double @HD header for bam

The @HD should be unique , no ? I don't get why it can be sorted and unsorted at the same time in a two lines header fashion.

samtools view -H sorted_test.bam |grep '@HD'
@HD VN:1.3  SO:coordinate
@HD VN:1.5  SO:unsorted GO:query

bam

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updated 2.6 years ago by Ram

• written 2.6 years ago by ZheFrench

How did that happen? Were two headers joined together at some step manually? Strictly speaking that breaks the SAM format spec since only one @HD line is expected though it is optional.

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written 2.6 years ago by GenoMax

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