From 1cba81c16fb07c228578c3fd71a2a64cc72f75a9 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 20 Jul 2010 22:08:04 +0000 Subject: [PATCH] updates to tribble with fixes for some bugs I've found in some new indexing code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3842 348d0f76-0448-11de-a6fe-93d51630548a --- .../builders/TribbleRMDTrackBuilder.java | 4 +++- .../TribbleRMDTrackBuilderUnitTest.java | 2 +- .../{tribble-121M.jar => tribble-122M.jar} | Bin 186721 -> 187414 bytes .../{tribble-121M.xml => tribble-122M.xml} | 2 +- 4 files changed, 5 insertions(+), 3 deletions(-) rename settings/repository/org.broad/{tribble-121M.jar => tribble-122M.jar} (89%) rename settings/repository/org.broad/{tribble-121M.xml => tribble-122M.xml} (64%) 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 110078246..60436fb15 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 @@ -31,6 +31,7 @@ import org.broad.tribble.*; import org.broad.tribble.index.Index; import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.linear.LinearIndex; +import org.broad.tribble.index.linear.LinearIndexCreator; import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.vcf.NameAwareCodec; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; @@ -279,6 +280,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen private static Index createIndexInMemory(File inputFile, FeatureCodec codec) throws IOException { // this can take a while, let them know what we're doing logger.info("Creating Tribble index in memory for file " + inputFile); - return new LinearIndex(16000,inputFile.getAbsolutePath()); + LinearIndexCreator creator = new LinearIndexCreator(inputFile,codec,null); + return creator.createIndex(); } } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java index 01a25663b..262c32b87 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java @@ -97,7 +97,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest { @Test public void testBuilderIndexDirectoryUnwritable() { - File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.vcf"); + File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf"); File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.idx"); Index ind = null; diff --git a/settings/repository/org.broad/tribble-121M.jar b/settings/repository/org.broad/tribble-122M.jar similarity index 89% rename from settings/repository/org.broad/tribble-121M.jar rename to settings/repository/org.broad/tribble-122M.jar index 56bf4a1cf80c1b62363da4b9a4dc47d799a36568..a39750e2f13175f384fb868cb6dd97c5c7e8d398 100644 GIT binary patch delta 8492 zcmb7J33yaRw*ITSliTUsY@Ku`VM{`gB?*Kzfv`qIHbHg_f{K8MARr*hqD>GLk=0hN zB5H7O*j#`}8VS4XJBW%igCl<9ED9guFupg+$otQ|okg8D-+TS#-dfJ7bLyO`I_JNY zOIu@CZjUtw^mVztkYC=C6=pM?yJSV-N}aQ0#pz6WUu(>sP`YZtMtN^FU9$}BcKsyH z-R>-DmS2hvDk<;x{OA($y=Dh#t};u!QvM^b&SrZ(eXd*D^%`7oi_q^Iww7j2_WOxa ze$i&Hj?Z0kz0*_M=X5*5DIM`z#dCC8D6?H^`Ne_@UXCdb7cY&Ivge&odt}h5;eRn% zhWc-86zVoUx|TI0UKy)|SpMzQBMHK^V_y6C94dID&$WIHTtEX?NTsHQmM!pxJ}*r# z?^xQxC9)?j7$>DQrKh6M=i+J!B{gATxglH!mOUq2p*ur`(p(t&$dqza+0_{7?!U3E zG#6~ls4L}L2M3AG<^MeD*HR{)aJg(_v->=CJ=X)|dO}&JJ3Khfi&S(lP~?S1M+2R_ zaHE4XI!mpK2VJG?COySo1aNB%U)|+(o4k5R-|a%}=|wN}jzu5z_2LfnGtl3Q6x?ZG 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