From b46c85e8b40fbbb6740c8e117940c322c5c30a84 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 18 Jul 2012 15:26:31 -0400 Subject: [PATCH] More bad BAM file catching --- .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 870492e42..36f67add5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -122,7 +122,8 @@ public class CommandLineGATK extends CommandLineExecutable { exitSystemWithUserError(new UserException.TooManyOpenFiles()); // malformed BAM looks like a SAM file - if ( message.indexOf("Cannot use index file with textual SAM file") != -1 ) + if ( message.indexOf("Cannot use index file with textual SAM file") != -1 || + message.indexOf("Cannot retrieve file pointers within SAM text files") != -1 ) exitSystemWithSamError(t); // can't close tribble index when writing