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Set SAMFileWriter to create index in ReadUtils to fix SplitSamFile issue

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Geraldine Van der Auwera 2013-11-26 15:53:29 -05:00
parent 5da901a8b1
commit 429582589f
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -152,8 +152,8 @@ public class ReadUtils {
public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) { public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) {
validateCompressionLevel(compression); validateCompressionLevel(compression);
if (file.endsWith(".bam")) if (file.endsWith(".bam"))
return new SAMFileWriterFactory().makeBAMWriter(header, presorted, new File(file), compression); return new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, presorted, new File(file), compression);
return new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, new File(file)); return new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(header, presorted, new File(file));
} }
public static int validateCompressionLevel(final int requestedCompressionLevel) { public static int validateCompressionLevel(final int requestedCompressionLevel) {