HISAT alignment, sam, bam, sorted.bam steps

[SAMtoBAM]

Hi there

I am trying braker3 at the moment and see that the RNAseq alignment step appears to perform the alignment to sam, compression to bam and sorting in 3 separate steps. If I am not mistaken the sorting step is performed during bam conversion, also you can directly pipe the alignment output directly to samtools sort therefore skipping the compression step Although it is clearly not going to improve the annotation outcome, it should certainly speed up these initial steps.

Thanks

[changchuanjun]

@SAMtoBAM 👍👍👍，I aggre with you, But I think this is a systematic work, and if the authors update the version, I assume they will accept the suggestion