From cd091d7309fe7a7b7eca864bf93dec6704bdbba9 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 8 Sep 2010 16:47:51 +0000 Subject: [PATCH] This walker can NOT be tree-reducible (in its current state). Given that it's meant to be run just once for any given transcript set, this is not at all a problem. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4231 348d0f76-0448-11de-a6fe-93d51630548a --- .../genomicannotator/TranscriptToGenomicInfo.java | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java index 30cbafb00..2da1b53d9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java @@ -43,7 +43,6 @@ import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.StingException; @@ -65,9 +64,8 @@ import org.broadinstitute.sting.utils.StingException; */ @Reference(window=@Window(start=-4,stop=4)) @By(DataSource.REFERENCE) -@Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name="transcripts",type=AnnotatorInputTableFeature.class) } ) -public class TranscriptToGenomicInfo extends RodWalker implements TreeReducible -{ +@Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name=TranscriptToGenomicInfo.ROD_NAME,type=AnnotatorInputTableFeature.class) } ) +public class TranscriptToGenomicInfo extends RodWalker { private static final String ROD_NAME = "transcripts"; //@Argument(fullName="pass-through", shortName="t", doc="Optionally specifies which columns from the transcript table should be copied verbatim (aka. passed-through) to the records in the output table. For example, -B transcripts,AnnotatorInputTable,/data/refGene.txt -t id will cause the refGene id column to be copied to the output table.", required=false) @@ -272,7 +270,7 @@ public class TranscriptToGenomicInfo extends RodWalker impleme try { generateOutputRecordsForROD(parsedTranscriptRod); } - catch(Exception e) { + catch(IOException e) { throw new RuntimeException(Thread.currentThread().getName() + " - Unexpected error occurred at position: [" + parsedTranscriptRod.txChrom + ":" + position + "] in transcript: " + parsedTranscriptRod, e); } @@ -760,8 +758,6 @@ public class TranscriptToGenomicInfo extends RodWalker impleme public Integer reduce(Integer value, Integer sum) { return sum + value; } - public Integer treeReduce(Integer lhs, Integer rhs) { return lhs + rhs; } - public void onTraversalDone(Integer result) { logger.info("Skipped " + skippedPositionsCounter + " in-transcript genomic positions out of "+ totalPositionsCounter + " total (" + ( totalPositionsCounter == 0 ? 0 : (100*skippedPositionsCounter)/totalPositionsCounter) + "%)"); logger.info("Skipped " + skippedTranscriptCounter + " transcripts out of "+ transcriptsProcessedCounter + " total (" + ( transcriptsProcessedCounter == 0 ? 0 : (100*skippedTranscriptCounter)/transcriptsProcessedCounter) + "%)");