Make ampliconclip primer counts output deterministic#2081
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The primer-counts output was being written with references in the order stored in the hash table, which is pseudo-randomised by the hash function. To get a more stable ordering, keep a list of references in the order they appear in the bed file, and then iterate through that. ampliconstats uses the same bad file reading code, but already outputs in the order of references in the bam header, so the updated loader allows it to skip building the reference list from the bad file. (ampliconclip could in theory work the same way, but as it doesn't insist that all bed references need to be in the bam header, and outputs zero counts for the missing ones, it's simpler to go with the bed file ordering so the output doesn't change more than it needs to.)
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The primer-counts output was being written with references in the order stored in the hash table, which is pseudo-randomised by the hash function. To get a more stable ordering, keep a list of references in the order they appear in the bed file, and then iterate through that.
ampliconstatsuses the same bad file reading code, but already outputs in the order of references in the bam header, so the updated loader allows it to skip building the reference list from the bed file. (ampliconclipcould in theory work the same way, but as it doesn't insist that all bed references need to be in the bam header, and outputs zero counts for the missing ones, it's simpler to go with the bed file ordering so the output doesn't change more than it needs to.)