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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

44
core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
View File

@ -135,13 +135,13 @@ public class TraversalEngine {
public void setSafetyChecking(final boolean 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;
}
public void setSortOnFly(final boolean 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;
}
@ -197,7 +197,7 @@ public class TraversalEngine {
scanner.close();
}
System.out.format("DEBUG: locStr: %s\n", locStr);
logger.debug("DEBUG: locStr: " + locStr);
this.locs = parseGenomeLocs(locStr);
}
@ -220,7 +220,7 @@ public class TraversalEngine {
Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";")));
GenomeLoc[] locs = (GenomeLoc[]) result.toArray(new GenomeLoc[0]);
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;
} 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));
@ -303,9 +303,9 @@ public class TraversalEngine {
this.lastProgressPrintTime = curTime;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
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
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
@ -313,7 +313,7 @@ public class TraversalEngine {
// 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.
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) {
printProgress(true, type, null);
System.out.println("Traversal reduce result is " + sum);
System.out.printf("Traversal skipped %d reads out of %d total (%.2f%%)%n", nSkippedReads, nReads, (nSkippedReads * 100.0) / nReads);
System.out.printf(" -> %d unmapped reads%n", nUnmappedReads);
System.out.printf(" -> %d non-primary reads%n", nNotPrimary);
System.out.printf(" -> %d reads with bad alignments%n", nBadAlignments);
System.out.printf(" -> %d reads with indels%n", nSkippedIndels);
logger.info(String.format("Traversal reduce result is " + sum));
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 non-primary reads", nNotPrimary));
logger.info(String.format(" -> %d reads with bad alignments", nBadAlignments));
logger.info(String.format(" -> %d reads with indels", nSkippedIndels));
}
// --------------------------------------------------------------------------------------------------------------
@ -372,7 +372,7 @@ public class TraversalEngine {
samReadIter = new VerifyingSamIterator(samReadIter);
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);
}
}
@ -385,7 +385,7 @@ public class TraversalEngine {
samReader.setValidationStringency(strictness);
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 (samReader.hasIndex()) {
@ -443,7 +443,7 @@ public class TraversalEngine {
protected void testReference() {
while (true) {
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));
}
}
@ -506,7 +506,7 @@ public class TraversalEngine {
if (result) {
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 {
nReads++;
}
@ -613,8 +613,8 @@ public class TraversalEngine {
// Iterate forward to get all reference ordered data covering this locus
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
@ -626,7 +626,7 @@ public class TraversalEngine {
}
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;
}
@ -656,7 +656,7 @@ public class TraversalEngine {
*/
protected <M, R> int traverseByRead(ReadWalker<M, R> walker) {
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)
verifyingSamReadIter.setCheckOrderP(false);
}
@ -698,7 +698,7 @@ public class TraversalEngine {
}
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;
}
}