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I want to use samtools to handle extremely high depth data. So I changed
iter->maxcnt = 8000;
in sam.c to 8000000.
Then it becomes very slow that it becomes not unusable.
I changed the same place in samtools 1.12 and it works like a charm.
Upon doing some debugging and compare the differences between 1.12 and 1.15,
I noticed that
ks_introsort(node, tv->n_nodes, tv->aux);
in bam_lpileup.c of 1.12 is replaced by
splaysort(node, tv->n_nodes, tv->aux);
in 1.15. After rename splaysort with
ks_introsort, 1.15 works as expected.
So my conclusion is that splaysort doesn't work
when maxcnt is large. Is this a bug or is it expected?
Why was ks_introsort replaced by splaysort in 1.15?