ropebwt3-3.9 (r259)

Notable changes:

• New feature: with option -p, the build command optionally runs partial
  suffix array construction and BWT merge at the same time.

(3.9 30 November 2024, r259)

Ropebwt3-3.8 (r249)

Notable changes:

• Improvement: a faster algorithm to locate a subset of positions in a suffix
  array interval. Given m highly similar genomes, the expected time is O(s/m)
  where s is the suffix array sample rate.

• New feature: added option mem -p to optionally output a semi-random subset
  of SMEM positions.

• New feature: added auxiliary script rb3tools.js for generating mappability
  filter and for simple SNP calling.

(3.8: 18 October 2024, r249)

Ropebwt3-3.7 (r226)

In this release, the sw command outputs the cs tag and can report all
end-to-end hits in a compact format with option --all-e2e.

(3.7: 17 September 2024, r226)

Ropebwt3-3.6 (r217)

Notable changes:

• Bugfix: fixed a rare assertion failure.

• Improvement: the stat command now works with the FMR format (#1).

• Breaking: the hapdiv command now gives the counts of alleles up to edit
  distance five.

(3.6: 10 September 2024, r217)

Ropebwt3-3.5 (r203)

Notable changes:

• New feature: added the end-to-end mode (-e) to sw. It outputs local
  haplotypes similar to the entire query string.

• New feature: hapdiv command to estimate local haplotype diversity. It
  applies the end-to-end mode to slide 101-mers and reports the number of
  haplotypes within certain edit distance threshold.

• Improvement: ~30% faster BWT construction for large datasets.

• Breaking: in sw, changed the default scoring to the BLASTN scoring

(3.5: 31 August 2024, r203)

Ropebwt3-3.4 (r167)

Notable changes:

• Improvement: in sw, removed out-of-band cells earlier. This speeds up
  BWA-SW by 20%.

• Improvement: sw now computes positions in each thread. This improves the
  multi-threading performance for short queries.

• Bugfix: with mem, ambiguous bases in query caused segmentation fault.
  Ropebwt3 now converts ambiguous bases to "A". This does not affect sw.

• Breaking: removed greedy MEM

(3.4: 20 August 2024, r167)

Ropebwt3-3.3 (r149)

Notable changes in the sw command:

• New feature: option to try SW only when there is a long MEM. This is not
  enabled by default.

• New feature: option to output unmapped reads in PAF

• Bugfix: backtracking the F state could be wrong in corner cases

• Bugfix: coordinates on the reverse strand were not flipped in PAF

• Breaking: don't output the reference sequence in the rs tag by default

Other new features:

• New feature: added the stat command to report the number of runs. Only
  working for the FMD format for now.

• New feature: added --min-gap to the mem command to output regions not
  covered by long MEMs.

(3.3: 6 August 2024, r149)

Ropebwt3-3.2 (r137)

This release implemented several critical features for sequence search:

• New feature: Travis Gagie's algorithm for finding long MEMs. It is faster
  and now the default algorithm for MEM finding.

• New feature: BWA-SW for local alignment. This algorithm allows mismatches
  and short gaps.

• New feature: sampled suffix array for obtaining mapping positions.

• Breaking: renamed match to mem.

(3.2: 23 July 2024, r137)

Ropebwt3-3.1 (r77)

Notable changes:

• New feature: the match command supports multi-threading.

• Improvement: generating suffix arrays (SA) with libsais16x64, a new addition
  to libsais by @IlyaGrebnov. libsais16x64 is faster and uses less memory for
  multi-string SA construction than libsais64. This reduces the peak memory of
  ropebwt3 for human genomes.

(3.1: 15 June 2024, r77)

Ropebwt3-3.0 (r67)

First release