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cruel hack: new toolkit-wide optional cmdline arguments added to allow for loading trio genotyping tracks; to be moved back to walker when walkers can register their data needs with the toolkit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@324 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-07 22:33:26 +00:00
parent 8ec427ab66
commit 1ade22121b
1 changed files with 24 additions and 3 deletions
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27
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -13,6 +13,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
import org.broadinstitute.sting.gatk.refdata.rodSAMPileup;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
@ -49,6 +50,12 @@ public class GenomeAnalysisTK extends CommandLineProgram {
public String DOWNSAMPLE_COVERAGE = null;
public String INTERVALS_FILE = null;
// added for mendelian walker.
//TODO: when walkers can ask for their tracks this should be removed!
public String MOTHER_GENOTYPE_FILE = null;
public String FATHER_GENOTYPE_FILE = null;
public String DAUGHTER_GENOTYPE_FILE = null;
// our walker manager
private WalkerManager walkerManager = null;
@ -116,6 +123,12 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("out", "o", "An output file presented to the walker. Will overwrite contents if file exists.", "outFileName" );
m_parser.addOptionalArg("err", "e", "An error output file presented to the walker. Will overwrite contents if file exists.", "errFileName" );
m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.", "outErrFileName");
//TODO: remove when walkers can ask for tracks
m_parser.addOptionalArg("mother", "MOM", "Mother's genotype (SAM pileup)", "MOTHER_GENOTYPE_FILE");
m_parser.addOptionalArg("father", "DAD", "Father's genotype (SAM pileup)", "FATHER_GENOTYPE_FILE");
m_parser.addOptionalArg("daughter", "KID", "Daughter's genotype (SAM pileup)", "DAUGHTER_GENOTYPE_FILE");
}
/**
@ -182,7 +195,15 @@ public class GenomeAnalysisTK extends CommandLineProgram {
ReferenceOrderedData<rodGFF> hapmapChip = new ReferenceOrderedData<rodGFF>("hapmap-chip", new File(HAPMAP_CHIP_FILE), rodGFF.class );
rods.add(hapmapChip);
}
}
//TODO: remove when walkers can ask for tracks
if ( MOTHER_GENOTYPE_FILE != null )
rods.add( new ReferenceOrderedData<rodSAMPileup>("mother", new File(MOTHER_GENOTYPE_FILE), rodSAMPileup.class ) );
if ( FATHER_GENOTYPE_FILE != null )
rods.add( new ReferenceOrderedData<rodSAMPileup>("father", new File(FATHER_GENOTYPE_FILE), rodSAMPileup.class ) );
if ( DAUGHTER_GENOTYPE_FILE != null )
rods.add( new ReferenceOrderedData<rodSAMPileup>("daughter", new File(DAUGHTER_GENOTYPE_FILE), rodSAMPileup.class ) );
}
initializeOutputStreams();
@ -211,9 +232,9 @@ public class GenomeAnalysisTK extends CommandLineProgram {
if ( WALK_ALL_LOCI )
this.engine = new TraverseByLociByReference(INPUT_FILE, REF_FILE_ARG, rods);
this.engine = new TraverseByLociByReference(INPUT_FILE, REF_FILE_ARG, rods);
else
this.engine = new TraverseByLoci(INPUT_FILE, REF_FILE_ARG, rods);
this.engine = new TraverseByLoci(INPUT_FILE, REF_FILE_ARG, rods);
}
}
catch (java.lang.ClassCastException e) {