Add lazy bathalign, and --nofs to skip frameshift calibration - #15
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kevinmoran1988 wants to merge 1 commit into
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Add lazy bathalign, and --nofs to skip frameshift calibration#15kevinmoran1988 wants to merge 1 commit into
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BATH dropped HMMER's hmmalign driver but kept the whole tracealign engine (tracealign.c, p7_tracealign_*) compiled into libhmmer.a. bathalign is a 288-line driver over that existing engine -- no new alignment code. Alphabet-generic, as the engine is; BATH3/f is a superset of HMMER3/f, so it reads both .bhmm and .hmm. Amino output is byte-identical to HMMER 3.4 hmmalign across --mapali, --outformat, --trim, and Stockholm and afa output, for models from bathbuild and hmmbuild alike. Note that bathbuild itself is amino-only, so non-amino models must come from hmmbuild. c2ba68e made frameshift tau calculation unconditional and dropped --fs, but left the gating in place: evalues.c still guards FS3/FS5 on cfg_b->fs and p7_hmmfile.c still guards the header lines on hmm->fs. --nofs re-exposes that switch against the new default. Alignment never reads the frameshift stats, so for a model built to be aligned against, the calibration is pure waste -- and it is roughly half of bathbuild's runtime (57.9s -> 30.2s over 400 dipteraODB12 alignments). Where the model exists only for alignment, building it dominates the cost of aligning. A --nofs model is byte-identical to a full one apart from the omitted FS3/FS5 STATS and FRAMESHIFT PROB lines, and gives identical bathsearch results when --fs/--fsonly are not used. When they are, bathsearch fails cleanly on the unset stats rather than mis-scoring.
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BATH dropped HMMER's hmmalign driver but kept the whole tracealign engine (tracealign.c, p7_tracealign_*) compiled into libhmmer.a. bathalign is a 288-line driver over that existing engine -- no new alignment code. Alphabet-generic, as the engine is; BATH3/f is a superset of HMMER3/f, so it reads both .bhmm and .hmm. Amino output is byte-identical to HMMER 3.4 hmmalign across --mapali, --outformat, --trim, and Stockholm and afa output, for models from bathbuild and hmmbuild alike. Note that bathbuild itself is amino-only, so non-amino models must come from hmmbuild.
c2ba68e made frameshift tau calculation unconditional and dropped --fs, but left the gating in place: evalues.c still guards FS3/FS5 on cfg_b->fs and p7_hmmfile.c still guards the header lines on hmm->fs. --nofs re-exposes that switch against the new default.
Alignment never reads the frameshift stats, so for a model built to be aligned against, the calibration is pure waste -- and it is roughly half of bathbuild's runtime (57.9s -> 30.2s over 400 dipteraODB12 alignments). Where the model exists only for alignment, building it dominates the cost of aligning.
A --nofs model is byte-identical to a full one apart from the omitted FS3/FS5 STATS and FRAMESHIFT PROB lines, and gives identical bathsearch results when --fs/--fsonly are not used. When they are, bathsearch fails cleanly on the unset stats rather than mis-scoring.