diff --git a/release-notes/00CHECKLIST b/release-notes/HMMER/00CHECKLIST similarity index 100% rename from release-notes/00CHECKLIST rename to release-notes/HMMER/00CHECKLIST diff --git a/release-notes/ANNOUNCE-1.8 b/release-notes/HMMER/ANNOUNCE-1.8 similarity index 100% rename from release-notes/ANNOUNCE-1.8 rename to release-notes/HMMER/ANNOUNCE-1.8 diff --git a/release-notes/ANNOUNCE-2.1 b/release-notes/HMMER/ANNOUNCE-2.1 similarity index 100% rename from release-notes/ANNOUNCE-2.1 rename to release-notes/HMMER/ANNOUNCE-2.1 diff --git a/release-notes/HISTORY b/release-notes/HMMER/HISTORY similarity index 100% rename from release-notes/HISTORY rename to release-notes/HMMER/HISTORY diff --git a/release-notes/RELEASE-1.5 b/release-notes/HMMER/RELEASE-1.5 similarity index 100% rename from release-notes/RELEASE-1.5 rename to release-notes/HMMER/RELEASE-1.5 diff --git a/release-notes/RELEASE-1.6 b/release-notes/HMMER/RELEASE-1.6 similarity index 100% rename from release-notes/RELEASE-1.6 rename to release-notes/HMMER/RELEASE-1.6 diff --git a/release-notes/RELEASE-1.7 b/release-notes/HMMER/RELEASE-1.7 similarity index 100% rename from release-notes/RELEASE-1.7 rename to release-notes/HMMER/RELEASE-1.7 diff --git a/release-notes/RELEASE-1.8 b/release-notes/HMMER/RELEASE-1.8 similarity index 100% rename from release-notes/RELEASE-1.8 rename to release-notes/HMMER/RELEASE-1.8 diff --git a/release-notes/RELEASE-1.8.3 b/release-notes/HMMER/RELEASE-1.8.3 similarity index 100% rename from release-notes/RELEASE-1.8.3 rename to release-notes/HMMER/RELEASE-1.8.3 diff --git a/release-notes/RELEASE-1.8.4 b/release-notes/HMMER/RELEASE-1.8.4 similarity index 100% rename from release-notes/RELEASE-1.8.4 rename to release-notes/HMMER/RELEASE-1.8.4 diff --git a/release-notes/RELEASE-2.0 b/release-notes/HMMER/RELEASE-2.0 similarity index 100% rename from release-notes/RELEASE-2.0 rename to release-notes/HMMER/RELEASE-2.0 diff --git a/release-notes/RELEASE-2.1 b/release-notes/HMMER/RELEASE-2.1 similarity index 100% rename from release-notes/RELEASE-2.1 rename to release-notes/HMMER/RELEASE-2.1 diff --git a/release-notes/RELEASE-2.1.1 b/release-notes/HMMER/RELEASE-2.1.1 similarity index 100% rename from release-notes/RELEASE-2.1.1 rename to release-notes/HMMER/RELEASE-2.1.1 diff --git a/release-notes/RELEASE-2.1.2 b/release-notes/HMMER/RELEASE-2.1.2 similarity index 100% rename from release-notes/RELEASE-2.1.2 rename to release-notes/HMMER/RELEASE-2.1.2 diff --git a/release-notes/RELEASE-2.1.3 b/release-notes/HMMER/RELEASE-2.1.3 similarity index 100% rename from release-notes/RELEASE-2.1.3 rename to release-notes/HMMER/RELEASE-2.1.3 diff --git a/release-notes/RELEASE-2.2 b/release-notes/HMMER/RELEASE-2.2 similarity index 100% rename from release-notes/RELEASE-2.2 rename to release-notes/HMMER/RELEASE-2.2 diff --git a/release-notes/RELEASE-2.3 b/release-notes/HMMER/RELEASE-2.3 similarity index 100% rename from release-notes/RELEASE-2.3 rename to release-notes/HMMER/RELEASE-2.3 diff --git a/release-notes/RELEASE-2.3.1 b/release-notes/HMMER/RELEASE-2.3.1 similarity index 100% rename from release-notes/RELEASE-2.3.1 rename to release-notes/HMMER/RELEASE-2.3.1 diff --git a/release-notes/RELEASE-2.3.2 b/release-notes/HMMER/RELEASE-2.3.2 similarity index 100% rename from release-notes/RELEASE-2.3.2 rename to release-notes/HMMER/RELEASE-2.3.2 diff --git a/release-notes/RELEASE-2.3.3 b/release-notes/HMMER/RELEASE-2.3.3 similarity index 100% rename from release-notes/RELEASE-2.3.3 rename to release-notes/HMMER/RELEASE-2.3.3 diff --git a/release-notes/RELEASE-3.0 b/release-notes/HMMER/RELEASE-3.0 similarity index 100% rename from release-notes/RELEASE-3.0 rename to release-notes/HMMER/RELEASE-3.0 diff --git a/release-notes/RELEASE-3.0a2 b/release-notes/HMMER/RELEASE-3.0a2 similarity index 100% rename from release-notes/RELEASE-3.0a2 rename to release-notes/HMMER/RELEASE-3.0a2 diff --git a/release-notes/RELEASE-3.0b1 b/release-notes/HMMER/RELEASE-3.0b1 similarity index 100% rename from release-notes/RELEASE-3.0b1 rename to release-notes/HMMER/RELEASE-3.0b1 diff --git a/release-notes/RELEASE-3.0b2 b/release-notes/HMMER/RELEASE-3.0b2 similarity index 100% rename from release-notes/RELEASE-3.0b2 rename to release-notes/HMMER/RELEASE-3.0b2 diff --git a/release-notes/RELEASE-3.0b3 b/release-notes/HMMER/RELEASE-3.0b3 similarity index 100% rename from release-notes/RELEASE-3.0b3 rename to release-notes/HMMER/RELEASE-3.0b3 diff --git a/release-notes/RELEASE-3.0rc1 b/release-notes/HMMER/RELEASE-3.0rc1 similarity index 100% rename from release-notes/RELEASE-3.0rc1 rename to release-notes/HMMER/RELEASE-3.0rc1 diff --git a/release-notes/RELEASE-3.0rc2 b/release-notes/HMMER/RELEASE-3.0rc2 similarity index 100% rename from release-notes/RELEASE-3.0rc2 rename to release-notes/HMMER/RELEASE-3.0rc2 diff --git a/release-notes/RELEASE-3.1b1 b/release-notes/HMMER/RELEASE-3.1b1 similarity index 100% rename from release-notes/RELEASE-3.1b1 rename to release-notes/HMMER/RELEASE-3.1b1 diff --git a/release-notes/RELEASE-3.1b2 b/release-notes/HMMER/RELEASE-3.1b2 similarity index 100% rename from release-notes/RELEASE-3.1b2 rename to release-notes/HMMER/RELEASE-3.1b2 diff --git a/release-notes/RELEASE-3.1rc1 b/release-notes/HMMER/RELEASE-3.1rc1 similarity index 100% rename from release-notes/RELEASE-3.1rc1 rename to release-notes/HMMER/RELEASE-3.1rc1 diff --git a/release-notes/RELEASE-3.2 b/release-notes/HMMER/RELEASE-3.2 similarity index 100% rename from release-notes/RELEASE-3.2 rename to release-notes/HMMER/RELEASE-3.2 diff --git a/release-notes/RELEASE-3.2.1 b/release-notes/HMMER/RELEASE-3.2.1 similarity index 100% rename from release-notes/RELEASE-3.2.1 rename to release-notes/HMMER/RELEASE-3.2.1 diff --git a/release-notes/RELEASE-3.3.1.md b/release-notes/HMMER/RELEASE-3.3.1.md similarity index 100% rename from release-notes/RELEASE-3.3.1.md rename to release-notes/HMMER/RELEASE-3.3.1.md diff --git a/release-notes/RELEASE-3.3.2.md b/release-notes/HMMER/RELEASE-3.3.2.md similarity index 100% rename from release-notes/RELEASE-3.3.2.md rename to release-notes/HMMER/RELEASE-3.3.2.md diff --git a/release-notes/RELEASE-3.3.md b/release-notes/HMMER/RELEASE-3.3.md similarity index 100% rename from release-notes/RELEASE-3.3.md rename to release-notes/HMMER/RELEASE-3.3.md diff --git a/release-notes/RELEASE-1.0.md b/release-notes/RELEASE-1.0.md new file mode 100644 index 00000000..289bfeab --- /dev/null +++ b/release-notes/RELEASE-1.0.md @@ -0,0 +1,15 @@ +# BATH 1.0 release notes (Feb 2025) + +BATH 1.0 is the first release of BATH. It is essentially a fork of the +HMMER 3.4 code base, extended to perform translated search (protein +query against DNA target) directly. bathsearch takes a protein query +and a DNA target and reports hits in the coordinates of the target +DNA. There is no need to compute ORFs in all six translation frames +first, and no bookkeeping to map hits on those ORFs back to the +encoding genome. + +BATH also introduces novel frameshift-aware algorithms to detect +frameshift-inducing nucleotide insertions and deletions (indels). + +Programs in this release: bathbuild, bathconvert, bathfetch, bathstat, +and bathsearch. diff --git a/release-notes/RELEASE-2.0.md b/release-notes/RELEASE-2.0.md new file mode 100644 index 00000000..cbc7db07 --- /dev/null +++ b/release-notes/RELEASE-2.0.md @@ -0,0 +1,63 @@ +# BATH 2.0 release notes (May 2026) + +This directory holds BATH release notes. The notes for HMMER, from +which BATH is derived, are in the HMMER/ subdirectory. + + +## new features: + +* Spliced alignment. With the new `--splice` option, bathsearch + models intron splice sites (GT-AG, GC-AG, and AT-AC, with empirical + signal probabilities) and joins ORF hits across introns into + gene-level exon chains. The new `--exontblout ` option writes a + tabular file with one row per exon, and `--min_intron ` and + `--max_intron ` bound the intron lengths considered. A single + search cannot yet combine `--splice` and `--fs`. + +* SIMD acceleration of the frameshift-aware and spliced dynamic + programming kernels: AVX, AVX2, and AVX-512 implementations on x86, + and NEON on ARM, with automatic fallback to SSE where newer + intrinsics are unavailable. + +* A local bias filtering stage that recomputes composition bias over + just the aligned region, to better reject short repetitive false + positives. + +* A new Forward-stage filter (F4): at least one ORF in a window must + pass a standard Forward P-value threshold before bathsearch + promotes the window to the frameshift or spliced Forward stage. + +* Reworked ORF and DNA window construction, including handling of + degenerate nucleotides: ORFs no longer span long runs of degenerate + nucleotides, and split codons in spliced alignments may contain + them. + + +## changes: + +* Frameshift-aware alignment is now opt-in. By default bathsearch + performs translated (non-frameshifted) search; `--fs` enables the + frameshift-aware pipeline. The frameshift probability is now a fixed + internal constant set at model build/convert time, and is no longer + a tunable option. + +* BATH 2.0 does not read model files built by BATH 1.x; run + bathconvert to update them. bathsearch prints this instruction when + it reads an old file. + +* Removed: PowerPC VMX/AltiVec support; MPI support in bathbuild; the + bathsearch bias-filter tuning options `--B1`, `--B2`, `--B3`; and + the envelope-coordinate columns in search output. + + +## bug fixes: + +* Fixed a bug in local bias filtering. + +* Reduced memory use by reusing dynamic programming matrices (the + Backward matrix for posterior probabilities, and the Forward matrix + for Viterbi alignment when posterior decoding fails). + + +For more information, see the +[git log](https://github.com/TravisWheelerLab/BATH/commits/main).