Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -130,12 +130,12 @@ public class CommandLineGATK extends CommandLineExecutable {
 
         // can't close tribble index when writing
         if ( message.indexOf("Unable to close index for") != -1 )
-            exitSystemWithUserError(new UserException(t.getCause().getMessage()));
+            exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage()));
 
         // disk is full
         if ( message.indexOf("No space left on device") != -1 )
             exitSystemWithUserError(new UserException(t.getMessage()));
-        if ( t.getCause().getMessage().indexOf("No space left on device") != -1 )
+        if ( t.getCause() != null && t.getCause().getMessage().indexOf("No space left on device") != -1 )
             exitSystemWithUserError(new UserException(t.getCause().getMessage()));
     }
 

public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java

@@ -62,6 +62,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         if (stub.getGenerateMD5())
             factory.setCreateMd5File(true);
         // Adjust max records in RAM.
+        // TODO -- this doesn't actually work because of a bug in Picard; do not use until fixed
         if(stub.getMaxRecordsInRam() != null)
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java

@@ -73,19 +73,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
     @Output(required=false, doc="Output bam")
     protected StingSAMFileWriter writer = null;
 
-    /**
-     * If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool
-     * may run out of memory.  We recommend that you additionally tell Java to use a temp directory with plenty of available
-     * space (by setting java.io.tempdir on the command-line).
-     */
-    @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false)
-    protected int MAX_RECORDS_IN_RAM = 500000;
-
-    public void initialize() {
-        // set up the output writer
-        if ( writer != null )
-            writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
-    }
+    public void initialize() {}
 
     private void emit(final SAMRecord read) {
         if ( writer != null )

public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

@@ -476,7 +476,6 @@ public class AlignmentUtils {
                     }
                     break;
                 case D:
-                case N:
                     if (!isDeletion) {
                         alignmentPos += elementLength;
                     } else {
@@ -498,6 +497,7 @@ public class AlignmentUtils {
                     break;
                 case H:
                 case P:
+                case N:
                     break;
                 default:
                     throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
@@ -516,16 +516,13 @@ public class AlignmentUtils {
             final int elementLength = ce.getLength();
 
             switch (ce.getOperator()) {
-                case I:
-                case S:
-                    break;
                 case D:
                 case N:
-                    alignmentLength += elementLength;
-                    break;
                 case M:
                     alignmentLength += elementLength;
                     break;
+                case I:
+                case S:
                 case H:
                 case P:
                     break;

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -373,13 +373,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     // --------------------------------------------------------------------------------------------------------------
     //
-    // testing SnpEff
+    // testing MinIndelFraction
     //
     // --------------------------------------------------------------------------------------------------------------
 
     final static String assessMinIndelFraction = baseCommandIndelsb37 + " -I " + validationDataLocation
             + "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";
-    
+
     @Test
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -403,4 +403,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
         executeTest("test minIndelFraction 1.0", spec);
     }
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing Ns in CIGAR
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Test
+    public void testNsInCigar() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
+                Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
+        executeTest("test calling on reads with Ns in CIGAR", spec);
+    }
 }