Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java

@@ -45,7 +45,7 @@ import java.util.*;
  *
  * The IntervalBinding<T> is a formal GATK argument that bridges between a walker and
  * the engine to construct intervals for traversal at runtime.  The IntervalBinding can
- * either be a RodBinding<T>, a string of one or more intervals, or a file with interval strings.
+ * either be a RodBinding<T>, a string of one interval, or a file with interval strings.
  * The GATK Engine takes care of initializing the binding when appropriate and determining intervals from it.
  *
  * Note that this class is immutable.

public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java

@@ -56,28 +56,30 @@ public class IntervalUtils {
     public static List<GenomeLoc> parseIntervalArguments(GenomeLocParser parser, String arg) {
         List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();    // running list of raw GenomeLocs
 
-        // separate argument on semicolon first
+        if ( arg.indexOf(';') != -1 ) {
-        for (String fileOrInterval : arg.split(";")) {
+            throw new UserException.BadArgumentValue("-L " + arg, "The legacy -L \"interval1;interval2\" syntax " +
-            // if any argument is 'unmapped', "parse" it to a null entry.  A null in this case means 'all the intervals with no alignment data'.
+                                                     "is no longer supported. Please use one -L argument for each " +
-            if (isUnmapped(fileOrInterval))
+                                                     "interval or an interval file instead.");
-                rawIntervals.add(GenomeLoc.UNMAPPED);
+        }
-            // if it's a file, add items to raw interval list
-            else if (isIntervalFile(fileOrInterval)) {
-                try {
-                    rawIntervals.addAll(intervalFileToList(parser, fileOrInterval));
-                }
-                catch ( UserException.MalformedGenomeLoc e ) {
-                    throw e;
-                }
-                catch ( Exception e ) {
-                    throw new UserException.MalformedFile(fileOrInterval, "Interval file could not be parsed in any supported format.", e);
-                }
-            }
 
-                // otherwise treat as an interval -> parse and add to raw interval list
+        // if any argument is 'unmapped', "parse" it to a null entry.  A null in this case means 'all the intervals with no alignment data'.
-            else {
+        if (isUnmapped(arg))
-                rawIntervals.add(parser.parseGenomeLoc(fileOrInterval));
+            rawIntervals.add(GenomeLoc.UNMAPPED);
+        // if it's a file, add items to raw interval list
+        else if (isIntervalFile(arg)) {
+            try {
+                rawIntervals.addAll(intervalFileToList(parser, arg));
             }
+            catch ( UserException.MalformedGenomeLoc e ) {
+                throw e;
+            }
+            catch ( Exception e ) {
+                throw new UserException.MalformedFile(arg, "Interval file could not be parsed in any supported format.", e);
+            }
+        }
+        // otherwise treat as an interval -> parse and add to raw interval list
+        else {
+            rawIntervals.add(parser.parseGenomeLoc(arg));
         }
 
         return rawIntervals;

public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java

@@ -52,7 +52,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     
     @Test
     public void testCallableLociWalker2() {
-        String gatk_args = commonArgs + " -format BED -L 1:10,000,000-10,000,100;1:10,000,110-10,000,120 -summary %s";
+        String gatk_args = commonArgs + " -format BED -L 1:10,000,000-10,000,100 -L 1:10,000,110-10,000,120 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
                 Arrays.asList("c671f65712d9575b8b3e1f1dbedc146e", "d287510eac04acf5a56f5cde2cba0e4a"));
         executeTest("formatBed by interval", spec);

public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java

@@ -12,25 +12,25 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         String md5_1 = "328d2d52cedfdc52da7d1abff487633d";
 
         WalkerTestSpec spec1a = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500 -L 1:10,100,000-10,101,000 -L 1:10,900,000-10,900,001 -o %s",
                  1,
                  Arrays.asList(md5_1));
         executeTest("testFastaReference", spec1a);
 
         WalkerTestSpec spec1b = new WalkerTestSpec(
-                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500 -L 1:10,100,000-10,101,000 -L 1:10,900,000-10,900,001 -o %s",
                  1,
                  Arrays.asList(md5_1));
         executeTest("testFastaReference", spec1b);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s",
                  1,
                  Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
         WalkerTestSpec spec3 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500 -L 1:10,029,200-10,029,500 -o %s",
                  1,
                  Arrays.asList("8b6cd2e20c381f9819aab2d270f5e641"));
         executeTest("testFastaAlternateReferenceSnps", spec3);

public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java

@@ -3,7 +3,10 @@ package org.broadinstitute.sting.utils.interval;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.SAMFileHeader;
 import org.apache.commons.io.FileUtils;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.IntervalBinding;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.testng.Assert;
@@ -983,4 +986,14 @@ public class IntervalUtilsUnitTest extends BaseTest {
                 data.toString(), data.original, actual, data.expected);
         Assert.assertEquals(actual, data.expected, description);
     }
+
+    @Test(expectedExceptions=UserException.BadArgumentValue.class)
+    public void testExceptionUponLegacyIntervalSyntax() throws Exception {
+        GenomeAnalysisEngine toolkit = new GenomeAnalysisEngine();
+        toolkit.setGenomeLocParser(new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference))));
+
+        // Attempting to use the legacy -L "interval1;interval2" syntax should produce an exception:
+        IntervalBinding<Feature> binding = new IntervalBinding<Feature>("1;2");
+        List<GenomeLoc> intervals = binding.getIntervals(toolkit);
+    }
 }