Fix off-by-one in HMM forward-backward posterior indexing#2519
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix off-by-one in HMM forward-backward posterior indexing#2519sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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The fwd-bwd probability array returned by hmm_get_fwd_bwd_prob() reserves positions [0..nstates-1] for initial state probabilities, so site i's posteriors start at (i+1)*nstates, not i*nstates. This is encoded in the HMM_PPROB macro but was not followed in: - vcfroh.c flush_viterbi(): fwd[i*2+state] -> fwd[(i+1)*2+state] - vcfcnv.c cnv_flush_viterbi(): fwd+isite*nstates -> fwd+(isite+1)*nstates Also fix hmm_set_tprob() in HMM.c: when called a second time with a different ntprob, the old tprob_arr was never reallocated because the guard was `if (!hmm->tprob_arr)`. Now compare against the previous ntprob_arr value and realloc when the size changes.
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Summary
fwd[i*2 + state]tofwd[(i+1)*2 + state]invcfroh.cand equivalent invcfcnv.c— thefwd[0..nstates-1]slot contains initial state probabilities, not site 0 posteriorshmm_set_tprob()inHMM.cto reallocatetprob_arrwhen called with a largerntprob, preventing heap buffer overflowTest plan