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gatk-3.8
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Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2010-03-16 22:01:23 +00:00
parent 933823c8bc
commit 849bd1f451
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
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@ -411,7 +411,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
*/ */
public SAMReaders(Reads sourceInfo) { public SAMReaders(Reads sourceInfo) {
for(File readsFile: sourceInfo.getReadsFiles()) { for(File readsFile: sourceInfo.getReadsFiles()) {
SAMFileReader2 reader = new SAMFileReader2(readsFile,false); SAMFileReader2 reader = new SAMFileReader2(readsFile,true);
reader.setValidationStringency(sourceInfo.getValidationStringency()); reader.setValidationStringency(sourceInfo.getValidationStringency());
// If no read group is present, hallucinate one. // If no read group is present, hallucinate one.