On 20 Apr 2016, at 13:50, Anne Philippi <[email protected]> wrote:
> I find a bug when I used fastq option of samtools:
> anne$ samtools fastq -nO input_sorted.bam -1 output_1.fastq -2 output_2.fastq
> Segmentation fault
This is most likely a bug that strikes when processing an alignment record
doesn't have an OQ aux field [1]. It has been fixed in the source code
repository [2], and will be fixed in the upcoming samtools release. In the
meantime, you could apply the fix below yourself or, if perhaps your
input_sorted.bam in fact doesn't have any OQ tags at all, just remove the -O
option.
John
[1] https://github.com/samtools/samtools/issues/517
[2]
https://github.com/samtools/samtools/commit/59ab663fb9c98bd454432070fd09bc13b7c488bc
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