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Enabled multiple argument for GATK driver; first step towards generalized -rods <name> <type> <file> argument structure 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@325 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-08 01:52:13 +00:00
parent 1ade22121b
commit b49f713336
2 changed files with 21 additions and 1 deletions
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15
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -8,6 +8,8 @@ import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Option;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
@ -96,6 +98,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
*/ */
private static Logger logger = Logger.getLogger(GenomeAnalysisTK.class); private static Logger logger = Logger.getLogger(GenomeAnalysisTK.class);
public static ArrayList<String> ROD_BINDINGS = null;
/** /**
* setup our arguments, both required and optional * setup our arguments, both required and optional
@ -129,6 +133,12 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("father", "DAD", "Father's genotype (SAM pileup)", "FATHER_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"); m_parser.addOptionalArg("daughter", "KID", "Daughter's genotype (SAM pileup)", "DAUGHTER_GENOTYPE_FILE");
// --rodBind <name> <type> <file>
Option rodBinder = OptionBuilder.withArgName("rodBind")
.hasArgs()
.withDescription( "Bind rod with <name> and <type> to <file>" )
.create("B");
m_parser.addOptionalArg(rodBinder, "ROD_BINDINGS");
} }
/** /**
@ -172,6 +182,11 @@ public class GenomeAnalysisTK extends CommandLineProgram {
final boolean TEST_ROD = false; final boolean TEST_ROD = false;
List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >(); List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >();
if ( ROD_BINDINGS != null ) {
System.out.printf("ROD BINDINGS are %s%n", Utils.join(":", ROD_BINDINGS));
}
if ( TEST_ROD ) { if ( TEST_ROD ) {
ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>("test", new File("trunk/data/gFFTest.gff"), rodGFF.class ); ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>("test", new File("trunk/data/gFFTest.gff"), rodGFF.class );
gff.testMe(); gff.testMe();

5
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
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@ -99,6 +99,11 @@ public class ArgumentParser {
} }
public void addOptionalArg(Option opt, String fieldname) {
// add it to the option
AddToOptionStorage(opt, fieldname);
}
/** /**
* Used locally to add to the options storage we have, for latter processing * Used locally to add to the options storage we have, for latter processing
* *