diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 254aea5a1..820290d3a 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -35,8 +35,8 @@ import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.interval.IntervalIndexCreator; import org.broad.tribble.index.linear.LinearIndexCreator; import org.broad.tribble.source.BasicFeatureSource; -import org.broad.tribble.util.LEDataOutputStream; -import org.broad.tribble.util.LEDataStreamUtils; +import org.broad.tribble.util.LittleEndianInputStream; +import org.broad.tribble.util.LittleEndianOutputStream; import org.broad.tribble.vcf.NameAwareCodec; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; @@ -46,9 +46,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.file.FSLockWithShared; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; +import java.io.*; import java.util.*; @@ -267,7 +265,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen locked = lock.exclusiveLock(); if (locked) { logger.info("Writing Tribble index to disk for file " + inputFile); - LEDataOutputStream stream = LEDataStreamUtils.createOutputStream(indexFile); + LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile)); index.write(stream); stream.close(); } diff --git a/settings/repository/org.broad/tribble-124M.jar b/settings/repository/org.broad/tribble-129M.jar similarity index 79% rename from settings/repository/org.broad/tribble-124M.jar rename to settings/repository/org.broad/tribble-129M.jar index 51780b5cb..0b00d42c6 100644 Binary files a/settings/repository/org.broad/tribble-124M.jar and b/settings/repository/org.broad/tribble-129M.jar differ diff --git a/settings/repository/org.broad/tribble-124M.xml b/settings/repository/org.broad/tribble-129M.xml similarity index 64% rename from settings/repository/org.broad/tribble-124M.xml rename to settings/repository/org.broad/tribble-129M.xml index ffb0daf3d..7814d5097 100644 --- a/settings/repository/org.broad/tribble-124M.xml +++ b/settings/repository/org.broad/tribble-129M.xml @@ -1,3 +1,3 @@ - +