minimap2 0.2.31.0 → 1.2.31.0

data/ext/minimap2/NEWS.md

@@ -1,1022 +0,0 @@
-Release 2.31-r1302 (19 May 2026)
---------------------------------
-
-Notable changes to minimap2:
-
- * Bugfix: supplementary and secondary alignments were occasionally flagged
-   incorrectly.
-
- * Bugfix: Smith-Waterman alignment for inversion alignment led to an
-   out-of-bound access in rare cases.
-
-Changes to paftools.js:
-
- * New feature: new `sim2bed` subcommand to get a BED file from simulated
-   reads.
-
- * New feature: new `badread2fa` subcommand to format reads simulated by
-   the Badread simulator.
-
-Change to the python binding:
-
- * New feature: mappy optionally writes the `ds` tag.
-
- * Bugfix: a use-after-free error (#1345)
-
-The two bugs in minimap2 had existed for years. They were caught by Jeremy Wang
-at UNC when he ported minimap2 to Rust. Due to the two bug fixes, this version
-occasionally produces alignment different from the last version.
-
-(2.31: 19 May 2026, r1302)
-
-
-
-Release 2.30-r1287 (15 June 2025)
----------------------------------
-
-Notable changes:
-
- * Improvement: consolidated `--spsc`.
-
- * Deprecation: subcommands `splice2bed`, `gff2bed`, `gff2junc`, `junceval` and
-   `exoneval` in `paftools.js` are deprecated by minigff. They will remain
-   indefinitely for backward compatibility.
-
-(2.30: 15 June 2025, r1287)
-
-
-
-Release 2.29-r1283 (18 April 2025)
-----------------------------------
-
-Notable changes to minimap2:
-
- * New feature: added the `splice:sr` preset for short RNA-seq read alignment.
-   Users may use `-j` to specify known gene annotation to improve spliced
-   alignment close to the ends of short reads. Also added `--write-junc` and
-   `--pass1` for 2-pass short-read RNA-seq alignment.
-
- * Experimental feature: read splice scores from a file specified by `--spsc`
-   and consider the scores during base alignment. The feature makes it possible
-   to apply advanced splice models and to improve spliced alignment.
-
- * Change: adjusted the mapping quality calculation for spliced alignment.
-
- * Bugfixes: a) missing overlap alignment when base alignment is requested
-   (#969); b) incorrect summary information for long genomes (#1192); c)
-   missing parameter check for `--score-N` (#1226).
-
- * Improvement: a) warn about absent junction files (#1229); b) report an error
-   if a wrong preset prefixed with "splice" is specified (#589).
-
-Notable changes to mappy:
-
- * Improvement: allow passing read name (#1260)
-
- * Improvement: exposed score for ambiguous bases (#1240)
-
-Minimap2 now supports short/long genomic/RNA-seq read alignment along with
-contig alignment and all-vs-all read overlapping. It produces identical genomic
-long-read or contig alignment to v2.27. Short genomic read alignment and the
-mapping quality of long RNA-seq read alignment may slightly differ in very rare
-cases.
-
-(2.29: 18 April 2025, r1283)
-
-
-
-Release 2.28-r1209 (27 March 2024)
-----------------------------------
-
-Notable changes to minimap2:
-
- * Bugfix: `--MD` was not working properly due to the addition of `--ds` in the
-   last release (#1181 and #1182).
-
- * New feature: added an experimental preset `lq:hqae` for aligning accurate
-   long reads back to their assembly. It has been observed that `map-hifi` and
-   `lr:hq` may produce many wrong alignments around centromeres when accurate
-   long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid
-   assembly constructed from them. This new preset produces much more accurate
-   alignment. It is still experimental and may be subjective to changes in
-   future.
-
- * Change: reduced the default `--cap-kalloc` to 500m to lower the peak
-   memory consumption (#855).
-
-Notable changes to mappy:
-
- * Bugfix: mappy option struct was out of sync with minimap2 (#1177).
-
-Minimap2 should output identical alignments to v2.27.
-
-(2.28: 27 March 2024, r1209)
-
-
-
-Release 2.27-r1193 (12 March 2024)
-----------------------------------
-
-Notable changes to minimap2:
-
- * New feature: added the `lr:hq` preset for accurate long reads at ~1% error
-   rate. This was suggested by Oxford Nanopore developers (#1127). It is not
-   clear if this preset also works well for PacBio HiFi reads.
-
- * New feature: added the `map-iclr` preset for Illumina Complete Long Reads
-   (#1069), provided by Illumina developers.
-
- * New feature: added option `-b` to specify mismatch penalty for base
-   transitions (i.e. A-to-G or C-to-T changes).
-
- * New feature: added option `--ds` to generate a new `ds:Z` tag that
-   indicates uncertainty in INDEL positions. It is an extension to `cs`. The
-   `mgutils-es6.js` script in minigraph parses `ds`.
-
- * Bugfix: avoided a NULL pointer dereference (#1154). This would not have an
-   effect on most systems but would still be good to fix.
-
- * Bugfix: reverted the value of `ms:i` to pre-2.22 versions (#1146). This was
-   an oversight. See fcd4df2 for details.
-
-Notable changes to paftools.js and mappy:
-
- * New feature: expose `bw_long` to mappy's Aligner class (#1124).
-
- * Bugfix: fixed several compatibility issues with k8 v1.0 (#1161 and #1166).
-   Subcommands "call", "pbsim2fq" and "mason2fq" were not working with v1.0.
-
-Minimap2 should output identical alignments to v2.26, except the ms tag.
-
-(2.27: 12 March 2024, r1193)
-
-
-
-Release 2.26-r1175 (29 April 2023)
-----------------------------------
-
-Fixed the broken Python package. This is the only change.
-
-(2.26: 25 April 2023, r1173)
-
-
-
-Release 2.25-r1173 (25 April 2023)
-----------------------------------
-
-Notable changes:
-
- * Improvement: use the miniprot splice model for RNA-seq alignment by default.
-   This model considers non-GT-AG splice sites and leads to slightly higher
-   (<0.1%) accuracy and sensitivity on real human data.
-
- * Change: increased the default `-I` to `8G` such that minimap2 would create a
-   uni-part index for a pair of mammalian genomes. This change may increase the
-   memory for all-vs-all read overlap alignment given large datasets.
-
- * New feature: output the sequences in secondary alignments with option
-   `--secondary-seq` (#687).
-
- * Bugfix: --rmq was not parsed correctly (#1010)
-
- * Bugfix: possibly incorrect coordinate when applying end bonus to the target
-   sequence (#1025). This is a ksw2 bug. It does not affect minimap2 as
-   minimap2 is not using the affected feature.
-
- * Improvement: incorporated several changes for better compatibility with
-   Windows (#1051) and for minimap2 integration at Oxford Nanopore Technologies
-   (#1048 and #1033).
-
- * Improvement: output the HD-line in SAM output (#1019).
-
- * Improvement: check minimap2 index file in mappy to prevent segmentation
-   fault for certain indices (#1008).
-
-For genomic sequences, minimap2 should give identical output to v2.24.
-Long-read RNA-seq alignment may occasionally differ from previous versions.
-
-(2.25: 25 April 2023, r1173)
-
-
-
-Release 2.24-r1122 (26 December 2021)
--------------------------------------
-
-This release improves alignment around long poorly aligned regions. Older
-minimap2 may chain through such regions in rare cases which may result in
-missing alignments later. The issue has become worse since the the change of
-the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
-release provides a better solution with a X-drop-like heuristic and by enabling
-two-bandwidth chaining in the assembly mode.
-
-(2.24: 26 December 2021, r1122)
-
-
-
-Release 2.23-r1111 (18 November 2021)
--------------------------------------
-
-Notable changes:
-
- * Bugfix: fixed missing alignments around long inversions (#806 and #816).
-   This bug affected v2.19 through v2.22.
-
- * Improvement: avoid extremely long mapping time for pathologic reads with
-   highly repeated k-mers not in the reference (#771). Use --q-occ-frac=0
-   to disable the new heuristic.
-
- * Change: use --cap-kalloc=1g by default.
-
-(2.23: 18 November 2021, r1111)
-
-
-
-Release 2.22-r1101 (7 August 2021)
-----------------------------------
-
-When choosing the best alignment, this release uses logarithm gap penalty and
-query-specific mismatch penalty. It improves the sensitivity to long INDELs in
-repetitive regions.
-
-Other notable changes:
-
- * Bugfix: fixed an indirect memory leak that may waste a large amount of
-   memory given highly repetitive reference such as a 16S RNA database (#749).
-   All versions of minimap2 have this issue.
-
- * New feature: added --cap-kalloc to reduce the peak memory. This option is
-   not enabled by default but may become the default in future releases.
-
-Known issue:
-
- * Minimap2 may take a long time to map a read (#771). So far it is not clear
-   if this happens to v2.18 and earlier versions.
-
-(2.22: 7 August 2021, r1101)
-
-
-
-Release 2.21-r1071 (6 July 2021)
---------------------------------
-
-This release fixed a regression in short-read mapping introduced in v2.19
-(#776). It also fixed invalid comparisons of uninitialized variables, though
-these are harmless (#752). Long-read alignment should be identical to v2.20.
-
-(2.21: 6 July 2021, r1071)
-
-
-
-Release 2.20-r1061 (27 May 2021)
---------------------------------
-
-This release fixed a bug in the Python module and improves the command-line
-compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset,
-users would get alignments more fragmented than v2.18. This could be an issue
-for existing pipelines specifying `-r`. This release resolves this issue.
-
-(2.20: 27 May 2021, r1061)
-
-
-
-Release 2.19-r1057 (26 May 2021)
---------------------------------
-
-This release includes a few important improvements backported from unimap:
-
- * Improvement: more contiguous alignment through long INDELs. This is enabled
-   by the minigraph chaining algorithm. All `asm*` presets now use the new
-   algorithm. They can find INDELs up to 100kb and may be faster for
-   chromosome-long contigs. The default mode and `map*` presets use this
-   algorithm to replace the long-join heuristic.
-
- * Improvement: better alignment in highly repetitive regions by rescuing
-   high-occurrence seeds. If the distance between two adjacent seeds is too
-   large, attempt to choose a fraction of high-occurrence seeds in-between.
-   Minimap2 now produces fewer clippings and alignment break points in long
-   satellite regions.
-
- * Improvement: allow to specify an interval of k-mer occurrences with `-U`.
-   For repeat-rich genomes, the automatic k-mer occurrence threshold determined
-   by `-f` may be too large and makes alignment impractically slow. The new
-   option protects against such cases. Enabled for `asm*` and `map-hifi`.
-
- * New feature: added the `map-hifi` preset for maping PacBio High-Fidelity
-   (HiFi) reads.
-
- * Change to the default: apply `--cap-sw-mem=100m` for genomic alignment.
-
- * Bugfix: minimap2 could not generate an index file with `-xsr` (#734).
-
-This release represents the most signficant algorithmic change since v2.1 in
-2017. With features backported from unimap, minimap2 now has similar power to
-unimap for contig alignment. Unimap will remain an experimental project and is
-no longer recommended over minimap2. Sorry for reverting the recommendation in
-short time.
-
-(2.19: 26 May 2021, r1057)
-
-
-
-Release 2.18-r1015 (9 April 2021)
----------------------------------
-
-This release fixes multiple rare bugs in minimap2 and adds additional
-functionality to paftools.js.
-
-Changes to minimap2:
-
- * Bugfix: a rare segfault caused by an off-by-one error (#489)
-
- * Bugfix: minimap2 segfaulted due to an uninitilized variable (#622 and #625).
-
- * Bugfix: minimap2 parsed spaces as field separators in BED (#721). This led
-   to issues when the BED name column contains spaces.
-
- * Bugfix: minimap2 `--split-prefix` did not work with long reference names
-   (#394).
-
- * Bugfix: option `--junc-bonus` didn't work (#513)
-
- * Bugfix: minimap2 didn't return 1 on I/O errors (#532)
-
- * Bugfix: the `de:f` tag (sequence divergence) could be negative if there were
-   ambiguous bases
-
- * Bugfix: fixed two undefined behaviors caused by calling memcpy() on
-   zero-length blocks (#443)
-
- * Bugfix: there were duplicated SAM @SQ lines if option `--split-prefix` is in
-   use (#400 and #527)
-
- * Bugfix: option -K had to be smaller than 2 billion (#491). This was caused
-   by a 32-bit integer overflow.
-
- * Improvement: optionally compile against SIMDe (#597). Minimap2 should work
-   with IBM POWER CPUs, though this has not been tested. To compile with SIMDe,
-   please use `make -f Makefile.simde`.
-
- * Improvement: more informative error message for I/O errors (#454) and for
-   FASTQ parsing errors (#510)
-
- * Improvement: abort given malformatted RG line (#541)
-
- * Improvement: better formula to estimate the `dv:f` tag (approximate sequence
-   divergence). See DOI:10.1101/2021.01.15.426881.
-
- * New feature: added the `--mask-len` option to fine control the removal of
-   redundant hits (#659). The default behavior is unchanged.
-
-Changes to mappy:
-
- * Bugfix: mappy caused segmentation fault if the reference index is not
-   present (#413).
-
- * Bugfix: fixed a memory leak via 238b6bb3
-
- * Change: always require Cython to compile the mappy module (#723). Older
-   mappy packages at PyPI bundled the C source code generated by Cython such
-   that end users did not need to install Cython to compile mappy. However, as
-   Python 3.9 is breaking backward compatibility, older mappy does not work
-   with Python 3.9 anymore. We have to add this Cython dependency as a
-   workaround.
-
-Changes to paftools.js:
-
- * Bugfix: the "part10-" line from asmgene was wrong (#581)
-
- * Improvement: compatibility with GTF files from GenBank (#422)
-
- * New feature: asmgene also checks missing multi-copy genes
-
- * New feature: added the misjoin command to evaluate large-scale misjoins and
-   megabase-long inversions.
-
-Although given the many bug fixes and minor improvements, the core algorithm
-stays the same. This version of minimap2 produces nearly identical alignments
-to v2.17 except very rare corner cases.
-
-Now unimap is recommended over minimap2 for aligning long contigs against a
-reference genome. It often takes less wall-clock time and is much more
-sensitive to long insertions and deletions.
-
-(2.18: 9 April 2021, r1015)
-
-
-
-Release 2.17-r941 (4 May 2019)
-------------------------------
-
-Changes since the last release:
-
- * Fixed flawed CIGARs like `5I6D7I` (#392).
-
- * Bugfix: TLEN should be 0 when either end is unmapped (#373 and #365).
-
- * Bugfix: mappy is unable to write index (#372).
-
- * Added option `--junc-bed` to load known gene annotations in the BED12
-   format. Minimap2 prefers annotated junctions over novel junctions (#197 and
-   #348). GTF can be converted to BED12 with `paftools.js gff2bed`.
-
- * Added option `--sam-hit-only` to suppress unmapped hits in SAM (#377).
-
- * Added preset `splice:hq` for high-quality CCS or mRNA sequences. It applies
-   better scoring and improves the sensitivity to small exons. This preset may
-   introduce false small introns, but the overall accuracy should be higher.
-
-This version produces nearly identical alignments to v2.16, except for CIGARs
-affected by the bug mentioned above.
-
-(2.17: 5 May 2019, r941)
-
-
-
-Release 2.16-r922 (28 February 2019)
-------------------------------------
-
-This release is 50% faster for mapping ultra-long nanopore reads at comparable
-accuracy. For short-read mapping, long-read overlapping and ordinary long-read
-mapping, the performance and accuracy remain similar. This speedup is achieved
-with a new heuristic to limit the number of chaining iterations (#324). Users
-can disable the heuristic by increasing a new option `--max-chain-iter` to a
-huge number.
-
-Other changes to minimap2:
-
- * Implemented option `--paf-no-hit` to output unmapped query sequences in PAF.
-   The strand and reference name columns are both `*` at an unmapped line. The
-   hidden option is available in earlier minimap2 but had a different 2-column
-   output format instead of PAF.
-
- * Fixed a bug that leads to wrongly calculated `de` tags when ambiguous bases
-   are involved (#309). This bug only affects v2.15.
-
- * Fixed a bug when parsing command-line option `--splice` (#344). This bug was
-   introduced in v2.13.
-
- * Fixed two division-by-zero cases (#326). They don't affect final alignments
-   because the results of the divisions are not used in both case.
-
- * Added an option `-o` to output alignments to a specified file. It is still
-   recommended to use UNIX pipes for on-the-fly conversion or compression.
-
- * Output a new `rl` tag to give the length of query regions harboring
-   repetitive seeds.
-
-Changes to paftool.js:
-
- * Added a new option to convert the MD tag to the long form of the cs tag.
-
-Changes to mappy:
-
- * Added the `mappy.Aligner.seq_names` method to return sequence names (#312).
-
-For NA12878 ultra-long reads, this release changes the alignments of <0.1% of
-reads in comparison to v2.15. All these reads have highly fragmented alignments
-and are likely to be problematic anyway. For shorter or well aligned reads,
-this release should produce mostly identical alignments to v2.15.
-
-(2.16: 28 February 2019, r922)
-
-
-
-Release 2.15-r905 (10 January 2019)
------------------------------------
-
-Changes to minimap2:
-
- * Fixed a rare segmentation fault when option -H is in use (#307). This may
-   happen when there are very long homopolymers towards the 5'-end of a read.
-
- * Fixed wrong CIGARs when option --eqx is used (#266).
-
- * Fixed a typo in the base encoding table (#264). This should have no
-   practical effect.
-
- * Fixed a typo in the example code (#265).
-
- * Improved the C++ compatibility by removing "register" (#261). However,
-   minimap2 still can't be compiled in the pedantic C++ mode (#306).
-
- * Output a new "de" tag for gap-compressed sequence divergence.
-
-Changes to paftools.js:
-
- * Added "asmgene" to evaluate the completeness of an assembly by measuring the
-   uniquely mapped single-copy genes. This command learns the idea of BUSCO.
-
- * Added "vcfpair" to call a phased VCF from phased whole-genome assemblies. An
-   earlier version of this script is used to produce the ground truth for the
-   syndip benchmark [PMID:30013044].
-
-This release produces identical alignment coordinates and CIGARs in comparison
-to v2.14. Users are advised to upgrade due to the several bug fixes.
-
-(2.15: 10 Janurary 2019, r905)
-
-
-
-Release 2.14-r883 (5 November 2018)
------------------------------------
-
-Notable changes:
-
- * Fixed two minor bugs caused by typos (#254 and #266).
-
- * Fixed a bug that made minimap2 abort when --eqx was used together with --MD
-   or --cs (#257).
-
- * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may
-   take a lot of memory in the splicing mode. This may lead to issues when we
-   run minimap2 on a cluster with a hard memory limit. The new option avoids
-   unlimited memory usage at the cost of missing a few long introns.
-
- * Conforming to C99 and C11 when possible (#261).
-
- * Warn about malformatted FASTA or FASTQ (#252 and #255).
-
-This release occasionally produces base alignments different from v2.13. The
-overall alignment accuracy remain similar.
-
-(2.14: 5 November 2018, r883)
-
-
-
-Release 2.13-r850 (11 October 2018)
------------------------------------
-
-Changes to minimap2:
-
- * Fixed wrongly formatted SAM when -L is in use (#231 and #233).
-
- * Fixed an integer overflow in rare cases.
-
- * Added --hard-mask-level to fine control split alignments (#244).
-
- * Made --MD work with spliced alignment (#139).
-
- * Replaced musl's getopt with ketopt for portability.
-
- * Log peak memory usage on exit.
-
-This release should produce alignments identical to v2.12 and v2.11.
-
-(2.13: 11 October 2018, r850)
-
-
-
-Release 2.12-r827 (6 August 2018)
----------------------------------
-
-Changes to minimap2:
-
- * Added option --split-prefix to write proper alignments (correct mapping
-   quality and clustered query sequences) given a multi-part index (#141 and
-   #189; mostly by @hasindu2008).
-
- * Fixed a memory leak when option -y is in use.
-
-Changes to mappy:
-
- * Support the MD/cs tag (#183 and #203).
-
- * Allow mappy to index a single sequence, to add extra flags and to change the
-   scoring system.
-
-Minimap2 should produce alignments identical to v2.11.
-
-(2.12: 6 August 2018, r827)
-
-
-
-Release 2.11-r797 (20 June 2018)
---------------------------------
-
-Changes to minimap2:
-
- * Improved alignment accuracy in low-complexity regions for SV calling. Thank
-   @armintoepfer for multiple offline examples.
-
- * Added option --eqx to encode sequence match/mismatch with the =/X CIGAR
-   operators (#156, #157 and #175).
-
- * When compiled with VC++, minimap2 generated wrong alignments due to a
-   comparison between a signed integer and an unsigned integer (#184). Also
-   fixed warnings reported by "clang -Wextra".
-
- * Fixed incorrect anchor filtering due to a missing 64- to 32-bit cast.
-
- * Fixed incorrect mapping quality for inversions (#148).
-
- * Fixed incorrect alignment involving ambiguous bases (#155).
-
- * Fixed incorrect presets: option `-r 2000` is intended to be used with
-   ava-ont, not ava-pb. The bug was introduced in 2.10.
-
- * Fixed a bug when --for-only/--rev-only is used together with --sr or
-   --heap-sort=yes (#166).
-
- * Fixed option -Y that was not working in the previous releases.
-
- * Added option --lj-min-ratio to fine control the alignment of long gaps
-   found by the "long-join" heuristic (#128).
-
- * Exposed `mm_idx_is_idx`, `mm_idx_load` and `mm_idx_dump` C APIs (#177).
-   Also fixed a bug when indexing without reference names (this feature is not
-   exposed to the command line).
-
-Changes to mappy:
-
- * Added `__version__` (#165).
-
- * Exposed the maximum fragment length parameter to mappy (#174).
-
-Changes to paftools:
-
- * Don't crash when there is no "cg" tag (#153).
-
- * Fixed wrong coverage report by "paftools.js call" (#145).
-
-This version may produce slightly different base-level alignment. The overall
-alignment statistics should remain similar.
-
-(2.11: 20 June 2018, r797)
-
-
-
-Release 2.10-r761 (27 March 2018)
----------------------------------
-
-Changes to minimap2:
-
- * Optionally output the MD tag for compatibility with existing tools (#63,
-   #118 and #137).
-
- * Use SSE compiler flags more precisely to prevent compiling errors on certain
-   machines (#127).
-
- * Added option --min-occ-floor to set a minimum occurrence threshold. Presets
-   intended for assembly-to-reference alignment set this option to 100. This
-   option alleviates issues with regions having high copy numbers (#107).
-
- * Exit with non-zero code on file writing errors (e.g. disk full; #103 and
-   #132).
-
- * Added option -y to copy FASTA/FASTQ comments in query sequences to the
-   output (#136).
-
- * Added the asm20 preset for alignments between genomes at 5-10% sequence
-   divergence.
-
- * Changed the band-width in the ava-ont preset from 500 to 2000. Oxford
-   Nanopore reads may contain long deletion sequencing errors that break
-   chaining.
-
-Changes to mappy, the Python binding:
-
- * Fixed a typo in Align.seq() (#126).
-
-Changes to paftools.js, the companion script:
-
- * Command sam2paf now converts the MD tag to cs.
-
- * Support VCF output for assembly-to-reference variant calling (#109).
-
-This version should produce identical alignment for read overlapping, RNA-seq
-read mapping, and genomic read mapping. We have also added a cook book to show
-the variety uses of minimap2 on real datasets. Please see cookbook.md in the
-minimap2 source code directory.
-
-(2.10: 27 March 2017, r761)
-
-
-
-Release 2.9-r720 (23 February 2018)
------------------------------------
-
-This release fixed multiple minor bugs.
-
-* Fixed two bugs that lead to incorrect inversion alignment. Also improved the
-  sensitivity to small inversions by using double Z-drop cutoff (#112).
-
-* Fixed an issue that may cause the end of a query sequence unmapped (#104).
-
-* Added a mappy API to retrieve sequences from the index (#126) and to reverse
-  complement DNA sequences. Fixed a bug where the `best_n` parameter did not
-  work (#117).
-
-* Avoided segmentation fault given incorrect FASTQ input (#111).
-
-* Combined all auxiliary javascripts to paftools.js. Fixed several bugs in
-  these scripts at the same time.
-
-(2.9: 24 February 2018, r720)
-
-
-
-Release 2.8-r672 (1 February 2018)
-----------------------------------
-
-Notable changes in this release include:
-
- * Speed up short-read alignment by ~10%. The overall mapping accuracy stays
-   the same, but the output alignments are not always identical to v2.7 due to
-   unstable sorting employed during chaining. Long-read alignment is not
-   affected by this change as the speedup is short-read specific.
-
- * Mappy now supports paired-end short-read alignment (#87). Please see
-   python/README.rst for details.
-
- * Added option --for-only and --rev-only to perform alignment against the
-   forward or the reverse strand of the reference genome only (#91).
-
- * Alleviated the issue with undesired diagonal alignment in the self mapping
-   mode (#10). Even if the output is not ideal, it should not interfere with
-   other alignments. Fully resolving the issue is intricate and may require
-   additional heuristic thresholds.
-
- * Enhanced error checking against incorrect input (#92 and #96).
-
-For long query sequences, minimap2 should output identical alignments to v2.7.
-
-(2.8: 1 February 2018, r672)
-
-
-
-Release 2.7-r654 (9 January 2018)
----------------------------------
-
-This release fixed a bug in the splice mode and added a few minor features:
-
- * Fixed a bug that occasionally takes an intron as a long deletion in the
-   splice mode. This was caused by wrong backtracking at the last CIGAR
-   operator. The current fix eliminates the error, but it is not optimal in
-   that it often produces a wrong junction when the last operator is an intron.
-   A future version of minimap2 may improve upon this.
-
- * Support high-end ARM CPUs that implement the NEON instruction set (#81).
-   This enables minimap2 to work on Raspberry Pi 3 and Odroid XU4.
-
- * Added a C API to construct a minimizer index from a set of C strings (#80).
-
- * Check scoring specified on the command line (#79). Due to the 8-bit limit,
-   excessively large score penalties fail minimap2.
-
-For genomic sequences, minimap2 should give identical alignments to v2.6.
-
-(2.7: 9 January 2018, r654)
-
-
-
-Release 2.6-r623 (12 December 2017)
------------------------------------
-
-This release adds several features and fixes two minor bugs:
-
- * Optionally build an index without sequences. This helps to reduce the
-   peak memory for read overlapping and is automatically applied when
-   base-level alignment is not requested.
-
- * Approximately estimate per-base sequence divergence (i.e. 1-identity)
-   without performing base-level alignment, using a MashMap-like method. The
-   estimate is written to a new dv:f tag.
-
- * Reduced the number of tiny terminal exons in RNA-seq alignment. The current
-   setting is conservative. Increase --end-seed-pen to drop more such exons.
-
- * Reduced the peak memory when aligning long query sequences.
-
- * Fixed a bug that is caused by HPC minimizers longer than 256bp. This should
-   have no effect in practice, but it is recommended to rebuild HPC indices if
-   possible.
-
- * Fixed a bug when identifying identical hits (#71). This should only affect
-   artifactual reference consisting of near identical sequences.
-
-For genomic sequences, minimap2 should give nearly identical alignments to
-v2.5, except the new dv:f tag.
-
-(2.6: 12 December 2017, r623)
-
-
-
-Release 2.5-r572 (11 November 2017)
------------------------------------
-
-This release fixes several bugs and brings a couple of minor improvements:
-
- * Fixed a severe bug that leads to incorrect mapping coordinates in rare
-   corner cases.
-
- * Fixed underestimated mapping quality for chimeric alignments when the whole
-   query sequence contain many repetitive minimizers, and for chimeric
-   alignments caused by Z-drop.
-
- * Fixed two bugs in Python binding: incorrect strand field (#57) and incorrect
-   sequence names for Python3 (#55).
-
- * Improved mapping accuracy for highly overlapping paired ends.
-
- * Added option -Y to use soft clipping for supplementary alignments (#56).
-
-(2.5: 11 November 2017, r572)
-
-
-
-Release 2.4-r555 (6 November 2017)
-----------------------------------
-
-As is planned, this release focuses on fine tuning the base algorithm. Notable
-changes include
-
- * Changed the mapping quality scale to match the scale of BWA-MEM. This makes
-   minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real
-   short-read data.
-
- * Improved the accuracy of splice alignment by modeling one additional base
-   close to the GT-AG signal. This model is used by default with `-x splice`.
-   For SIRV control data, however, it is recommended to add `--splice-flank=no`
-   to disable this feature as the SIRV splice signals are slightly different.
-
- * Tuned the parameters for Nanopore Direct RNA reads. The recommended command
-   line is `-axsplice -k14 -uf` (#46).
-
- * Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This
-   bug is very rare but it affects all versions of minimap2. It is also
-   recommended to re-index reference genomes created with `map-pb`. For human,
-   two minimizers in an old index are wrong.
-
- * Changed option `-L` in sync with the final decision of hts-specs: a fake
-   CIGAR takes the form of `<readLen>S<refLen>N`. Note that `-L` only enables
-   future tools to recognize long CIGARs. It is not possible for older tools to
-   work with such alignments in BAM (#43 and #51).
-
- * Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate
-   alignment.
-
-The minimap2 technical note hosted at arXiv has also been updated to reflect
-recent changes.
-
-(2.4: 6 November 2017, r555)
-
-
-
-Release 2.3-r531 (22 October 2017)
-----------------------------------
-
-This release come with many improvements and bug fixes:
-
- * The **sr** preset now supports paired-end short-read alignment. Minimap2 is
-   3-4 times as fast as BWA-MEM, but is slightly less accurate on simulated
-   reads.
-
- * Meticulous improvements to assembly-to-assembly alignment (special thanks to
-   Alexey Gurevich from the QUAST team): a) apply a small penalty to matches
-   between ambiguous bases; b) reduce missing alignments due to spurious
-   overlaps; c) introduce the short form of the `cs` tag, an improvement to the
-   SAM MD tag.
-
- * Make sure gaps are always left-aligned.
-
- * Recognize `U` bases from Oxford Nanopore Direct RNA-seq (#33).
-
- * Fixed slightly wrong chaining score. Fixed slightly inaccurate coordinates
-   for split alignment.
-
- * Fixed multiple reported bugs: 1) wrong reference name for inversion
-   alignment (#30); 2) redundant SQ lines when multiple query files are
-   specified (#39); 3) non-functioning option `-K` (#36).
-
-This release has implemented all the major features I planned five months ago,
-with the addition of spliced long-read alignment. The next couple of releases
-will focus on fine tuning of the base algorithms.
-
-(2.3: 22 October 2017, r531)
-
-
-
-Release 2.2-r409 (17 September 2017)
-------------------------------------
-
-This is a feature release. It improves single-end short-read alignment and
-comes with Python bindings. Detailed changes include:
-
- * Added the **sr** preset for single-end short-read alignment. In this mode,
-   minimap2 runs faster than BWA-MEM, but is slightly less accurate on
-   simulated data sets. Paired-end alignment is not supported as of now.
-
- * Improved mapping quality estimate with more accurate identification of
-   repetitive hits. This mainly helps short-read alignment.
-
- * Implemented **mappy**, a Python binding for minimap2, which is available
-   from PyPI and can be installed with `pip install --user mappy`. Python users
-   can perform read alignment without the minimap2 executable.
-
- * Restructured the indexing APIs and documented key minimap2 APIs in the
-   header file minimap.h. Updated example.c with the new APIs. Old APIs still
-   work but may become deprecated in future.
-
-This release may output alignments different from the previous version, though
-the overall alignment statistics, such as the number of aligned bases and long
-gaps, remain close.
-
-(2.2: 17 September 2017, r409)
-
-
-
-Release 2.1.1-r341 (6 September 2017)
--------------------------------------
-
-This is a maintenance release that is expected to output identical alignment to
-v2.1. Detailed changes include:
-
- * Support CPU dispatch. By default, minimap2 is compiled with both SSE2 and
-   SSE4 based implementation of alignment and automatically chooses the right
-   one at runtime. This avoids unexpected errors on older CPUs (#21).
-
- * Improved Windows support as is requested by Oxford Nanopore (#19). Minimap2
-   now avoids variable-length stacked arrays, eliminates alloca(), ships with
-   getopt_long() and provides timing functions implemented with Windows APIs.
-
- * Fixed a potential segmentation fault when specifying -k/-w/-H with
-   multi-part index (#23).
-
- * Fixed two memory leaks in example.c
-
-(2.1.1: 6 September 2017, r341)
-
-
-
-Release 2.1-r311 (25 August 2017)
----------------------------------
-
-This release adds spliced alignment for long noisy RNA-seq reads. On a SMRT
-Iso-Seq and a Oxford Nanopore data sets, minimap2 appears to outperform
-traditional mRNA aligners. For DNA alignment, this release gives almost
-identical output to v2.0. Other changes include:
-
- * Added option `-R` to set the read group header line in SAM.
-
- * Optionally output the `cs:Z` tag in PAF to encode both the query and the
-   reference sequences in the alignment.
-
- * Fixed an issue where DP alignment uses excessive memory.
-
-The minimap2 technical report has been updated with more details and the
-evaluation of spliced alignment:
-
- * Li, H. (2017). Minimap2: fast pairwise alignment for long nucleotide
-   sequences. [arXiv:1708.01492v2](https://arxiv.org/abs/1708.01492v2).
-
-(2.1: 25 August 2017, r311)
-
-
-
-Release 2.0-r275 (8 August 2017)
---------------------------------
-
-This release is identical to version 2.0rc1, except the version number. It is
-described and evaluated in the following technical report:
-
- * Li, H. (2017). Minimap2: fast pairwise alignment for long DNA sequences.
-   [arXiv:1708.01492v1](https://arxiv.org/abs/1708.01492v1).
-
-(2.0: 8 August 2017, r275)
-
-
-
-Release 2.0rc1-r232 (30 July 2017)
-----------------------------------
-
-This release improves the accuracy of long-read alignment and added several
-minor features.
-
- * Improved mapping quality estimate for short alignments containing few seed
-   hits.
-
- * Fixed a minor bug that affects the chaining accuracy towards the ends of a
-   chain. Changed the gap cost for chaining to reduce false seeding.
-
- * Skip potentially wrong seeding and apply dynamic programming more frequently.
-   This slightly increases run time, but greatly reduces false long gaps.
-
- * Perform local alignment at Z-drop break point to recover potential inversion
-   alignment. Output the SA tag in the SAM format. Added scripts to evaluate
-   mapping accuracy for reads simulated with pbsim.
-
-This release completes features intended for v2.0. No major features will be
-added to the master branch before the final v2.0.
-
-(2.0rc1: 30 July 2017, r232)
-
-
-
-Release r191 (19 July 2017)
----------------------------
-
-This is the first public release of minimap2, an aligner for long reads and
-assemblies. This release has a few issues and is generally not recommended for
-production uses.
-
-(19 July 2017, r191)