Add base qualities for unaligned sequences in GAF output#88
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A note to other @vgteam contributors: The author of this pull request has on their Github profile that they work for BGI. I've been talking to the UC Santa Cruz export control office, because BGI is on a list of people who it is illegal for people in the US to export products or services to. The export control office is very keen that nobody in the US offer any technical review or technical feedback on this pull request, because they think that it would be illegal to do so. So please don't review this pull request, because reviewing it would be illegal. For more information, we can contact export@ucsc.edu. |
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Description
This PR ensures that base quality strings (QUAL) are preserved and included when writing unaligned sequences to GAF (Graph Alignment Format) file.
Motivation
Preserving sequence data integrity. Quality scores are critical for downstream variant calling, error correction, and filtering. Dropping these scores for unaligned reads makes it impossible to re-evaluate those sequences later without referring back to the original raw files.