zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
ebanks 2010-09-08 16:47:51 +00:00
parent ae9cba1c73
commit cd091d7309
1 changed files with 3 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
View File

@ -43,7 +43,6 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker; 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.gatk.walkers.Window;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
@ -65,9 +64,8 @@ import org.broadinstitute.sting.utils.StingException;
*/ */
@Reference(window=@Window(start=-4,stop=4)) @Reference(window=@Window(start=-4,stop=4))
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name="transcripts",type=AnnotatorInputTableFeature.class) } ) @Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name=TranscriptToGenomicInfo.ROD_NAME,type=AnnotatorInputTableFeature.class) } )
public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> implements TreeReducible<Integer> public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
{
private static final String ROD_NAME = "transcripts"; 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) //@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<Integer, Integer> impleme
try { try {
generateOutputRecordsForROD(parsedTranscriptRod); 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); 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<Integer, Integer> impleme
public Integer reduce(Integer value, Integer sum) { return sum + value; } 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) { 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 " + 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) + "%)"); logger.info("Skipped " + skippedTranscriptCounter + " transcripts out of "+ transcriptsProcessedCounter + " total (" + ( transcriptsProcessedCounter == 0 ? 0 : (100*skippedTranscriptCounter)/transcriptsProcessedCounter) + "%)");