Merge pull request #159 from broadinstitute/md_bqsr_ion

Trivial BQSR bug fixes and improvement

protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java

@@ -237,7 +237,9 @@ public class CycleCovariate implements StandardCovariate {
 
         // Unknown platforms
         else {
-            throw new UserException("The platform (" + read.getReadGroup().getPlatform() + ") associated with read group " + read.getReadGroup() + " is not a recognized platform. Implemented options are e.g. illumina, 454, and solid");
+            throw new UserException("The platform (" + read.getReadGroup().getPlatform()
+                    + ") associated with read group " + read.getReadGroup()
+                    + " is not a recognized platform. Allowable options are " + NGSPlatform.knownPlatformsString());
         }
     }
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java

@@ -82,7 +82,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                     " -I " + bam +
                     " -L " + interval +
                     args +
-                    " -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) +
+                    " -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : (reference.equals(b37KGReference) ? b37dbSNP129 : hg18dbSNP132)) +
                     " --allow_potentially_misencoded_quality_scores" +  // TODO -- remove me when we get new SOLiD bams
                     " -o %s" +
                     " -sortAllCols";
@@ -115,6 +115,8 @@ public class BQSRIntegrationTest extends WalkerTest {
                 {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "c1c3cda8caceed619d3d439c3990cd26")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "c9953f020a65c1603a6d71aeeb1b95f3")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5bfff0c699345cca12a9b33acf95588f")},
+                // make sure we work with ION torrent bam
+                {new BQSRTest(b37KGReference, privateTestDir + "iontorrent.bam", "20:10,000,000-10,200,000", "", "7375c7b692e76b651c278a9fb478fa1c")},
         };
     }
 
@@ -257,4 +259,17 @@ public class BQSRIntegrationTest extends WalkerTest {
                 UserException.class);
         executeTest("testPRFailWithLowMaxCycle", spec);
     }
+
+    @Test
+    public void testPRFailWithBadPL() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                " -T BaseRecalibrator" +
+                        " -R " + b37KGReference +
+                        " -I " + privateTestDir + "badPLForBQSR.bam" +
+                        " -L 1:10,000,000-10,200,000" +
+                        " -o %s",
+                1,
+                UserException.class);
+        executeTest("testPRFailWithBadPL", spec);
+    }
 }

public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java

@@ -28,6 +28,9 @@ package org.broadinstitute.sting.utils;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
+import java.util.LinkedList;
+import java.util.List;
+
 /**
  * A canonical, master list of the standard NGS platforms.  These values
  * can be obtained (efficiently) from a GATKSAMRecord object with the
@@ -117,4 +120,17 @@ public enum NGSPlatform {
     public static boolean isKnown(final String platform) {
         return fromReadGroupPL(platform) != UNKNOWN;
     }
+
+    /**
+     * Get a human-readable list of platform names
+     * @return the list of platform names
+     */
+    public static String knownPlatformsString() {
+        final List<String> names = new LinkedList<String>();
+        for ( final NGSPlatform pl : values() ) {
+            for ( final String name : pl.BAM_PL_NAMES )
+                names.add(name);
+        }
+        return Utils.join(",", names);
+    }
 }

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

@@ -72,6 +72,11 @@ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
         return mNGSPlatform;
     }
 
+    @Override
+    public String toString() {
+        return "GATKSAMReadGroupRecord @RG:" + getReadGroupId();
+    }
+
     ///////////////////////////////////////////////////////////////////////////////
     // *** The following methods are overloaded to cache the appropriate data ***//
     ///////////////////////////////////////////////////////////////////////////////