From 814937f3b66b84169a915f9cd5912a4cc55d5285 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 1 Dec 2011 18:52:42 +0000
Subject: [PATCH] throw SAMException if BAM index not present
---
.../artemis/components/alignment/BamView.java | 28 +++++++++++++------
1 file changed, 20 insertions(+), 8 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index c5b4e5483..64f11d106 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -94,6 +94,7 @@ import org.apache.log4j.Level;
import net.sf.picard.sam.BuildBamIndex;
import net.sf.samtools.AlignmentBlock;
+import net.sf.samtools.SAMException;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
@@ -413,14 +414,25 @@ public class BamView extends JPanel
File bamIndexFile = getBamIndexFile(bam);
if(!bamIndexFile.exists())
{
- System.out.println("Index file not found so using picard to index the BAM.");
- System.out.println("This requires BAM to be sorted by coordinate and for the\n"+
- "sort order to be in the header line, HD.");
- System.out.println("If this does not work run:\nsamtools index "+bam);
- // Use Picard to index the file
- // requires reads to be sorted by coordinate
- new BuildBamIndex().instanceMain(
- new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000" });
+ try
+ {
+ logger4j.warn("Index file not found so using picard to index the BAM.");
+ // Use Picard to index the file
+ // requires reads to be sorted by coordinate
+ new BuildBamIndex().instanceMain(
+ new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000" });
+ }
+ catch(SAMException e)
+ {
+ String ls = System.getProperty("line.separator");
+ String msg =
+ "BAM index file is missing. The BAM file needs to be sorted and indexed"+ls+
+ "This can be done using samtools (http://samtools.sf.net/):"+ls+ls+
+ "samtools sort <in.bam> <out.prefix>"+ls+
+ "samtools index <sorted.bam>";
+
+ throw new SAMException(msg);
+ }
}
final SAMFileReader samFileReader;
--
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