# HG changeset patch
# User shian_su <registertonysu@gmail.com>
# Date 1406697225 -36000
# Node ID f1076bfb0ed19b094a1ef38850220556a89abb3a
# Parent  548802b3492fa092d6987daaf9a12c2ea3b4fe04
- Fixed tool to actually make use of barcode location options
  - Stored variables now properly used in processHairpinReads function

diff -r 548802b3492f -r f1076bfb0ed1 hairpinTool.R
--- a/hairpinTool.R	Fri May 02 17:22:24 2014 +1000
+++ b/hairpinTool.R	Wed Jul 30 15:13:45 2014 +1000
@@ -35,6 +35,7 @@
 #                            plots
 #       19.selectVals       -String specifying members selected for barcode
 #                            plots
+#    ###
 #
 # OUT:  Bar Plot of Counts Per Index
 #       Bar Plot of Counts Per Hairpin
@@ -57,7 +58,7 @@
 library(edgeR, quietly=TRUE, warn.conflicts=FALSE)
 library(limma, quietly=TRUE, warn.conflicts=FALSE)
 
-if (packageVersion("edgeR") < "3.5.23") {
+if (packageVersion("edgeR") < "3.5.27") {
   stop("Please update 'edgeR' to version >= 3.5.23 to run this tool")
 }
 
@@ -359,6 +360,7 @@
   # Use EdgeR hairpin process and capture outputs
   hpReadout <- capture.output(
   data <- processHairpinReads(fastqPath, samplePath, annoPath,
+                              barcodeStart=barStart, barcodeEnd=barEnd,
                               hairpinStart=hpStart, hairpinEnd=hpEnd, 
                               verbose=TRUE)
   )
@@ -470,6 +472,17 @@
 linkData <- rbind(linkData, newEntry)
 invisible(dev.off())
 
+# BCV Plot
+png(bcvPng, width=600, height=600)
+plotBCV(data, main="BCV Plot")
+imageData <- rbind(imageData, c("BCV Plot", "bcv.png"))
+invisible(dev.off())
+
+pdf(bcvPdf)
+plotBCV(data, main="BCV Plot")
+newEntry <- c("BCV Plot (.pdf)", "bcv.pdf")
+invisible(dev.off())
+
 if (workMode=="classic") {
   # Assess differential representation using classic exact testing methodology 
   # in edgeR
diff -r 548802b3492f -r f1076bfb0ed1 hairpinTool.xml
--- a/hairpinTool.xml	Fri May 02 17:22:24 2014 +1000
+++ b/hairpinTool.xml	Wed Jul 30 15:13:45 2014 +1000
@@ -1,11 +1,12 @@
-<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.9">
+<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.11">
   <description>
     Analyse hairpin differential representation using edgeR
   </description>
     
   <requirements>
-    <requirement type="R-module" version="3.5.27">edgeR</requirement>
-    <requirement type="R-module" version="3.18.13">limma</requirement>
+    <requirement type="R-module" version="3.6.2">edgeR</requirement>
+    <requirement type="R-module" version="3.20.7">limma</requirement>
+    <requirement type="package" version="3.0.3">R_3_0_3</requirement>
   </requirements>
   
   <stdio>