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Improved command-line-arg validation at startup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-18 02:46:17 +00:00
parent 04e14ef85a
commit 3c022e4b0c
1 changed files with 41 additions and 3 deletions
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44
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
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@ -23,13 +23,17 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
@ -43,6 +47,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.AnnotatorROD;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.By;
@ -51,6 +57,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
@ -72,7 +79,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> {
protected String sampleName = null;
@Argument(fullName="select", shortName="s", doc="Optionally specifies which subset of columns from which -B inputs should be used for annotations. For example, -B mydbsnp,AnnotatorInputTable,/path/to/mydbsnp.txt -B mytable,AnnotatorInputTable,/path/mytable.txt -s mydbsnp.avHet,mydbsnp.name,mytable.column3 will cause annotations to only be generated from the 3 columns specified using -s.", required=false)
protected String[] COLUMNS = {};
protected String[] SELECT_COLUMNS = {};
@Argument(fullName="oneToMany", shortName="m", doc="If more than one record from the same file matches a particular locus (for example, multiple dbSNP records with the same position), create multiple entries in the ouptut VCF file - one for each match. If a particular tabular file has J matches, and another tabular file has K matches for a given locus, then J*K output VCF records will be generated - one for each pair of K, J. If this flag is not provided, the multiple records are still generated, but they are stored in the INFO field of a single output VCF record, with their annotation keys differentiated by appending '_i' with i varying from 1 to K*J. ", required=false)
protected Boolean ONE_TO_MANY = false;
@ -116,10 +123,41 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> {
logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
}
engine = new VariantAnnotatorEngine(getToolkit(), new String[] { }, new String[] { "GenomicAnnotation" });
//read all ROD file headers and construct a set of all column names to be used for validation of command-line args
final HashSet<String> allColumnNames = new HashSet<String>();
try {
for(ReferenceOrderedDataSource ds : getToolkit().getRodDataSources()) {
if(! AnnotatorROD.class.isAssignableFrom(ds.getReferenceOrderedData().getType())) {
continue; //skip all non-AnnotatorROD files.
}
final ArrayList<String> header = AnnotatorROD.readHeader(ds.getReferenceOrderedData().getFile());
for(String columnName : header) {
allColumnNames.add(ds.getName() + "." + columnName);
}
}
} catch(IOException e) {
throw new StingException("Failed when attempting to read file header. ", e);
}
//parse the SELECT_COLUMNS arg and validate the column names
List<String> parsedSelectColumns = new LinkedList<String>();
for(String token : SELECT_COLUMNS) {
parsedSelectColumns.addAll(Arrays.asList(token.split(",")));
}
SELECT_COLUMNS = parsedSelectColumns.toArray(SELECT_COLUMNS);
for(String columnName : SELECT_COLUMNS) {
if(!allColumnNames.contains(columnName)) {
throw new StingException("The column name '" + columnName + "' provided to -s doesn't match any of the column names in any of the -B files.");
}
}
//instanciate teh VariantAnnotatorEngine
engine = new VariantAnnotatorEngine(getToolkit(), new String[] { }, new String[] { "GenomicAnnotation" });
engine.setOneToMany( Boolean.TRUE.equals( ONE_TO_MANY ) );
engine.setRequestedColumns(COLUMNS);
engine.setRequestedColumns(SELECT_COLUMNS);
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();