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added support for Picard IntervalList files to --interval_file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@334 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-08 16:49:43 +00:00
parent 295c269a64
commit 0b81a76420
1 changed files with 26 additions and 8 deletions
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22
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -4,6 +4,8 @@ import edu.mit.broad.picard.filter.FilteringIterator;
import edu.mit.broad.picard.filter.SamRecordFilter; import edu.mit.broad.picard.filter.SamRecordFilter;
import edu.mit.broad.picard.reference.ReferenceSequence; import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.sam.SamFileHeaderMerger; import edu.mit.broad.picard.sam.SamFileHeaderMerger;
import edu.mit.broad.picard.directed.IntervalList;
import edu.mit.broad.picard.util.Interval;
import net.sf.functionalj.Function1; import net.sf.functionalj.Function1;
import net.sf.functionalj.FunctionN; import net.sf.functionalj.FunctionN;
import net.sf.functionalj.Functions; import net.sf.functionalj.Functions;
@ -207,6 +209,21 @@ public abstract class TraversalEngine {
* @param file_name * @param file_name
*/ */
public void setLocationFromFile(final String file_name) { public void setLocationFromFile(final String file_name) {
// first try to read it as an interval file since that's well structured
// we'll fail quickly if it's not a valid file. Then try to parse it as
// a location string file
try {
IntervalList il = IntervalList.fromFile(new File(file_name));
// iterate through the list of merged intervals and add then as GenomeLocs
ArrayList<GenomeLoc> locList = new ArrayList<GenomeLoc>();
for(Interval interval : il.getUniqueIntervals()) {
locList.add(new GenomeLoc(interval.getSequence(), interval.getStart(), interval.getEnd()));
}
this.locs = locList;
} catch (Exception e) {
try { try {
xReadLines reader = new xReadLines(new File(file_name)); xReadLines reader = new xReadLines(new File(file_name));
List<String> lines = reader.readLines(); List<String> lines = reader.readLines();
@ -214,11 +231,12 @@ public abstract class TraversalEngine {
String locStr = Utils.join(";", lines); String locStr = Utils.join(";", lines);
logger.debug("locStr: " + locStr); logger.debug("locStr: " + locStr);
setLocation(locStr); setLocation(locStr);
} catch (Exception e) { } catch (Exception e2) {
e.printStackTrace(); e2.printStackTrace();
System.exit(-1); System.exit(-1);
} }
} }
}