From 91f04cef9a91a1e7da8540d34da7cbe950489fb4 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 8 Apr 2011 15:03:42 +0000
Subject: [PATCH] report number of mapped reads
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15897 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/components/alignment/BamUtils.java | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index b4ddf4df1..68f3f421f 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -116,8 +116,14 @@ class BamUtils
DecimalFormat df = new DecimalFormat("0.00##");
StringBuffer buff = new StringBuffer();
- for(String bam : bamList)
- buff.append("#BAM: "+bam+"\n");
+ for(int j=0; j<bamList.size(); j++)
+ {
+ String bam = bamList.get(j);
+ buff.append("#BAM: "+bam);
+ if(mappedReads != null)
+ buff.append(" Mapped Reads/million: "+ df.format( ((float)mappedReads[j]) / 1000000.f) );
+ buff.append("\n");
+ }
buff.append("\n");
for (String fId : featureReadCount.keySet() ) {
--
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