v0.12.6

Buildable Source Tarball: wfmash-v0.12.6.tar.gz

What's Changed

• Add error when the index is empty by @bkille in #219
• Don't include endpoint in L2 range by @bkille in #220
• make the script more robust by @AndreaGuarracino in #222

Full Changelog: v0.8.4...v0.12.6

mashmap3 and more

Buildable Source Tarball: wfmash-v0.12.5.tar.gz

This closes an integration process that pulled in minmer-based mashmap3. The CLI has been updated to make it easy to run large all-to-all alignment jobs in parts on a cluster using the -P[pfx], --target-prefix=[pfx] and target list options. We have included a new --one-to-one mapping option that ensures symmetry between mapping query and target ranges (they must each be the best option).

wfmash 0.10.5 - Prefisso

Buildable Source Tarball: wfmash-v0.10.5.tar.gz

This release fixes the issue of getting N exact mappings when less than N mappings are requested. Moreover, now it is possible to specify a prefix, or a list of sequences, to filter target sequences. Finally, wfmash building with cmake is improved.

This introduces:

• fix the build to use cmake everywhere #180 #181 by @ekg
• avoid exact mapping duplicates #182 by @ekg
• subset targets by list or prefix #183 by @ekg

wfmash 0.10.4 - Euristico

Buildable Source Tarball: wfmash-v0.10.4.tar.gz

This release strongly improves the runtime performance of the alignments without affecting their accuracy (in all alignments tested). We apply an heuristic BiWFlign/BiWFλ and the mapping chaining is less aggressive, improving also the runtime during the mapping phase with the price of getting a bit more mappings.

This introduces:

• make gcc 11.4.0 and 13.1.0 happy #177 by @AndreaGuarracino
• update WFA2-lib #179 by @AndreaGuarracino
• Heuristic BiWFλ and less aggressive mapping chaining #176 by @AndreaGuarracino

wfmash 0.10.3 - Vendetta

Buildable Source Tarball: wfmash-v0.10.3.tar.gz

This release reimplements the bidirectional wfλ, with a very tiny, but consistent, performance improvement.

This introduces:

• Fix versioning #170 by @AndreaGuarracino
• Refactored BiWFλ (BiWFlambda) #169 by @smarco @AndreaGuarracino

wfmash 0.10.2 - Eseguito

Buildable Source Tarball: wfmash-v0.10.2.tar.gz

Minor change. This release is used to update the conda release.

This introduces:

• executable scripts #167 by @AndreaGuarracino

wfmash 0.10.1 - Bibidirezionale

Buildable Source Tarball: wfmash-v0.10.1.tar.gz

Minor changes. This release is used to update the conda release.

This introduces:

• always emit long version format #164 by @AndreaGuarracino
• add -O/--invert-filtering parameter #165 by @AndreaGuarracino

wfmash 0.10.0 - Bidirezionale

Buildable Source Tarball: wfmash-v0.10.0.tar.gz

The main change is the introduction of the bidirectional wfλ, which allows a full exploration of the high-order alignment matrix without blowing up with the memory. This leads to more and better anchors that tend to simplify the alignments during the patching phase, therefore even improving the runtime.

This introduces (in reverse chronological order):

• WFA2-lib update #148 #149 by @smarco @AndreaGuarracino
• bug fixes in reduction #151 #152 #155 by @AndreaGuarracino
• implementation of BiWFλ, bidirectional flavor of wfλ #153 by @AndreaGuarracino
• better head and tail patchings #158 by @AndreaGuarracino
• fix trace plot for short/medium sequences #159 by @AndreaGuarracino
• tune parameter for high divergence #160 by @AndreaGuarracino

Citazioni

Fixes several bugs (including a memory leak), updates WFA2-lib and documentation.

wfmash 0.9.1 - Mutamento

Buildable Source Tarball: wfmash-v0.9.1.tar.gz

Major changes in this release are an improvement of mapping merging and updates to the base level alignment code which allow for exact patching of large gaps in the alignment traceback.

Fixes and updates:

• signed 32-bit overflow on large plant chromosomes
• avoid overfiltering due to equal scores on multiple targets
• mapping min-hash sparsification (hash mapping struct and keep hashes below a threshold) to sample from very large all-vs-all alignment problems
• simplify mapping merging and cap the merge distance at the wavefront reduction distance used in wflign
• reduce wavefronts while following the diagonal, to handle wflign of sequences with very different lengths without alignment failure
• universal minimizer spaced seeds: ALeS seeds now work with unbiased universal minimizer scheme
• integration of WFA2-lib and application of biWFA for O(s)-memory patching of large gaps in alignment traceback