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Instead of addressing a position on the genome with a (reference_id, reference_start) tuple, we now use a single 64-bit `ref_start` integer. Advantages: - Slightly simpler code in some places - This should allow us to later reduce the number of bits needed for the reference coordinate. - A downside is that recovering the chromosome a position is on requires a binary search, but this only needs to be done essentially once when converting the output to SAM. The randstrobes generated in N regions change slightly because the pseudorandom nucleotide that the N wildcards are replaced with depends on the position, which is now relative to the start of the genome and not the start of the contig. Closes #227 See #597
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Instead of addressing a position on the genome with a (reference_id, reference_start) tuple, this uses a single 64-bit
ref_startinteger.Advantages:
A downside is that recovering the chromosome a position is on requires a binary search. This is in this draft only done once when converting the output to SAM and comes at essentially no cost.
However, there are a couple of places in the code (currently marked with a
TODOcomment) where we iterate over anchors or chains from left to right and where we would previously do something when transitioning from one contig to another. Now, we can theoretically 1) chain from one contig to another and 2) pair one read with one on another contig. We’ll have to think a bit more about how much we need to prevent this.The randstrobes generated in N regions change slightly because the pseudorandom nucleotide that the N wildcards are replaced with depends on the position, which is now relative to the start of the genome and not the start of the contig.
Closes #227
See #597