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reconciled TraversalEngine 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@21 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-02 21:51:25 +00:00
parent 46c3f1a0ac
commit 851e1df072
4 changed files with 17 additions and 14 deletions
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3
java/build.xml
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@ -6,6 +6,7 @@
<property name="src" location="trunk/java/"/> <property name="src" location="trunk/java/"/>
<property name="build" location="out/production/AnalysisTK"/> <property name="build" location="out/production/AnalysisTK"/>
<property name="dist" location="dist"/> <property name="dist" location="dist"/>
<property name="jars" location="trunk/java/jars/functionalj.jar"/>
<target name="init"> <target name="init">
<!-- Create the time stamp --> <!-- Create the time stamp -->
@ -17,7 +18,7 @@
<target name="compile" depends="init" <target name="compile" depends="init"
description="compile the source " > description="compile the source " >
<!-- Compile the java code from ${src} into ${build} --> <!-- Compile the java code from ${src} into ${build} -->
<javac srcdir="${src}" destdir="${build}"/> <javac srcdir="${src}" destdir="${build}" classpath="${jars}"/>
</target> </target>
<target name="dist" depends="compile" <target name="dist" depends="compile"

20
java/src/edu/mit/broad/sting/atk/TraversalEngine.java
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@ -146,17 +146,18 @@ public class TraversalEngine {
// functions for dealing with the reference sequence // functions for dealing with the reference sequence
// //
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
public void printProgress(final String type) { printProgress( false, type ); } public void printProgress(final String type, GenomeLoc loc) { printProgress( false, type, loc ); }
public void printProgress( boolean mustPrint, final String type ) { public void printProgress( boolean mustPrint, final String type, GenomeLoc loc ) {
final long nRecords = this.nRecords; final long nRecords = this.nRecords;
if ( mustPrint || nRecords % 100000 == 0 ) { if ( mustPrint || nRecords % 100000 == 0 ) {
final double elapsed = (System.currentTimeMillis() - startTime) / 1000.0; final double elapsed = (System.currentTimeMillis() - startTime) / 1000.0;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords; final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
if ( loc != null )
System.out.printf("Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type); System.out.printf("Traversed to %s, processing %d %s %.2f secs (%.2f secs per 1M %s)%n", loc, nRecords, type, elapsed, secsPer1MReads, type);
else
System.out.printf("Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type);
System.out.printf(" -> %s%n", samReadingTracker.progressMeter()); System.out.printf(" -> %s%n", samReadingTracker.progressMeter());
} }
} }
@ -297,14 +298,15 @@ public class TraversalEngine {
done = true; done = true;
} }
printProgress("loci");
} }
printProgress("loci", locus.getLocation());
if ( pastFinalLocation(locus.getLocation()) ) if ( pastFinalLocation(locus.getLocation()) )
done = true; done = true;
} }
printProgress( true, "loci" ); printProgress( true, "loci", null );
System.out.println("Traversal reduce result is " + sum); 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("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 unmapped reads%n", nUnmappedReads );
@ -345,7 +347,7 @@ public class TraversalEngine {
break; break;
} }
printProgress("reads"); printProgress("reads", loc);
} }
if ( pastFinalLocation(loc) ) if ( pastFinalLocation(loc) )
@ -353,7 +355,7 @@ public class TraversalEngine {
//System.out.printf("Done? %b%n", done); //System.out.printf("Done? %b%n", done);
} }
printProgress( true, "reads" ); printProgress( true, "reads", null );
System.out.println("Traversal reduce result is " + sum); System.out.println("Traversal reduce result is " + sum);
walker.onTraveralDone(); walker.onTraveralDone();
return 0; return 0;

2
scripts/TraverseTest.sh
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@ -1 +1 @@
java -Xmx1024m -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $* java -Xmx4096m -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*

2
scripts/TraverseTestProf.sh
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@ -1 +1 @@
java -Xmx1024m -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $* java -Xmx4096m -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.AnalysisTK $*