# HG changeset patch
# User kyost
# Date 1525415087 14400
# Node ID 3cd53127a8383172efcb7f3e5951beaf285912df
# Parent  72571a30f17bc01c8968999413e6ac7000eaaaed
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb

diff -r 72571a30f17b -r 3cd53127a838 ATAC_Primer_Tool.ga
diff -r 72571a30f17b -r 3cd53127a838 concatenate_ordered.xml
diff -r 72571a30f17b -r 3cd53127a838 filter_bam.bash
--- a/filter_bam.bash	Wed May 02 13:20:21 2018 -0400
+++ b/filter_bam.bash	Fri May 04 02:24:47 2018 -0400
@@ -29,7 +29,7 @@
 
 #create bed file of fragments for each bam file
 
-samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file
+samtools view -b -F 4 -L $ext_peak_file $bam_file > $filtered_bam_file
 
 rm name
 rm count
diff -r 72571a30f17b -r 3cd53127a838 filter_bam.xml
diff -r 72571a30f17b -r 3cd53127a838 find_qPCR_regions.R
--- a/find_qPCR_regions.R	Wed May 02 13:20:21 2018 -0400
+++ b/find_qPCR_regions.R	Fri May 04 02:24:47 2018 -0400
@@ -1,8 +1,7 @@
 ## Command to run tool:
 # Rscript --vanilla find_qPCR_regions.R o.coverage.bed f9.coverage.bed lib_sizes.txt cor_cutoff cov_cutoff output_file
 
-# Set up R error handling to go to stderr
-options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
+options(warn=-1)
 
 # Avoid crashing Galaxy with an UTF8 error on German LC settings
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -58,9 +57,6 @@
 	a_split <- asplit[[i]]
 	b_split <- bsplit[[i]]
 	
-	if (sd(t(a_split[1,5:m])) == 0 || sd(t(b_split[-1,5:m])) == 0 ){
-		next
-	}
 
 	#calculate correlation between total peak reads and spanning reads in each window
     corb <- data.frame(cor(t(a_split[1,5:m])
@@ -83,7 +79,7 @@
     
 	#keep windows for which correlation with total peak reads is above threshold and 
 	#number of spanning reads is above cutoff
-    regions <- data[which(data$correlation > corr_cut & data3$averageReadDepth > cov_cut),]
+    regions <- data[which(data$correlation >= corr_cut & data3$averageReadDepth >= cov_cut),]
     regions <- regions[,2:4]
 	
 	#collapse windows to non-overlappin regions
@@ -93,7 +89,7 @@
     nregion <- 1
     if (nrow(regions)>=2){
 		for (j in 2:nrow(regions)) {
-			if (as.numeric(regions[j,2]) <= (as.numeric(regions[j-1,3]))) {
+			if (as.numeric(regions[j,2]) < (as.numeric(regions[j-1,3]))) {
 				collapsed_regions[nrow(collapsed_regions),3] <- regions[j,3]
 			}else{
 				collapsed_regions <- rbind(collapsed_regions, regions[j,])
diff -r 72571a30f17b -r 3cd53127a838 find_qPCR_regions.xml
diff -r 72571a30f17b -r 3cd53127a838 make_window_bed.R
diff -r 72571a30f17b -r 3cd53127a838 make_window_bed.xml
diff -r 72571a30f17b -r 3cd53127a838 window_coverage.xml