From 6e3c69870d8119f0fa5bf0152bddbd8fcf93464c Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <pdimens@live.com>
Date: Thu, 3 Feb 2022 13:18:28 -0500
Subject: [PATCH] swap order for ordering function call (top/htop convenience)

---
 rules/LepMap3/distances.smk | 4 ++--
 rules/LepMap3/order.smk     | 2 +-
 rules/LepMap3/reorder.smk   | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/rules/LepMap3/distances.smk b/rules/LepMap3/distances.smk
index ef94e55..b03f166 100644
--- a/rules/LepMap3/distances.smk
+++ b/rules/LepMap3/distances.smk
@@ -19,10 +19,10 @@ rule calculate_distances:
         """
         cp {input.lg} {output.distance}
         
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
+        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
         sed -i -e 's/LG \= 0/LG \= {params.lg}/g' {output.sex_averagedtmp}
         sed -n '/\*\*\* LG \=/,$p' {output.sex_averagedtmp} > {output.sex_averaged} 
         awk '/#java/{{flag=1}} flag; /*** LG =/{{flag=0}}' {output.sex_averagedtmp} > {log.sex_averaged}
 
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
+        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
         """
\ No newline at end of file
diff --git a/rules/LepMap3/order.smk b/rules/LepMap3/order.smk
index 4d36f46..f820f5c 100644
--- a/rules/LepMap3/order.smk
+++ b/rules/LepMap3/order.smk
@@ -15,7 +15,7 @@ rule order_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 map={input.filt_map} {params.extra} data=- numThreads={threads} chromosome={params.chrom} &> {output.runlog}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 chromosome={params.chrom} map={input.filt_map} {params.extra} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
diff --git a/rules/LepMap3/reorder.smk b/rules/LepMap3/reorder.smk
index 18e570a..c798918 100644
--- a/rules/LepMap3/reorder.smk
+++ b/rules/LepMap3/reorder.smk
@@ -16,7 +16,7 @@ rule reorder_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 {params.extra} map={input.filt_map} data=- numThreads={threads} evaluateOrder={input.lg_order} &> {output.runlog}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg_order} {params.extra} map={input.filt_map} data=- numThreads={threads} &> {output.runlog}
         sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
         grep "recombin" {output.runlog} > {log.recomb}
         awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}