From 060c7ce8aea6939c77aca62d87e8f5665bab1d80 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 10 Nov 2011 14:03:22 -0500 Subject: [PATCH] It wouldn't harm integrationtests if we had our logic right... :-) --- .../sting/gatk/filters/MalformedReadFilter.java | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java index 46d28185b..37a6cfc36 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java @@ -129,8 +129,14 @@ public class MalformedReadFilter extends ReadFilter { * @return true if they have the same number. False otherwise. */ private static boolean checkMismatchingBasesAndQuals(SAMRecord read, boolean filterMismatchingBaseAndQuals) { - if (!filterMismatchingBaseAndQuals) - throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +" [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals"); - return (read.getReadLength() == read.getBaseQualities().length); + boolean result; + if (read.getReadLength() == read.getBaseQualities().length) + result = true; + else if (filterMismatchingBaseAndQuals) + result = false; + else + throw new UserException.MalformedBAM(read, String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals]", read.getReadName(), read.getReadLength(), read.getBaseQualities().length)); + + return result; } }