam: $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam cat $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam > $(TOIL_OS)/$(BASENAME)_merged.gam