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Updated to use Tribble-based GATKFeature instead of TabularROD 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-19 03:42:12 +00:00
parent 42ee16f256
commit 984c51efd3
1 changed files with 6 additions and 5 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
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@ -48,9 +48,9 @@ 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.refdata.features.sampileup.AnnotatorInputTableCodec;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
@ -123,14 +123,15 @@ 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.");
}
//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.
if(! ds.getReferenceOrderedData().getType().equals(AnnotatorInputTableCodec.class)) {
continue; //skip all non-AnnotatorInputTable files.
}
final ArrayList<String> header = AnnotatorROD.readHeader(ds.getReferenceOrderedData().getFile());
final ArrayList<String> header = AnnotatorInputTableCodec.readHeader(ds.getReferenceOrderedData().getFile());
for(String columnName : header) {
allColumnNames.add(ds.getName() + "." + columnName);
}
@ -148,7 +149,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> {
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.");
throw new StingException("The column name '" + columnName + "' provided to -s doesn't match any of the column names in any of the -B files. Here is the list of available column names: " + allColumnNames);
}
}