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Counts of records failing filters are displayed sorted 

-- Stops random ordering of the output, as the counts are returned sorted by string name of the class
-- Deleted now unused sh*tty assessors in Utils
This commit is contained in:
Mark DePristo 2011-10-06 18:42:26 -07:00
parent d1e70d6ec2
commit 0b88af4af9
3 changed files with 11 additions and 33 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
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@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Collections; import java.util.Collections;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
import java.util.TreeMap;
/** /**
* Holds a bunch of basic information about the traversal. * Holds a bunch of basic information about the traversal.
@ -102,8 +103,12 @@ public class ReadMetrics implements Cloneable {
counter.put(filter.getClass(), c + 1L); counter.put(filter.getClass(), c + 1L);
} }
public Map<Class,Long> getCountsByFilter() { public Map<String,Long> getCountsByFilter() {
return Collections.unmodifiableMap(counter); final TreeMap<String, Long> sortedCounts = new TreeMap<String, Long>();
for(Map.Entry<Class,Long> counterEntry: counter.entrySet()) {
sortedCounts.put(counterEntry.getKey().getSimpleName(),counterEntry.getValue());
}
return sortedCounts;
} }
/** /**

8
public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -364,8 +364,8 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
// count up the number of skipped reads by summing over all filters // count up the number of skipped reads by summing over all filters
long nSkippedReads = 0L; long nSkippedReads = 0L;
for ( Map.Entry<Class, Long> countsByFilter: cumulativeMetrics.getCountsByFilter().entrySet()) for ( final long countsByFilter : cumulativeMetrics.getCountsByFilter().values())
nSkippedReads += countsByFilter.getValue(); nSkippedReads += countsByFilter;
logger.info(String.format("Total runtime %.2f secs, %.2f min, %.2f hours", elapsed, elapsed / 60, elapsed / 3600)); logger.info(String.format("Total runtime %.2f secs, %.2f min, %.2f hours", elapsed, elapsed / 60, elapsed / 3600));
if ( cumulativeMetrics.getNumReadsSeen() > 0 ) if ( cumulativeMetrics.getNumReadsSeen() > 0 )
@ -373,10 +373,10 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
nSkippedReads, nSkippedReads,
cumulativeMetrics.getNumReadsSeen(), cumulativeMetrics.getNumReadsSeen(),
100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen()))); 100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen())));
for ( Map.Entry<Class, Long> filterCounts : cumulativeMetrics.getCountsByFilter().entrySet() ) { for ( Map.Entry<String, Long> filterCounts : cumulativeMetrics.getCountsByFilter().entrySet() ) {
long count = filterCounts.getValue(); long count = filterCounts.getValue();
logger.info(String.format(" -> %d reads (%.2f%% of total) failing %s", logger.info(String.format(" -> %d reads (%.2f%% of total) failing %s",
count, 100.0 * MathUtils.ratio(count,cumulativeMetrics.getNumReadsSeen()), Utils.getClassName(filterCounts.getKey()))); count, 100.0 * MathUtils.ratio(count,cumulativeMetrics.getNumReadsSeen()), filterCounts.getKey()));
} }
if ( performanceLog != null ) performanceLog.close(); if ( performanceLog != null ) performanceLog.close();

27
public/java/src/org/broadinstitute/sting/utils/Utils.java
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@ -58,33 +58,6 @@ public class Utils {
return (int)(maxElements / JAVA_DEFAULT_HASH_LOAD_FACTOR) + 2; return (int)(maxElements / JAVA_DEFAULT_HASH_LOAD_FACTOR) + 2;
} }
public static String getClassName(Class c) {
String FQClassName = c.getName();
int firstChar;
firstChar = FQClassName.lastIndexOf ('.') + 1;
if ( firstChar > 0 ) {
FQClassName = FQClassName.substring ( firstChar );
}
return FQClassName;
}
// returns package and class name
public static String getFullClassName(Class c) {
return c.getName();
}
// returns the package without the classname, empty string if
// there is no package
public static String getPackageName(Class c) {
String fullyQualifiedName = c.getName();
int lastDot = fullyQualifiedName.lastIndexOf ('.');
if (lastDot==-1){ return ""; }
return fullyQualifiedName.substring (0, lastDot);
}
/** /**
* Compares two objects, either of which might be null. * Compares two objects, either of which might be null.
* *