Merge pull request #587 from broadinstitute/eb_actually_fail_on_reduced_bams

Make sure to fail in all cases where the BAM being used was created by ReduceReads.

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java

@@ -168,14 +168,15 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    final static String assessMinIndelFraction = baseCommandIndelsb37 + " -I " + validationDataLocation
+    final static String assessMinIndelFraction = "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R "
-            + "978604.bam -L 1:978,586-978,626 -o %s --sites_only -rf Sample -goodSM 7377 -goodSM 22-0022 -goodSM 134 -goodSM 344029-53 -goodSM 14030";
+            + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -I "
+            + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,500,000 -o %s";
 
     @Test
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("af0b881d0a931f0789706f0289b72a64"));
+                Arrays.asList("0d9a3129f680c4a4f41b08154fd836a4"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -183,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("aa97a7941a861d57a3b746b3f6301eb6"));
+                Arrays.asList("e910304c25a277b63d8fa8167d4a8b88"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 
@@ -191,7 +192,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction100() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 1", 1,
-                Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
+                Arrays.asList("83e72fd13291cec00fa5a468a2656c94"));
         executeTest("test minIndelFraction 1.0", spec);
     }
 

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -154,6 +154,15 @@ public class SAMDataSource {
      */
     private final ThreadAllocation threadAllocation;
 
+    /**
+     * Static set of unsupported programs that create bam files.
+     * The key is the PG record ID and the value is the name of the tool that created it
+     */
+    private static Map<String, String> unsupportedPGs = new HashMap<>();
+    static {
+        unsupportedPGs.put("GATK ReduceReads", "ReduceReads");
+    }
+
     /**
      * Create a new SAM data source given the supplied read metadata.
      *
@@ -324,7 +333,6 @@ public class SAMDataSource {
         // and read group id (merged) -> read group id (original) mappings.
         for(SAMReaderID id: readerIDs) {
             SAMFileReader reader = readers.getReader(id);
-            checkForReducedBamFile(reader.getFileHeader());
 
             ReadGroupMapping mappingToMerged = new ReadGroupMapping();
 
@@ -356,9 +364,11 @@ public class SAMDataSource {
      * @param header the SAM header for a given file
      * @throws UserException if the header is from a reduced bam
      */
-    private void checkForReducedBamFile(final SAMFileHeader header) {
+    private void checkForUnsupportedBamFile(final SAMFileHeader header) {
-        if ( header.getProgramRecord("GATK ReduceReads") != null )
+        for ( final SAMProgramRecord PGrecord : header.getProgramRecords() ) {
-            throw new UserException("The GATK no longer supports running off of BAMs produced by ReduceReads");
+            if ( unsupportedPGs.containsKey(PGrecord.getId()) )
+                throw new UserException("The GATK no longer supports running off of BAMs produced by " + unsupportedPGs.get(PGrecord.getId()));
+        }
     }
 
     public void close() {
@@ -837,6 +847,8 @@ public class SAMDataSource {
             for(final SAMReaderID readerID: readerIDs) {
                 final ReaderInitializer init = new ReaderInitializer(readerID).call();
 
+                checkForUnsupportedBamFile(init.reader.getFileHeader());
+
                 if (removeProgramRecords) {
                     init.reader.getFileHeader().setProgramRecords(new ArrayList<SAMProgramRecord>());
                 }

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java

@@ -227,4 +227,26 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 new ArrayList<ReadFilter>(),
                 false);
     }
+
+    @Test(expectedExceptions = UserException.class)
+    public void testFailOnReducedReadsRemovingProgramRecords() {
+        readers.add(new SAMReaderID(new File(privateTestDir + "old.reduced.bam"), new Tags()));
+
+        SAMDataSource data = new SAMDataSource(readers,
+                new ThreadAllocation(),
+                null,
+                genomeLocParser,
+                false,
+                SAMFileReader.ValidationStringency.SILENT,
+                null,
+                null,
+                new ValidationExclusion(),
+                new ArrayList<ReadFilter>(),
+                Collections.<ReadTransformer>emptyList(),
+                false,
+                (byte) -1,
+                true,
+                false,
+                null);
+    }
 }