Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4270 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -26,6 +26,8 @@
 package org.broadinstitute.sting.commandline;
 
 import org.apache.log4j.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
@@ -350,17 +352,19 @@ public abstract class CommandLineProgram {
      * @param msg the message
      * @param e   the error
      */
-    public static void exitSystemWithError(final String msg, Exception e) {
+    public static void exitSystemWithError(String msg, final Exception e) {
         errorPrintf("------------------------------------------------------------------------------------------%n");
         errorPrintf("stack trace %n");
         e.printStackTrace();
 
         errorPrintf("------------------------------------------------------------------------------------------%n");
-        errorPrintf("A GATK RUNTIME ERROR has occurred:%n");
+        errorPrintf("A GATK RUNTIME ERROR has occurred (version %s):%n", CommandLineGATK.getVersionNumber());
         errorPrintf("%n");
         errorPrintf("Please visit to wiki to see if this is a known problem%n");
         errorPrintf("If not, please post the error, with stack trace, to the GATK forum%n");
         printDocumentationReference();
+        if ( msg == null ) // some exceptions don't have detailed messages
+            msg = "Code exception (see stack trace for error itself)";
         errorPrintf("%n");
         errorPrintf("MESSAGE: %s%n", msg.trim());
         errorPrintf("------------------------------------------------------------------------------------------%n");
@@ -368,8 +372,12 @@ public abstract class CommandLineProgram {
     }
 
     public static void exitSystemWithUserError(UserException e) {
+        if ( e.getMessage() == null )
+            throw new ReviewedStingException("UserException found with no message!", e);
+
         errorPrintf("------------------------------------------------------------------------------------------%n");
-        errorPrintf("A USER ERROR has occurred.  The invalid arguments or inputs must be corrected before the GATK can proceed%n");
+        errorPrintf("A USER ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
+        errorPrintf("The invalid arguments or inputs must be corrected before the GATK can proceed%n");
         errorPrintf("%n");
         errorPrintf("See the documentation (rerun with -h) for this tool to view allowable command-line argument.%n");
         printDocumentationReference();

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java

@@ -183,17 +183,17 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
         if ( outputFormat == OutputFormat.STATE_PER_BASE ) {
             out.println(state.toString());
+        }
+
+        // format is integrating
+        if ( integrator.state == null )
+            integrator.state = state;
+        else if ( state.getLocation().getStart() != integrator.state.getLocation().getStop() + 1 ||
+                integrator.state.changingState(state.getState()) ) {
+            out.println(integrator.state.toString());
+            integrator.state = state;
         } else {
-            // format is integrating
+            integrator.state.update(state.getLocation());
-            if ( integrator.state == null )
-                integrator.state = state;
-            else if ( state.getLocation().getStart() != integrator.state.getLocation().getStop() + 1 ||
-                    integrator.state.changingState(state.getState()) ) {
-                out.println(integrator.state.toString());
-                integrator.state = state;
-            } else {
-                integrator.state.update(state.getLocation());
-            }
         }
 
         return integrator;
@@ -207,7 +207,8 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
     public void onTraversalDone(Integrator result) {
         // print out the last state
         if ( result != null ) {
-            out.println(result.state.toString());
+            if ( outputFormat == OutputFormat.BED )  // get the last interval
+                out.println(result.state.toString());
 
             try {
                 PrintStream summaryOut = new PrintStream(summaryFile);
@@ -215,7 +216,6 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
                 for ( CalledState state : CalledState.values() ) {
                     summaryOut.printf("%30s %d%n", state, result.counts[state.ordinal()]);
                 }
-
                 summaryOut.close();
             } catch (FileNotFoundException e) {
                 throw new UserException.CouldNotCreateOutputFile(summaryFile, e);

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

@@ -32,14 +32,24 @@ import java.util.Arrays;
 public class CallableLociWalkerIntegrationTest extends WalkerTest {
     final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
 
+    final static String SUMMARY_MD5 = "ed4c255bb78313b8e7982127caf3d6c4";
+
     @Test
-    public void testCallableLociWalker1() {
+    public void testCallableLociWalkerBed() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("884c9c2d96419d990a708d2bd98fcefa", "ed4c255bb78313b8e7982127caf3d6c4"));
+                Arrays.asList("884c9c2d96419d990a708d2bd98fcefa", SUMMARY_MD5));
         executeTest("formatBed", spec);
     }
 
+    @Test
+    public void testCallableLociWalkerPerBase() {
+        String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
+        WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
+                Arrays.asList("fb4524f8b3b213060c0c5b85362b5902", SUMMARY_MD5));
+        executeTest("format_state_per_base", spec);
+    }
+    
     @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";