Inappropriate call if not paired read

[ziaursani]

I want to extract reads from a bam file but get the following error.

An exception occurred in the Actor thread Actor Thread 3
java.lang.IllegalStateException: Inappropriate call if not paired read
at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:901)

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Error is very long consisting of many lines. Can some one please help me with this?

thanks

Zia

[ziaursani]

I have used following statement for extraction of reads

java -jar build/libs/bazam.jar -bam test.bam > tmp.fastq

but I am getting error as described above.

[ghost]

Gave the tool a whirl. One of my alignment files threw this as well. The problem stems from this func returning false. Not totally sure what that func does yet.