# HG changeset patch
# User clifinder
# Date 1582762056 18000
# Node ID 3471a9785135627d7dc828aecd50c237ef12b4d4
# Parent  3e33703874415b012d4bbddd4e3577253f2fc441
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit e141f9b9038a22c92f827daa298bcc53356b4bdc"

diff -r 3e3370387441 -r 3471a9785135 script/CLIFinder_results.R
--- a/script/CLIFinder_results.R	Fri Feb 14 17:03:24 2020 -0500
+++ b/script/CLIFinder_results.R	Wed Feb 26 19:07:36 2020 -0500
@@ -110,7 +110,7 @@
   
   for (i in 0:nfastq)
   {
-    mcols(grfus)[grfus$dup>1, 11+i] <- mcols(grfus)[grfus$dup>1, 11+i] + mcols(grchim2)[position[duplicated(position[, 1]), 2], 9+i]
+    mcols(grfus)[position[duplicated(position[, 1]), 1], 11+i] <- mcols(grfus)[position[duplicated(position[, 1]), 1], 11+i] + mcols(grchim2)[position[duplicated(position[, 1]), 2], 9+i]
   }
   
   grfus2 <- grfus
@@ -123,9 +123,9 @@
   suppressWarnings(position3 <- as.data.frame(findOverlaps(gr3[gr3$dup>1], grfus2)))
   grfus$info [position3[, 2]] <- "overlap sens opposé"
   
-  min <- ddply(as.data.frame(grchim2), .(seqnames, end, strand), function(x)x[x$L1.start == min(x$L1.start), ])
+  min <- ddply(as.data.frame(grfus), .(seqnames, end, strand), function(x)x[x$L1.start == min(x$L1.start), ])
   min <- ddply(data.frame(min), .(seqnames, start, strand), function(x)x[x$L1.start == min(x$L1.start), ])
-  max <- ddply(as.data.frame(grchim2), .(seqnames, end, strand), function(x)x[x$L1.end == max(x$L1.end), ])
+  max <- ddply(as.data.frame(grfus), .(seqnames, end, strand), function(x)x[x$L1.end == max(x$L1.end), ])
   max <- ddply(data.frame(max), .(seqnames, start, strand), function(x)x[x$L1.end == max(x$L1.end), ])
   
   grfus1 <- as.data.frame(grfus)