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

Another midway commit for teh engineerz 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2890 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-25 21:24:02 +00:00
parent 3289826892
commit 10cc71ceb0
1 changed files with 32 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

46
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
View File

@ -17,10 +17,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.*;
/**
* A parallelizable walker designed to quickly aggregate relevant coverage statistics across samples in the input
@ -85,6 +82,27 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
if ( getToolkit().getArguments().outFileName == null ) {
throw new StingException("This walker requires that you specify an output file (-o)");
}
if ( ! omitDepthOutput ) { // print header
out.printf("%s\t%s\t%s","Locus","Total_Depth","Average_Depth");
// get all the samples
HashSet<String> allSamples = new HashSet<String>(); // since the DOCS object uses a HashMap, this will be in the same order
for ( Set<String> sampleSet : getToolkit().getSamplesByReaders()) {
for (String s : sampleSet) {
allSamples.add(s);
}
}
for ( String s : allSamples) {
out.printf("\t%s_%s","Depth_for",s);
}
out.printf("%n");
} else {
out.printf("Per-Locus Depth of Coverage output was omitted");
}
}
public boolean isReduceByInterval() {
@ -104,16 +122,6 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
if ( ! omitLocusTable ) {
stats.initializeLocusCounts();
}
if ( ! omitDepthOutput ) { // print header
out.printf("%s\t%s\t%s","Locus","Total_Depth","Average_Depth");
for ( String s : stats.getAllSamples()) {
out.printf("\t%s_%s","Depth_for",s);
}
out.printf("%n");
} else {
out.printf("Per-Locus Depth of Coverage output was omitted");
}
return stats;
}
@ -312,11 +320,20 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
////////////////////////////////////////////////////////////////////////////////////
public void onTraversalDone(DepthOfCoverageStats coverageProfiles) {
logger.info("I am in the final ONTRAVERSALDONE");
logger.info(coverageProfiles.getTotalLoci()+" loci covered");
if ( out == null) {
logger.info("Out is now null");
} else {
logger.info(" ::: TESTING OUT ::: ");
out.println("====This is a test====");
}
///////////////////
// OPTIONAL OUTPUTS
//////////////////
if ( ! omitSampleSummary ) {
logger.info("Printing sample summary");
File summaryStatisticsFile = deriveFromStream("summary_statistics");
File perSampleStatisticsFile = deriveFromStream("sample_statistics");
printSummary(out,summaryStatisticsFile,coverageProfiles);
@ -324,6 +341,7 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
}
if ( ! omitLocusTable ) {
logger.info("Printing locus summary");
File perLocusStatisticsFile = deriveFromStream("locus_statistics");
printPerLocus(perLocusStatisticsFile,coverageProfiles);
}