From db303d0a36462e0290b0f410db97595b97ee3f4f Mon Sep 17 00:00:00 2001
From: Anton Kriese <kriese_a@molgen.mpg.de>
Date: Fri, 3 Jun 2022 15:10:59 +0200
Subject: [PATCH] read alternative references' regions; this fixes the error,
 that all references use the same region in IGV

---
 workflow/Snakefile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index a3d813e..8faf366 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -127,6 +127,7 @@ rule pca_plot:
 
 rule create_igv_batch:
     input:
+        "results/{sample}/{region}/cut_refs.fa"
     output:
         "results/{sample}/{region}/igv_batch_{ref}.txt"
     params:
@@ -135,13 +136,15 @@ rule create_igv_batch:
         path_to_resources = Path(".").absolute()
     shell:
         """
+            REF_REGION=$(grep {wildcards.ref} {input} | cut -d' ' -f2)
             cat > {output} <<-EOF
 genome {params.path_to_resources}/resources/references/{params.ref_file}
 load {params.path_to_resources}/resources/samples/{wildcards.sample}/{wildcards.ref}/PacBio.bam
-goto {params.region}
+goto $REF_REGION
 snapshot {params.path_to_resources}/results/{wildcards.sample}/{wildcards.region}/igv_{wildcards.ref}_screenshot.png
 exit
 EOF
+            unset REF_REGION
         """
         # load "resources/{wildcards.sample}/Illumina.bam"
         # load "results/{wildcards.sample}/{wildcards.region}/MSA"