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

@ minor fixes to CoverageAndPowerWalker and AnalyzePowerWalker (switching to By Reference traversal, spitting out Syzygy position for sanity check) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1465 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-08-27 21:44:18 +00:00
parent bd1e679bc5
commit 6012f7602b
2 changed files with 18 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

21
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
View File

@ -6,6 +6,8 @@ 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.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.playground.utils.PoolUtils;
import java.io.FileNotFoundException;
@ -26,6 +28,7 @@ import net.sf.samtools.SAMRecord;
* Time: 3:47:47 PM
* To change this template use File | Settings | File Templates.
*/
@By(DataSource.REFERENCE)
public class AnalyzePowerWalker extends CoverageAndPowerWalker{
// runs CoverageAndPowerWalker except compares to Syzygy outputs in a file
@ -44,7 +47,7 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
super.initialize();
try {
syzyFileReader = new BufferedReader(new FileReader(pathToSyzygyFile));
syzyFileReader.readLine();
System.out.println(syzyFileReader.readLine());
} catch (FileNotFoundException e) {
String newErrMsg = "Syzygy input file " + pathToSyzygyFile + " could be incorrect. File not found.";
throw new StingException(newErrMsg,e);
@ -62,23 +65,27 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
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.calculatePower(splitReads,false,context);
Pair<double[],byte[]> powPair = super.calculatePower(splitReads,false,context);
boolean syzyFileIsReady;
boolean syzyFileIsReady=true;
try {
syzyFileIsReady = syzyFileReader.ready();
}
catch(IOException e) {
syzyFileIsReady = false;
throw new StingException("Input file reader was not ready before an attempt to read from it", e);
}
if(!syzyFileIsReady) {
throw new StingException("Input file reader was not ready before an attempt to read from it.");
throw new StingException("Input file reader was not ready before an attempt to read from it, but there was no IOException");
} else if(!outOfLinesInSyzyFile) {
Pair<Double,String> syzyPow = getSyzyPowFromFile();
out.printf("%s: %d %d %f %f (%s)%n", context.getLocation(), context.getReads().size(),powpair.second,powpair.first,syzyPow.first,syzyPow.second);
out.printf("%s: %d %d %d %d %d %d %f %f %f %f |%s%n", context.getLocation(), splitReads.getFirst().getFirst().size(), splitReads.getFirst().getSecond().size(),
context.getReads().size(), powPair.getSecond()[0], powPair.getSecond()[1], powPair.getSecond()[2],
powPair.getFirst()[0], powPair.getFirst()[1], powPair.getFirst()[2], syzyPow.getFirst(), syzyPow.getSecond());
} else {
out.printf("%s: %d %d %f%n", context.getLocation(), context.getReads().size(),powpair.second,powpair.first);
out.printf("%s: $d %d %d %d %d %d %d %f %f %f%n", context.getLocation(), splitReads.getFirst().getFirst().size(), splitReads.getFirst().getSecond().size(),
context.getReads().size(), powPair.getSecond()[0], powPair.getSecond()[1], powPair.getSecond()[2],
powPair.getFirst()[0], powPair.getFirst()[1], powPair.getFirst()[2]);
}
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
View File

@ -7,6 +7,8 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.ListUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.playground.utils.PoolUtils;
@ -21,6 +23,8 @@ import java.util.*;
* Time: 11:57:07 AM
* To change this template use File | Settings | File Templates.
*/
@By(DataSource.REFERENCE)
public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>, Pair<Long, Long>> {
@Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false)
public boolean suppress_printing = false;