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@ Fixed issues with AnalyzePowerWalker which depended on CoverageAndPowerWalker. The latter was changed but not the former. Now fixed 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1464 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-08-27 20:23:41 +00:00
parent a17dad5fa9
commit bd1e679bc5
2 changed files with 21 additions and 8 deletions
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22
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.playground.utils.PoolUtils;
import java.io.FileNotFoundException;
import java.io.FileReader;
@ -13,8 +14,11 @@ import java.io.BufferedReader;
import java.io.IOException;
import java.util.StringTokenizer;
import java.util.NoSuchElementException;
import java.util.List;
import java.rmi.NoSuchObjectException;
import net.sf.samtools.SAMRecord;
/**
* Created by IntelliJ IDEA.
* User: chartl
@ -29,8 +33,6 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
String pathToSyzygyFile = null;
@Argument(fullName = "ColumnOffset", shortName = "co", doc = "Offset of column containing the power in the pf", required = true)
int colOffset = 0;
@Argument(fullName = "linesToClear", shortName="clr", doc = "Clear so many lines from the read file before starting (default - just the header line)", required = false)
int clrLines = 1;
BufferedReader syzyFileReader;
final String pfFileDelimiter = " ";
@ -42,9 +44,7 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
super.initialize();
try {
syzyFileReader = new BufferedReader(new FileReader(pathToSyzygyFile));
for(int clear = 0; clear < clrLines; clear++) {
syzyFileReader.readLine();
}
syzyFileReader.readLine();
} catch (FileNotFoundException e) {
String newErrMsg = "Syzygy input file " + pathToSyzygyFile + " could be incorrect. File not found.";
throw new StingException(newErrMsg,e);
@ -56,11 +56,13 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
}
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)
public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)
{
Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
if ( !super.suppress_printing )
{
Pair<Double,Byte> powpair = super.boostrapSamplingPowerCalc(context);
Pair<double[],byte[]> powpair = super.calculatePower(splitReads,false,context);
boolean syzyFileIsReady;
try {
@ -80,7 +82,7 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
}
}
return context.getReads().size();
return new Pair(splitReads.getFirst().getFirst().size(), splitReads.getFirst().getFirst().size());
}
public Pair<Double,String> getSyzyPowFromFile() {
@ -107,4 +109,8 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
throw new StingException(errMsg);
}
}
public String createHeaderString() {
return (super.createHeaderString() + " PowSyz");
}
}

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
View File

@ -43,6 +43,9 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
}
public Pair<Long,Long> reduceInit() {
if ( ! suppress_printing ) { // print header
out.printf("%s%n",createHeaderString());
}
return new Pair(0l,0l);
}
@ -154,6 +157,10 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
return power;
}
public String createHeaderString() {
return "Chrom:Pos CvgF CvgR CvgC QmedF QmedR QmedC PowF PowR PowC";
}
// class methods
public static Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> coinTossPartition(List<SAMRecord> reads, List<Integer> offsets, double snpProb) {