Updated Hoadley scripts

melkebir · melkebir · commit f9e894344c40 · 2017-09-19T11:05:34.000-04:00
diff --git a/result/hoadley_2016/run_A1.sh b/result/hoadley_2016/run_A1.sh
@@ -14,4 +14,4 @@ $2 breast adrenal liver lung spinal > A1/migration_trees.txt
 
 $3 ../../data/hoadley_2016/A1/F.tsv > A1/mutation_trees.txt
 
-$1 -n -c ../../data/hoadley_2016/coloring.txt -barT A1/mutation_trees.txt -G A1/migration_trees.txt -F ../../data/hoadley_2016/A1/F.tsv -p breast -t 4 -m 1 -o A1/ > A1/results.txt
+$1 -c ../../data/hoadley_2016/coloring.txt -barT A1/mutation_trees.txt -G A1/migration_trees.txt -F ../../data/hoadley_2016/A1/F.tsv -p breast -t 4 -m 1 -o A1/ > A1/results.txt
diff --git a/result/hoadley_2016/run_A7.sh b/result/hoadley_2016/run_A7.sh
@@ -14,4 +14,4 @@ $2 breast brain kidney liver lung rib > A7/migration_trees.txt
 
 $3 ../../data/hoadley_2016/A7/F.tsv > A7/mutation_trees.txt
 
-$1 -n -c ../../data/hoadley_2016/coloring.txt -barT A7/mutation_trees.txt -G A7/migration_trees.txt -F ../../data/hoadley_2016/A7/F.tsv -p breast -t 4 -m 1 -o A7/ > A7/results.txt
+$1 -c ../../data/hoadley_2016/coloring.txt -barT A7/mutation_trees.txt -G A7/migration_trees.txt -F ../../data/hoadley_2016/A7/F.tsv -p breast -t 4 -m 1 -o A7/ > A7/results.txt

Original file line number	Diff line number	Diff line change
`@@ -14,4 +14,4 @@ $2 breast adrenal liver lung spinal > A1/migration_trees.txt`
`14`	`14`
`15`	`15`	`$3 ../../data/hoadley_2016/A1/F.tsv > A1/mutation_trees.txt`
`16`	`16`
`17`		`-$1 -n -c ../../data/hoadley_2016/coloring.txt -barT A1/mutation_trees.txt -G A1/migration_trees.txt -F ../../data/hoadley_2016/A1/F.tsv -p breast -t 4 -m 1 -o A1/ > A1/results.txt`
	`17`	`+$1 -c ../../data/hoadley_2016/coloring.txt -barT A1/mutation_trees.txt -G A1/migration_trees.txt -F ../../data/hoadley_2016/A1/F.tsv -p breast -t 4 -m 1 -o A1/ > A1/results.txt`
Original file line number	Diff line number	Diff line change
`@@ -14,4 +14,4 @@ $2 breast brain kidney liver lung rib > A7/migration_trees.txt`
`14`	`14`
`15`	`15`	`$3 ../../data/hoadley_2016/A7/F.tsv > A7/mutation_trees.txt`
`16`	`16`
`17`		`-$1 -n -c ../../data/hoadley_2016/coloring.txt -barT A7/mutation_trees.txt -G A7/migration_trees.txt -F ../../data/hoadley_2016/A7/F.tsv -p breast -t 4 -m 1 -o A7/ > A7/results.txt`
	`17`	`+$1 -c ../../data/hoadley_2016/coloring.txt -barT A7/mutation_trees.txt -G A7/migration_trees.txt -F ../../data/hoadley_2016/A7/F.tsv -p breast -t 4 -m 1 -o A7/ > A7/results.txt`