minimap2 0.2.31.0 → 1.2.31.0

data/ext/minimap2/README.md

@@ -1,429 +0,0 @@
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-## <a name="started"></a>Getting Started
-**ALERT:** `minimap2.com` is a [phishing site](https://github.com/lh3/minimap2/issues/1316). Please don't use anything from that website.
-```sh
-git clone https://github.com/lh3/minimap2
-cd minimap2 && make
-# long sequences against a reference genome
-./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
-# create an index first and then map
-./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa
-./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam
-# use presets (no test data)
-./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio CLR genomic reads
-./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
-./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+)
-./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam       # Nanopore Q20 genomic reads (v2.27+)
-./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
-./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
-./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore direct RNA-seq
-./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam    # PacBio Kinnex/Iso-seq (RNA-seq)
-./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam  # use annotated junctions
-./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam     # short-read RNA-seq (v2.29+)
-./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam
-./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf             # intra-species asm-to-asm alignment
-./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf     # PacBio read overlap
-./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf    # Nanopore read overlap
-# man page for detailed command line options
-man ./minimap2.1
-```
-
-## Table of Contents
-
-- [Getting Started](#started)
-- [Users' Guide](#uguide)
-  - [Installation](#install)
-  - [General usage](#general)
-  - [Use cases](#cases)
-    - [Map long noisy genomic reads](#map-long-genomic)
-    - [Map long mRNA/cDNA reads](#map-long-splice)
-    - [Find overlaps between long reads](#long-overlap)
-    - [Map short genomic reads](#short-genomic)
-    - [Map short RNA-seq reads](#short-rna-seq)
-    - [Full genome/assembly alignment](#full-genome)
-  - [Advanced features](#advanced)
-    - [Working with >65535 CIGAR operations](#long-cigar)
-    - [The cs optional tag](#cs)
-    - [Working with the PAF format](#paftools)
-  - [Algorithm overview](#algo)
-  - [Getting help](#help)
-  - [Citing minimap2](#cite)
-- [Developers' Guide](#dguide)
-- [Limitations](#limit)
-
-## <a name="uguide"></a>Users' Guide
-
-Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
-sequences against a large reference database. Typical use cases include: (1)
-mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2)
-finding overlaps between long reads with error rate up to ~15%; (3)
-splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads
-against a reference genome; (4) aligning Illumina single- or paired-end reads;
-(5) assembly-to-assembly alignment; (6) full-genome alignment between two
-closely related species with divergence below ~15%.
-
-For ~10kb noisy reads sequences, minimap2 is tens of times faster than
-mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more
-accurate on simulated long reads and produces biologically meaningful alignment
-ready for downstream analyses. For >100bp Illumina short reads, minimap2 is
-three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data.
-Detailed evaluations are available from the [minimap2 paper][doi] or the
-[preprint][preprint].
-
-### <a name="install"></a>Installation
-
-Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
-the [release page][release] with:
-```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.31/minimap2-2.31_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.31_x64-linux/minimap2
-```
-If you want to compile from the source, you need to have a C compiler, GNU make
-and zlib development files installed. Then type `make` in the source code
-directory to compile. If you see compilation errors, try `make sse2only=1`
-to disable SSE4 code, which will make minimap2 slightly slower.
-
-Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
-compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To
-compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1
-aarch64=1`.
-
-Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
-implementation to the different SIMD instruction sets. To compile using SIMDe,
-use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
-with the ARM related command lines given above.
-
-### <a name="general"></a>General usage
-
-Without any options, minimap2 takes a reference database and a query sequence
-file as input and produce approximate mapping, without base-level alignment
-(i.e. coordinates are only approximate and no CIGAR in output), in the [PAF format][paf]:
-```sh
-minimap2 ref.fa query.fq > approx-mapping.paf
-```
-You can ask minimap2 to generate CIGAR at the `cg` tag of PAF with:
-```sh
-minimap2 -c ref.fa query.fq > alignment.paf
-```
-or to output alignments in the [SAM format][sam]:
-```sh
-minimap2 -a ref.fa query.fq > alignment.sam
-```
-Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input. You
-don't need to convert between FASTA and FASTQ or decompress gzip'd files first.
-
-For the human reference genome, minimap2 takes a few minutes to generate a
-minimizer index for the reference before mapping. To reduce indexing time, you
-can optionally save the index with option **-d** and replace the reference
-sequence file with the index file on the minimap2 command line:
-```sh
-minimap2 -d ref.mmi ref.fa                     # indexing
-minimap2 -a ref.mmi reads.fq > alignment.sam   # alignment
-```
-***Importantly***, it should be noted that once you build the index, indexing
-parameters such as **-k**, **-w**, **-H** and **-I** can't be changed during
-mapping. If you are running minimap2 for different data types, you will
-probably need to keep multiple indexes generated with different parameters.
-This makes minimap2 different from BWA which always uses the same index
-regardless of query data types.
-
-### <a name="cases"></a>Use cases
-
-Minimap2 uses the same base algorithm for all applications. However, due to the
-different data types it supports (e.g. short vs long reads; DNA vs mRNA reads),
-minimap2 needs to be tuned for optimal performance and accuracy. It is usually
-recommended to choose a preset with option **-x**, which sets multiple
-parameters at the same time. The default setting is the same as `map-ont`.
-
-#### <a name="map-long-genomic"></a>Map long noisy genomic reads
-
-```sh
-minimap2 -ax map-pb  ref.fa pacbio-reads.fq > aln.sam   # for PacBio CLR reads
-minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam      # for Oxford Nanopore reads
-minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam    # for Illumina Complete Long Reads
-```
-The difference between `map-pb` and `map-ont` is that `map-pb` uses
-homopolymer-compressed (HPC) minimizers as seeds, while `map-ont` uses ordinary
-minimizers as seeds. Empirical evaluation suggests HPC minimizers improve
-performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning
-Nanopore reads. `map-iclr` uses an adjusted alignment scoring matrix that
-accounts for the low overall error rate in the reads, with transversion errors
-being less frequent than transitions.
-
-#### <a name="map-long-splice"></a>Map long mRNA/cDNA reads
-
-```sh
-minimap2 -ax splice:hq -uf ref.fa iso-seq.fq > aln.sam       # PacBio Iso-seq/traditional cDNA
-minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam        # Nanopore 2D cDNA-seq
-minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam  # Nanopore Direct RNA-seq
-minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa    # mapping against SIRV control
-```
-There are different long-read RNA-seq technologies, including tranditional
-full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq.
-They produce data of varying quality and properties. By default, `-x splice`
-assumes the read orientation relative to the transcript strand is unknown. It
-tries two rounds of alignment to infer the orientation and write the strand to
-the `ts` SAM/PAF tag if possible. For Iso-seq, Direct RNA-seq and tranditional
-full-length cDNAs, it would be desired to apply `-u f` to force minimap2 to
-consider the forward transcript strand only. This speeds up alignment with
-slight improvement to accuracy. For noisy Nanopore Direct RNA-seq reads, it is
-recommended to use a smaller k-mer size for increased sensitivity to the first
-or the last exons.
-
-Minimap2 rates an alignment by the score of the max-scoring sub-segment,
-*excluding* introns, and marks the best alignment as primary in SAM. When a
-spliced gene also has unspliced pseudogenes, minimap2 slightly prefers
-the spliced alignment. By default, minimap2 outputs up to five secondary
-alignments (i.e. likely pseudogenes in the context of RNA-seq mapping). This
-can be tuned with option **-N**.
-
-For long RNA-seq reads, minimap2 may produce chimeric alignments potentially
-caused by gene fusions/structural variations or by an intron longer than the
-max intron length **-G** (200k by default). For now, it is not recommended to
-apply an excessively large **-G** as this slows down minimap2 and sometimes
-leads to false alignments.
-
-It is worth noting that by default `-x splice` prefers GT[A/G]..[C/T]AG
-over GT[C/T]..[A/G]AG, and then over other splicing signals. Considering
-one additional base improves the junction accuracy for noisy reads, but
-reduces the accuracy when aligning against the widely used SIRV control data.
-This is because SIRV does not honor the evolutionarily conservative splicing
-signal. If you are studying SIRV, you may apply `--splice-flank=no` to let
-minimap2 only model GT..AG, ignoring the additional base.
-
-Since v2.17, minimap2 can optionally take annotated genes as input and
-prioritize on annotated splice junctions. To use this feature, you can 
-```sh
-paftools.js gff2bed anno.gff > anno.bed
-minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam
-```
-Here, `anno.gff` is the gene annotation in the GTF or GFF3 format (`gff2bed`
-automatically tests the format). The output of `gff2bed` is in the 12-column
-BED format, or the BED12 format. With the `--junc-bed` option, minimap2 adds a
-bonus score (tuned by `--junc-bonus`) if an aligned junction matches a junction
-in the annotation. Option `--junc-bed` also takes 5-column BED, including the
-strand field. In this case, each line indicates an oriented junction.
-
-**Note:** `--junc-bed` is intended for long noisy RNA-seq reads only.
-Applying the option to short RNA-seq reads would increase run time with little
-improvement to junction accuracy.
-
-#### <a name="long-overlap"></a>Find overlaps between long reads
-
-```sh
-minimap2 -x ava-pb  reads.fq reads.fq > ovlp.paf    # PacBio CLR read overlap
-minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf    # Oxford Nanopore read overlap
-```
-Similarly, `ava-pb` uses HPC minimizers while `ava-ont` uses ordinary
-minimizers. It is usually not recommended to perform base-level alignment in
-the overlapping mode because it is slow and may produce false positive
-overlaps. However, if performance is not a concern, you may try to add `-a` or
-`-c` anyway.
-
-#### <a name="short-genomic"></a>Map short genomic reads
-
-```sh
-minimap2 -ax sr ref.fa reads-se.fq > aln.sam           # single-end alignment
-minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam     # paired-end alignment
-minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam  # paired-end alignment
-```
-When two read files are specified, minimap2 reads from each file in turn and
-merge them into an interleaved stream internally. Two reads are considered to
-be paired if they are adjacent in the input stream and have the same name (with
-the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
-mixed.
-
-#### <a name="short-rna-seq"></a>Map short RNA-seq reads
-
-```sh
-minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam           # single-end
-minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam        # paired-end
-minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam  # use annotation
-# 2-pass alignment
-minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed
-minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam
-```
-The new preset `splice:sr` was added in v2.29. It functions similarly to `sr`
-except that it performs spliced alignment.
-
-#### <a name="full-genome"></a>Full genome/assembly alignment
-
-```sh
-minimap2 -ax asm5 ref.fa asm.fa > aln.sam       # assembly to assembly/ref alignment
-```
-For cross-species full-genome alignment, the scoring system needs to be tuned
-according to the sequence divergence.
-
-### <a name="advanced"></a>Advanced features
-
-#### <a name="long-cigar"></a>Working with >65535 CIGAR operations
-
-Due to a design flaw, BAM does not work with CIGAR strings with >65535
-operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2
-may align ~1% of read bases with long CIGARs beyond the capability of BAM. If
-you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an
-error and abort. Older samtools and other tools may create corrupted BAM.
-
-To avoid this issue, you can add option `-L` at the minimap2 command line.
-This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR
-at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and
-sorting) still work with such BAM records; tools that read CIGAR will
-effectively ignore these records. It has been decided that future tools
-will seamlessly recognize long-cigar records generated by option `-L`.
-
-**TL;DR**: if you work with ultra-long reads and use tools that only process
-BAM files, please add option `-L`.
-
-#### <a name="cs"></a>The cs optional tag
-
-The `cs` SAM/PAF tag encodes bases at mismatches and INDELs. It matches regular
-expression `/(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/`. Like CIGAR, `cs`
-consists of series of operations.  Each leading character specifies the
-operation; the following sequence is the one involved in the operation.
-
-The `cs` tag is enabled by command line option `--cs`. The following alignment,
-for example:
-```txt
-CGATCGATAAATAGAGTAG---GAATAGCA
-||||||   ||||||||||   |||| |||
-CGATCG---AATAGAGTAGGTCGAATtGCA
-```
-is represented as `:6-ata:10+gtc:4*at:3`, where `:[0-9]+` represents an
-identical block, `-ata` represents a deletion, `+gtc` an insertion and `*at`
-indicates reference base `a` is substituted with a query base `t`. It is
-similar to the `MD` SAM tag but is standalone and easier to parse.
-
-If `--cs=long` is used, the `cs` string also contains identical sequences in
-the alignment. The above example will become
-`=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both
-reference and query sequences in one string. The `cs` tag also encodes intron
-positions and splicing signals (see the [minimap2 manpage][manpage-cs] for
-details).
-
-#### <a name="paftools"></a>Working with the PAF format
-
-Minimap2 also comes with a (java)script [paftools.js](misc/paftools.js) that
-processes alignments in the PAF format. It calls variants from
-assembly-to-reference alignment, lifts over BED files based on alignment,
-converts between formats and provides utilities for various evaluations. For
-details, please see [misc/README.md](misc/README.md).
-
-### <a name="algo"></a>Algorithm overview
-
-In the following, minimap2 command line options have a dash ahead and are
-highlighted in bold. The description may help to tune minimap2 parameters.
-
-1. Read **-I** [=*4G*] reference bases, extract (**-k**,**-w**)-minimizers and
-   index them in a hash table.
-
-2. Read **-K** [=*200M*] query bases. For each query sequence, do step 3
-   through 7:
-
-3. For each (**-k**,**-w**)-minimizer on the query, check against the reference
-   index. If a reference minimizer is not among the top **-f** [=*2e-4*] most
-   frequent, collect its the occurrences in the reference, which are called
-   *seeds*.
-
-4. Sort seeds by position in the reference. Chain them with dynamic
-   programming. Each chain represents a potential mapping. For read
-   overlapping, report all chains and then go to step 8. For reference mapping,
-   do step 5 through 7:
-
-5. Let *P* be the set of primary mappings, which is an empty set initially. For
-   each chain from the best to the worst according to their chaining scores: if
-   on the query, the chain overlaps with a chain in *P* by **--mask-level**
-   [=*0.5*] or higher fraction of the shorter chain, mark the chain as
-   *secondary* to the chain in *P*; otherwise, add the chain to *P*.
-
-6. Retain all primary mappings. Also retain up to **-N** [=*5*] top secondary
-   mappings if their chaining scores are higher than **-p** [=*0.8*] of their
-   corresponding primary mappings.
-
-7. If alignment is requested, filter out an internal seed if it potentially
-   leads to both a long insertion and a long deletion. Extend from the
-   left-most seed. Perform global alignments between internal seeds.  Split the
-   chain if the accumulative score along the global alignment drops by **-z**
-   [=*400*], disregarding long gaps. Extend from the right-most seed.  Output
-   chains and their alignments.
-
-8. If there are more query sequences in the input, go to step 2 until no more
-   queries are left.
-
-9. If there are more reference sequences, reopen the query file from the start
-   and go to step 1; otherwise stop.
-
-### <a name="help"></a>Getting help
-
-Manpage [minimap2.1][manpage] provides detailed description of minimap2
-command line options and optional tags. The [FAQ](FAQ.md) page answers several
-frequently asked questions. If you encounter bugs or have further questions or
-requests, you can raise an issue at the [issue page][issue].  There is not a
-specific mailing list for the time being.
-
-### <a name="cite"></a>Citing minimap2
-
-If you use minimap2 in your work, please cite:
-
-> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.
-> *Bioinformatics*, **34**:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
-
-and/or:
-
-> Li, H. (2021). New strategies to improve minimap2 alignment accuracy.
-> *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
-
-## <a name="dguide"></a>Developers' Guide
-
-Minimap2 is not only a command line tool, but also a programming library.
-It provides C APIs to build/load index and to align sequences against the
-index. File [example.c](example.c) demonstrates typical uses of C APIs. Header
-file [minimap.h](minimap.h) gives more detailed API documentation. Minimap2
-aims to keep APIs in this header stable. File [mmpriv.h](mmpriv.h) contains
-additional private APIs which may be subjected to changes frequently.
-
-This repository also provides Python bindings to a subset of C APIs. File
-[python/README.rst](python/README.rst) gives the full documentation;
-[python/minimap2.py](python/minimap2.py) shows an example. This Python
-extension, mappy, is also [available from PyPI][mappypypi] via `pip install
-mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
-
-## <a name="limit"></a>Limitations
-
-* Minimap2 may produce suboptimal alignments through long low-complexity
-  regions where seed positions may be suboptimal. This should not be a big
-  concern because even the optimal alignment may be wrong in such regions.
-
-* Minimap2 requires SSE2 instructions on x86 CPUs or NEON on ARM CPUs. It is
-  possible to add non-SIMD support, but it would make minimap2 slower by
-  several times.
-
-* Minimap2 does not work with a single query or database sequence ~2
-  billion bases or longer (2,147,483,647 to be exact). The total length of all
-  sequences can well exceed this threshold.
-
-* Minimap2 often misses small exons.
-
-
-
-[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
-[sam]: https://samtools.github.io/hts-specs/SAMv1.pdf
-[minimap]: https://github.com/lh3/minimap
-[smartdenovo]: https://github.com/ruanjue/smartdenovo
-[longislnd]: https://www.ncbi.nlm.nih.gov/pubmed/27667791
-[gaba]: https://github.com/ocxtal/libgaba
-[ksw2]: https://github.com/lh3/ksw2
-[preprint]: https://arxiv.org/abs/1708.01492
-[release]: https://github.com/lh3/minimap2/releases
-[mappypypi]: https://pypi.python.org/pypi/mappy
-[mappyconda]: https://anaconda.org/bioconda/mappy
-[issue]: https://github.com/lh3/minimap2/issues
-[k8]: https://github.com/attractivechaos/k8
-[manpage]: https://lh3.github.io/minimap2/minimap2.html
-[manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10
-[doi]: https://doi.org/10.1093/bioinformatics/bty191
-[doi2]: https://doi.org/10.1093/bioinformatics/btab705
-[simde]: https://github.com/nemequ/simde
-[unimap]: https://github.com/lh3/unimap

data/ext/minimap2/code_of_conduct.md

@@ -1,30 +0,0 @@
-## Contributor Code of Conduct
-
-As contributors and maintainers of this project, we pledge to respect all
-people who contribute through reporting issues, posting feature requests,
-updating documentation, submitting pull requests or patches, and other
-activities.
-
-We are committed to making participation in this project a harassment-free
-experience for everyone, regardless of level of experience, gender, gender
-identity and expression, sexual orientation, disability, personal appearance,
-body size, race, age, or religion.
-
-Examples of unacceptable behavior by participants include the use of sexual
-language or imagery, derogatory comments or personal attacks, trolling, public
-or private harassment, insults, or other unprofessional conduct.
-
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct. Project maintainers or
-contributors who do not follow the Code of Conduct may be removed from the
-project team.
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by opening an issue or contacting the maintainer via email.
-
-This Code of Conduct is adapted from the [Contributor Covenant][cc], [version
-1.0.0][v1].
-
-[cc]: http://contributor-covenant.org/
-[v1]: http://contributor-covenant.org/version/1/0/0/