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added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-25 03:12:54 +00:00
parent ff98e28abf
commit 8bdf49a01f
2 changed files with 3 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -339,7 +339,7 @@ public class TraversalEngine {
*/ */
protected <T> void printOnTraversalDone(final String type, T sum) { protected <T> void printOnTraversalDone(final String type, T sum) {
printProgress(true, type, null); printProgress(true, type, null);
logger.info(String.format("Traversal reduce result is " + sum)); System.out.printf(String.format("Traversal reduce result is %d%n", sum)); // TODO: fixme -- how do we use this logger?
logger.info(String.format("Traversal skipped %d reads out of %d total (%.2f%%)", nSkippedReads, nReads, (nSkippedReads * 100.0) / nReads)); logger.info(String.format("Traversal skipped %d reads out of %d total (%.2f%%)", nSkippedReads, nReads, (nSkippedReads * 100.0) / nReads));
logger.info(String.format(" -> %d unmapped reads", nUnmappedReads)); logger.info(String.format(" -> %d unmapped reads", nUnmappedReads));
logger.info(String.format(" -> %d non-primary reads", nNotPrimary)); logger.info(String.format(" -> %d non-primary reads", nNotPrimary));
@ -652,7 +652,7 @@ public class TraversalEngine {
samReader = initializeSAMFile(readsFile); samReader = initializeSAMFile(readsFile);
for ( GenomeLoc interval : locs ) { for ( GenomeLoc interval : locs ) {
System.out.printf("Processing locus %s%n", interval.toString()); logger.debug(String.format("Processing locus %s", interval.toString()));
CloseableIterator<SAMRecord> readIter = samReader.queryOverlapping( interval.getContig(), CloseableIterator<SAMRecord> readIter = samReader.queryOverlapping( interval.getContig(),
(int)interval.getStart(), (int)interval.getStart(),

2
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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@ -15,7 +15,7 @@ import java.util.List;
public class DepthOfCoverageWalker extends BasicLociWalker<Integer, Integer> { public class DepthOfCoverageWalker extends BasicLociWalker<Integer, Integer> {
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) { public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
System.out.printf("%s: %d%n", context.getLocation(), context.getReads().size() ); System.out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
return 0; return 1;
} }
public Integer reduceInit() { return 0; } public Integer reduceInit() { return 0; }