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Test-drive the GATK tools and Best Practices pipelines on Terra
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Debug message from htsjdk.samtools.FixBAMFile
I use htsjdk.samtools.FixBAMFile to fix occasional bin errors when use BWA-backtrack with old datasets:
java -cp htsjdk.jar htsjdk.samtools.FixBAMFile source.bam fixed.bam
This bin fixing issue is discussed in more details here:
When I use an old htsjdk version (i.e. htsjdk-1.133.jar) it fixes bam files without any messages. When I use the newer htsjdk versions (e.g. htsjdk-2.4.1.jar or htsjdk-2.7.0.jar) they apparently do the job, but report a debug message like the following:
DEBUG 2016-11-02 20:03:38 BlockCompressedOutputStream Using deflater: Deflater
What is this message about? Is it OK to use the versions producing such message?