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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:
http://gatkforums.broadinstitute.org/gatk/discussion/4290/sam-bin-field-error-for-the-gatk-run
https://sourceforge.net/p/samtools/mailman/message/31853465/
https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/FixBAMFile.java

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?

Thank you

Issue · Github
by Sheila

Issue Number
1405
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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