From 0c2016c19a0ea1ced97ab0dccd893432e911f60f Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 15 Oct 2009 12:07:44 +0000
Subject: [PATCH] Improved error messages -- now easier to read, points to the
 GATK Error Messages wiki, and avoids double printing of stack traces

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../iterators/MergingSamRecordIterator2.java   | 10 ++++------
 .../utils/cmdLine/CommandLineProgram.java      | 18 +++++++++++-------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index bac7f1c52..265df5879 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -99,15 +99,13 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
      */
     private void checkSortOrder(SAMFileReader reader) {
         if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
+            String msg = String.format("The GATK requires your bam have %s sort order, but your BAM file header %s.  Continuing beyond this point is unsafe -- please update your BAM file to have a compatible sort order using samtools sort or Picard MergeBamFiles",
+                    this.sortOrder, reader.getFileHeader().getAttribute("SO") == null ? "is missing the SO sort order flag" : "has an SO flag set to " + reader.getFileHeader().getAttribute("SO"));
             if (reads.getSafetyChecking()) {
-                throw new PicardException("Files are not compatible with sort order: " + reader.getFileHeader().getSortOrder() +
-                        " vrs " + this.sortOrder + ".  Make sure that the SO flag in your bam file is set (The reader attribute for sort order equals "
-                        + reader.getFileHeader().getAttribute("SO") + " in this case).");
+                throw new PicardException(msg);
             } else if (!warnedUserAboutSortOrder) {
                 warnedUserAboutSortOrder = true;
-                Utils.warnUser("Files are not compatible with sort order: " + reader.getFileHeader().getSortOrder() +
-                        " vrs " + this.sortOrder + ".  Make sure that the SO flag in your bam file is set (The reader attribute for sort order equals "
-                        + reader.getFileHeader().getAttribute("SO") + " in this case).");
+                Utils.warnUser(msg);
             }
 
         }
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index 855e53e62..ff7ccb6e2 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -228,12 +228,12 @@ public abstract class CommandLineProgram {
                 }
             }
 
-            // regardless of what happens next, generate the header information
-            generateHeaderInformation(clp, args);
-
             // set the default logger level
             clp.setupLoggerLevel();
 
+            // regardless of what happens next, generate the header information
+            generateHeaderInformation(clp, args);
+
             // call the execute
             CommandLineProgram.result = clp.execute();
 
@@ -249,8 +249,8 @@ public abstract class CommandLineProgram {
             // we catch all exceptions here. if it makes it to this level, we're in trouble.  Let's bail!
             // TODO: what if the logger is the exception? hmm...
             logger.fatal("Exception caught by base Command Line Program, with message: " + e.getMessage());
-            logger.fatal("with cause: " + e.getCause());
-            e.printStackTrace();
+            if ( e.getCause() != null ) logger.fatal("with cause: " + e.getCause());
+            //e.printStackTrace();
             throw new RuntimeException(e);
         }
     }
@@ -338,8 +338,12 @@ public abstract class CommandLineProgram {
      */
     private static void printExitSystemMsg(final String msg) {
         System.out.printf("------------------------------------------------------------------------------------------%n");
-        System.out.printf("An error has occurred.  Please check your command line arguments for any typos or inconsistencies.%n%n");
-        System.out.printf("For assistance, please email us at gsahelp@broad.mit.edu, or review our documentation at http://www.broadinstitute.org/gsa/wiki.%n");
+        System.out.printf("The following error has occurred:%n%n");
+        System.out.printf("%s:%n%n", msg);
+        System.out.printf("Please check your command line arguments for any typos or inconsistencies.%n");
+        System.out.printf("Help for dealing with common GATK error messages can be found at http://www.broadinstitute.org/gsa/wiki/index.php/GATK_Error_Messages%n");
+        System.out.printf("  Or see our general docs documentation at http://www.broadinstitute.org/gsa/wiki%n");
+        System.out.printf("Please email us at gsahelp@broad.mit.edu to report bugs or with help resolving undocumented issues%n");
     }
 
     /**