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

Deprecated 'O' in favor of 'o' in the cleaner 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4085 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-23 18:09:24 +00:00
parent 55a8306a0d
commit c9c6ff49c2
3 changed files with 15 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -56,7 +56,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
@Argument(fullName="variants_out",shortName="varout",doc="Please use --out instead",required=false)
@Deprecated
public boolean varout;
protected String varout;
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
protected File verboseFile = null;

25
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -46,7 +46,6 @@ import org.broadinstitute.sting.utils.collections.Pair;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintStream;
import java.util.*;
/**
@ -70,15 +69,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
protected double MISMATCH_THRESHOLD = 0.15;
@Output
protected PrintStream out;
@Output(fullName = "err", shortName = "e", doc = "An error output file presented to the walker. Will overwrite contents if file exists.", required = false)
protected PrintStream err;
@Output(fullName="output", shortName="O", required=false, doc="Output bam")
@Output(required=false, doc="Output bam")
protected String writerFilename = null;
@Argument(fullName="output",shortName="O",doc="Please use --out instead",required=false)
@Deprecated
protected String oldOArg;
@Argument(fullName="bam_compression", shortName="compress", required=false, doc="Compression level to use for output bams [default:5]")
protected Integer compressionLevel = 5;
@ -203,8 +200,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
try {
indelOutput = new FileWriter(new File(OUT_INDELS));
} catch (Exception e) {
logger.warn("Failed to create output file "+ OUT_INDELS+". Indel output will be suppressed");
err.println(e.getMessage());
logger.error("Failed to create output file "+ OUT_INDELS+". Indel output will be suppressed");
logger.error(e.getMessage());
indelOutput = null;
}
}
@ -212,8 +209,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
try {
statsOutput = new FileWriter(new File(OUT_STATS));
} catch (Exception e) {
logger.warn("Failed to create output file "+ OUT_STATS+". Cleaning stats output will be suppressed");
err.println(e.getMessage());
logger.error("Failed to create output file "+ OUT_STATS+". Cleaning stats output will be suppressed");
logger.error(e.getMessage());
statsOutput = null;
}
}
@ -221,8 +218,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
try {
snpsOutput = new FileWriter(new File(OUT_SNPS));
} catch (Exception e) {
logger.warn("Failed to create output file "+ OUT_SNPS+". Cleaning snps output will be suppressed");
err.println(e.getMessage());
logger.error("Failed to create output file "+ OUT_SNPS+". Cleaning snps output will be suppressed");
logger.error(e.getMessage());
snpsOutput = null;
}
}

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -11,7 +11,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testRealignerLod5() {
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "c4ef635f2597b12b93a73199f07e509b"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
Arrays.asList(md5s));
executeTest("test realigner lod5", spec);
@ -21,7 +21,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testRealignerLod50() {
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "3735a510513b6fa4161d92155e026283"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
Arrays.asList(md5s));
executeTest("test realigner lod50", spec);
@ -31,7 +31,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testRealignerKnownsOnly() {
String[] md5s = {"7084d4e543bc756730ab306768028530", "74652bd8240291293ec921f8ecfa1622"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
"-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,
Arrays.asList(md5s));
executeTest("test realigner known indels only", spec);