# HG changeset patch
# User shian_su <registertonysu@gmail.com>
# Date 1407818547 -36000
# Node ID 8923d4ea858bc21ab68c369ed5a6099c972b4574
# Parent  f1076bfb0ed19b094a1ef38850220556a89abb3a
- Added check for zero library size, will now filter out zero library size
  samples and generate report of filtered samples in html output

diff -r f1076bfb0ed1 -r 8923d4ea858b hairpinTool.R
--- a/hairpinTool.R	Wed Jul 30 15:13:45 2014 +1000
+++ b/hairpinTool.R	Tue Aug 12 14:42:27 2014 +1000
@@ -404,6 +404,14 @@
   data$samples$group <- make.names(data$samples$group)
 }
 
+# Filter out any samples with zero counts
+if (any(data$samples$lib.size == 0)) {
+  sampleSel <- data$samples$lib.size != 0
+  filteredSamples <- paste(data$samples$ID[!sampleSel], collapse=", ")
+  data$counts <- data$counts[, sampleSel]
+  data$samples <- data$samples[sampleSel, ]
+}
+
 # Filter hairpins with low counts
 preFilterCount <- nrow(data)
 sel <- rowSums(cpm(data$counts) > cpmReq) >= sampleReq
@@ -791,6 +799,12 @@
   ListItem(tempStr)
 }
 
+if (exists("filteredSamples")) {
+  tempStr <- paste("The following samples were filtered out for having zero",
+                   "library size: ", filteredSamples)
+  ListItem(tempStr)
+}
+
 if (workMode == "classic") {
   ListItem("An exact test was performed on each hairpin.")
 } else if (workMode == "glm") {
diff -r f1076bfb0ed1 -r 8923d4ea858b hairpinTool.xml
--- a/hairpinTool.xml	Wed Jul 30 15:13:45 2014 +1000
+++ b/hairpinTool.xml	Tue Aug 12 14:42:27 2014 +1000
@@ -1,4 +1,4 @@
-<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.11">
+<tool id="shRNAseq" name="shRNAseq Tool" version="1.0.12">
   <description>
     Analyse hairpin differential representation using edgeR
   </description>