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add all the input in Traversal Engine over to the logging engine 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@157 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-03-23 20:46:55 +00:00
parent d174417fbd
commit b56a73538d
1 changed files with 22 additions and 22 deletions
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44
core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -135,13 +135,13 @@ public class TraversalEngine {
public void setSafetyChecking(final boolean beSafeP) { public void setSafetyChecking(final boolean beSafeP) {
if (!beSafeP) if (!beSafeP)
System.out.printf("*** Turning off safety checking, I hope you know what you are doing. Errors will result in debugging assert failures and other inscrutable messages...%n"); logger.warn("*** Turning off safety checking, I hope you know what you are doing. Errors will result in debugging assert failures and other inscrutable messages...");
this.beSafeP = beSafeP; this.beSafeP = beSafeP;
} }
public void setSortOnFly(final boolean SORT_ON_FLY) { public void setSortOnFly(final boolean SORT_ON_FLY) {
if (SORT_ON_FLY) if (SORT_ON_FLY)
System.out.println("Sorting read file on the fly: max reads allowed is " + MAX_ON_FLY_SORTS); logger.info("Sorting read file on the fly: max reads allowed is " + MAX_ON_FLY_SORTS);
this.SORT_ON_FLY = SORT_ON_FLY; this.SORT_ON_FLY = SORT_ON_FLY;
} }
@ -197,7 +197,7 @@ public class TraversalEngine {
scanner.close(); scanner.close();
} }
System.out.format("DEBUG: locStr: %s\n", locStr); logger.debug("DEBUG: locStr: " + locStr);
this.locs = parseGenomeLocs(locStr); this.locs = parseGenomeLocs(locStr);
} }
@ -220,7 +220,7 @@ public class TraversalEngine {
Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";"))); Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";")));
GenomeLoc[] locs = (GenomeLoc[]) result.toArray(new GenomeLoc[0]); GenomeLoc[] locs = (GenomeLoc[]) result.toArray(new GenomeLoc[0]);
Arrays.sort(locs); Arrays.sort(locs);
System.out.printf(" Locations are: %s%n", Utils.join("\n", Functions.map(Operators.toString, Arrays.asList(locs)))); logger.debug(" Locations are: " + Utils.join("\n", Functions.map(Operators.toString, Arrays.asList(locs))));
return locs; return locs;
} catch (Exception e) { } catch (Exception e) {
logger.fatal(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str)); logger.fatal(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str));
@ -303,9 +303,9 @@ public class TraversalEngine {
this.lastProgressPrintTime = curTime; this.lastProgressPrintTime = curTime;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords; final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
if (loc != null) if (loc != null)
System.out.printf("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)%n", loc, nRecords, type, elapsed, secsPer1MReads, type); logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, type, elapsed, secsPer1MReads, type));
else else
System.out.printf("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type); logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, type, elapsed, secsPer1MReads, type));
// Currently samReadingTracker will print misleading info if we're not processing the whole file // Currently samReadingTracker will print misleading info if we're not processing the whole file
@ -313,7 +313,7 @@ public class TraversalEngine {
// traversal is not being performed. For now, don't bother printing progress. // traversal is not being performed. For now, don't bother printing progress.
// TODO: Create a sam indexed read tracker that tracks based on percentage through the query. // TODO: Create a sam indexed read tracker that tracks based on percentage through the query.
if (samReadingTracker != null && this.locs == null) if (samReadingTracker != null && this.locs == null)
System.out.printf("[PROGRESS] -> %s%n", samReadingTracker.progressMeter()); logger.info(String.format("[PROGRESS] -> %s", samReadingTracker.progressMeter()));
} }
} }
@ -326,12 +326,12 @@ 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);
System.out.println("Traversal reduce result is " + sum); logger.info(String.format("Traversal reduce result is " + sum));
System.out.printf("Traversal skipped %d reads out of %d total (%.2f%%)%n", 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));
System.out.printf(" -> %d unmapped reads%n", nUnmappedReads); logger.info(String.format(" -> %d unmapped reads", nUnmappedReads));
System.out.printf(" -> %d non-primary reads%n", nNotPrimary); logger.info(String.format(" -> %d non-primary reads", nNotPrimary));
System.out.printf(" -> %d reads with bad alignments%n", nBadAlignments); logger.info(String.format(" -> %d reads with bad alignments", nBadAlignments));
System.out.printf(" -> %d reads with indels%n", nSkippedIndels); logger.info(String.format(" -> %d reads with indels", nSkippedIndels));
} }
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
@ -372,7 +372,7 @@ public class TraversalEngine {
samReadIter = new VerifyingSamIterator(samReadIter); samReadIter = new VerifyingSamIterator(samReadIter);
if (THREADED_IO) { if (THREADED_IO) {
System.out.printf("Enabling threaded I/O with buffer of %d reads%n", THREADED_IO_BUFFER_SIZE); logger.info(String.format("Enabling threaded I/O with buffer of %d reads", THREADED_IO_BUFFER_SIZE));
samReadIter = new ThreadedIterator<SAMRecord>(samReadIter, THREADED_IO_BUFFER_SIZE); samReadIter = new ThreadedIterator<SAMRecord>(samReadIter, THREADED_IO_BUFFER_SIZE);
} }
} }
@ -385,7 +385,7 @@ public class TraversalEngine {
samReader.setValidationStringency(strictness); samReader.setValidationStringency(strictness);
final SAMFileHeader header = samReader.getFileHeader(); final SAMFileHeader header = samReader.getFileHeader();
System.err.println("Sort order is: " + header.getSortOrder()); logger.info(String.format("Sort order is: " + header.getSortOrder()));
// If the file has an index, querying functions are available. Use them if possible... // If the file has an index, querying functions are available. Use them if possible...
if (samReader.hasIndex()) { if (samReader.hasIndex()) {
@ -443,7 +443,7 @@ public class TraversalEngine {
protected void testReference() { protected void testReference() {
while (true) { while (true) {
ReferenceSequence ref = refFile.nextSequence(); ReferenceSequence ref = refFile.nextSequence();
System.out.printf("%s %d %d%n", ref.getName(), ref.length(), System.currentTimeMillis()); logger.debug(String.format("%s %d %d", ref.getName(), ref.length(), System.currentTimeMillis()));
printProgress(true, "loci", new GenomeLoc("foo", 1)); printProgress(true, "loci", new GenomeLoc("foo", 1));
} }
} }
@ -506,7 +506,7 @@ public class TraversalEngine {
if (result) { if (result) {
nSkippedReads++; nSkippedReads++;
//System.out.printf(" [filter] %s => %b %s%n", rec.getReadName(), result, why); //System.out.printf(" [filter] %s => %b %s", rec.getReadName(), result, why);
} else { } else {
nReads++; nReads++;
} }
@ -613,8 +613,8 @@ public class TraversalEngine {
// Iterate forward to get all reference ordered data covering this locus // Iterate forward to get all reference ordered data covering this locus
final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, locus.getLocation()); final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, locus.getLocation());
if (DEBUGGING)
System.out.printf(" Reference: %s:%d %c%n", refSite.getCurrentContig().getName(), refSite.getPosition(), refBase); logger.debug(String.format(" Reference: %s:%d %c", refSite.getCurrentContig().getName(), refSite.getPosition(), refBase));
// //
// Execute our contract with the walker. Call filter, map, and reduce // Execute our contract with the walker. Call filter, map, and reduce
@ -626,7 +626,7 @@ public class TraversalEngine {
} }
if (this.maxReads > 0 && this.nRecords > this.maxReads) { if (this.maxReads > 0 && this.nRecords > this.maxReads) {
System.out.println("Maximum number of reads encountered, terminating traversal " + this.nRecords); logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + this.nRecords));
done = true; done = true;
} }
@ -656,7 +656,7 @@ public class TraversalEngine {
*/ */
protected <M, R> int traverseByRead(ReadWalker<M, R> walker) { protected <M, R> int traverseByRead(ReadWalker<M, R> walker) {
if (refFileName == null && !walker.requiresOrderedReads() && verifyingSamReadIter != null) { if (refFileName == null && !walker.requiresOrderedReads() && verifyingSamReadIter != null) {
System.out.println("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing."); logger.warn(String.format("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing."));
if (verifyingSamReadIter != null) if (verifyingSamReadIter != null)
verifyingSamReadIter.setCheckOrderP(false); verifyingSamReadIter.setCheckOrderP(false);
} }
@ -698,7 +698,7 @@ public class TraversalEngine {
} }
if (this.maxReads > 0 && this.nRecords > this.maxReads) { if (this.maxReads > 0 && this.nRecords > this.maxReads) {
System.out.println("Maximum number of reads encountered, terminating traversal " + this.nRecords); logger.warn(String.format(("Maximum number of reads encountered, terminating traversal " + this.nRecords)));
done = true; done = true;
} }
} }