From c0084c741bec3a89a911916582abc67d13efef3e Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 25 Apr 2012 11:23:16 -0400 Subject: [PATCH] Pilot BCF2 Implementation: Checkpointing the code * Not working yet, still very much a work-in-progress with lots of placeholders * Needed to check this in to enable possible collaboration, since it's going slower than anticipated and the conference deadline looms. --- .../sting/utils/exceptions/UserException.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index fd0cf7869..a1ffaea4f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -215,6 +215,12 @@ public class UserException extends ReviewedStingException { } } + public static class MalformedBCF2 extends UserException { + public MalformedBCF2( String message ) { + super(String.format("Malformed BCF2 file: %s", message)); + } + } + public static class MalformedVCFHeader extends UserException { public MalformedVCFHeader(String message) { super(String.format("The provided VCF file has a malformed header: %s", message));