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NEWS.md

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Release 3.9-r259 (30 November 2024)

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)

Release 3.8-r249 (18 October 2024)

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)

Release 3.7-r226 (17 September 2024)

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)

Release 3.6-r217 (10 September 2024)

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)

Release 3.5-r203 (31 August 2024)

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)

Release 3.4-r167 (20 August 2024)

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)

Release 3.3-r149 (6 August 2024)

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)

Release 3.2-r137 (23 July 2024)

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)

Release 3.1-r77 (15 June 2024)

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)

Release 3.0-r67 (11 June 2024)

First release.