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Almost ready to stop doing eagar decoding; waiting on Eric 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1914 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-10-27 15:28:05 +00:00
parent e96b1791ab
commit 726378be8b
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java
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@ -45,6 +45,8 @@ import java.io.File;
* @version 0.1 * @version 0.1
*/ */
class ReadStreamResource { class ReadStreamResource {
final static boolean eagerDecode = true;
/** our log, which we want to capture anything from this class */ /** our log, which we want to capture anything from this class */
protected static Logger logger = Logger.getLogger(ReadStreamPointer.class); protected static Logger logger = Logger.getLogger(ReadStreamPointer.class);
@ -124,7 +126,7 @@ class ReadStreamResource {
// right now this is pretty damn heavy, it copies the file list into a reader list every time // right now this is pretty damn heavy, it copies the file list into a reader list every time
List<SAMFileReader> lst = new ArrayList<SAMFileReader>(); List<SAMFileReader> lst = new ArrayList<SAMFileReader>();
for (File f : reads.getReadsFiles()) { for (File f : reads.getReadsFiles()) {
SAMFileReader reader = new SAMFileReader(f, true); SAMFileReader reader = new SAMFileReader(f, eagerDecode);
reader.setValidationStringency(reads.getValidationStringency()); reader.setValidationStringency(reads.getValidationStringency());
final SAMFileHeader header = reader.getFileHeader(); final SAMFileHeader header = reader.getFileHeader();