Clip Reads error - removing soft clipped bases of aligned read

Hi
I want to conduct some computations using a python script directly on some aligned bam files, and to do this I need to remove the soft clipped bases.
I tried to do this using clip reads with -CR HARDCLIP_BASES. I appreciate this is unsupported, but thought I'd report the bug anyway (see below).
Im using GaTK 2.7-2, and the file will work with -QT 30 -CR WRITE_N's so I don't think the file is the problem.
Is there any other way to remove the soft clipped bases portion of an aligned read with GaTK?
Thanks

INFO 08:29:31,022 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:29:31,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29
INFO 08:29:31,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 08:29:31,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 08:29:31,032 HelpFormatter - Program Args: -T ClipReads -I clipin.bam -R /u/ref.fa -CR HARDCLIP_BASES -o clippedout.bam -os clipstats.txt
INFO 08:29:31,032 HelpFormatter - Date/Time: 2013/10/24 08:29:31
INFO 08:29:31,032 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:29:31,032 HelpFormatter - --------------------------------------------------------------------------------
INFO 08:29:31,260 GenomeAnalysisEngine - Strictness is SILENT
INFO 08:29:31,390 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 08:29:31,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 08:29:31,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 08:29:31,544 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 08:29:31,551 GenomeAnalysisEngine - Done preparing for traversal
INFO 08:29:31,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 08:29:31,552 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 08:29:31,557 ReadShardBalancer$1 - Loading BAM index data
INFO 08:29:31,559 ReadShardBalancer$1 - Done loading BAM index data
INFO 08:30:01,990 ProgressMeter - chr28:18627293 1.31e+06 30.0 s 23.0 s 78.8% 38.0 s 8.0 s
INFO 08:30:13,397 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException
at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:51)
at net.sf.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:41)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:329)
at java.util.TimSort.sort(TimSort.java:203)
at java.util.Arrays.sort(Arrays.java:727)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:203)
at net.sf.samtools.util.SortingCollection.doneAdding(SortingCollection.java:175)
at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:250)
at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:43)
at net.sf.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:190)
at org.broadinstitute.sting.gatk.io.storage.SAMFileWriterStorage.close(SAMFileWriterStorage.java:99)
at org.broadinstitute.sting.gatk.io.OutputTracker.close(OutputTracker.java:130)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:118)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

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