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Guard mappers from truncated quality strings#4492

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adamnovak merged 6 commits intomasterfrom
guard-quality
Jan 17, 2025
Merged

Guard mappers from truncated quality strings#4492
adamnovak merged 6 commits intomasterfrom
guard-quality

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Changelog Entry

To be copied to the draft changelog by merger:

  • vg giraffe, vg mpmap, and vg map will now fail early with an error when encountering a read with a quality string of the wrong length (as from a truncated FASTQ)

Description

This should protect users from weirder internal errors when FASTQs get truncated. It will print errors like:

error [vg::alignment.cpp]: Read m84039_230418_213342_s3/240455777/ccs has 20540 bases of sequence but only 18671 base quality values. Was the quality information truncated?

@adamnovak adamnovak merged commit 6554344 into master Jan 17, 2025
@faithokamoto faithokamoto deleted the guard-quality branch August 21, 2025 19:01
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