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Commit 4b120c8e authored by tcarver's avatar tcarver
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provide command line if index file not found and picard fails to index

the BAM
parent 8497c589
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......@@ -413,8 +413,10 @@ 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("(requires BAM to be sorted by coordinate and for the sort order to be in the header line, HD)");
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(
......
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