minimap2 0.2.30.3 → 1.2.31.0

data/ext/minimap2/minimap2.1

@@ -1,844 +0,0 @@
-.TH minimap2 1 "15 June 2025" "minimap2-2.30 (r1287)" "Bioinformatics tools"
-.SH NAME
-.PP
-minimap2 - mapping and alignment between collections of DNA sequences
-.SH SYNOPSIS
-* Indexing the target sequences (optional):
-.RS 4
-minimap2
-.RB [ -x
-.IR preset ]
-.B -d
-.I target.mmi
-.I target.fa
-.br
-minimap2
-.RB [ -H ]
-.RB [ -k
-.IR kmer ]
-.RB [ -w
-.IR miniWinSize ]
-.RB [ -I
-.IR batchSize ]
-.B -d
-.I target.mmi
-.I target.fa
-.RE
-
-* Long-read alignment with CIGAR:
-.RS 4
-minimap2
-.B -a
-.RB [ -x
-.IR preset ]
-.I target.mmi
-.I query.fa
->
-.I output.sam
-.br
-minimap2
-.B -c
-.RB [ -H ]
-.RB [ -k
-.IR kmer ]
-.RB [ -w
-.IR miniWinSize ]
-.RB [ ... ]
-.I target.fa
-.I query.fa
->
-.I output.paf
-.RE
-
-* Long-read overlap without CIGAR:
-.RS 4
-minimap2
-.B -x
-ava-ont
-.RB [ -t
-.IR nThreads ]
-.I target.fa
-.I query.fa
->
-.I output.paf
-.RE
-.SH DESCRIPTION
-.PP
-Minimap2 is a fast sequence mapping and alignment program that can find
-overlaps between long noisy reads, or map long reads or their assemblies to a
-reference genome optionally with detailed alignment (i.e. CIGAR). At present,
-it works efficiently with query sequences from a few kilobases to ~100
-megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
-SAM format.
-.SH OPTIONS
-.SS Indexing options
-.TP 10
-.BI -k \ INT
-Minimizer k-mer length [15]
-.TP
-.BI -w \ INT
-Minimizer window size [10]. A minimizer is the smallest k-mer
-in a window of w consecutive k-mers.
-.TP
-.B -H
-Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
-contracting homopolymer runs to a single base. An HPC minimizer is a minimizer
-on the HPC sequence.
-.TP
-.BI -I \ NUM
-Load at most
-.I NUM
-target bases into RAM for indexing [8G]. If there are more than
-.I NUM
-bases in
-.IR target.fa ,
-minimap2 needs to read
-.I query.fa
-multiple times to map it against each batch of target sequences. This would create a multi-part index.
-.I NUM
-may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
-multi-part index. See also option
-.BR --split-prefix .
-.TP
-.B --idx-no-seq
-Don't store target sequences in the index. It saves disk space and memory but
-the index generated with this option will not work with
-.B -a
-or
-.BR -c .
-When base-level alignment is not requested, this option is automatically applied.
-.TP
-.BI -d \ FILE
-Save the minimizer index of
-.I target.fa
-to
-.I FILE
-[no dump]. Minimap2 indexing is fast. It can index the human genome in a couple
-of minutes. If even shorter startup time is desired, use this option to save
-the index. Indexing options are fixed in the index file. When an index file is
-provided as the target sequences, options
-.BR -H ,
-.BR -k ,
-.BR -w ,
-.B -I
-will be effectively overridden by the options stored in the index file.
-.TP
-.BI --alt \ FILE
-List of ALT contigs [null]
-.TP
-.BI --alt-drop \ FLOAT
-Drop ALT hits by
-.I FLOAT
-fraction when ranking and computing mapping quality [0.15]
-.SS Mapping options
-.TP 10
-.BI -f \ FLOAT | INT1 [, INT2 ]
-If fraction, ignore top
-.I FLOAT
-fraction of most frequent minimizers [0.0002]. If integer,
-ignore minimizers occuring more than
-.I INT1
-times.
-.I INT2
-is only effective in the
-.B --sr
-or
-.B -xsr
-mode, which sets the threshold for a second round of seeding.
-.TP
-.BI -U \ INT1 [, INT2 ]
-Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
-.RI max{ INT1 ,\ min{ INT2 ,
-.BR -f }}.
-This option prevents excessively small or large
-.B -f
-estimated from the input reference. Available since r1034 and deprecating
-.B --min-occ-floor
-in earlier versions of minimap2.
-.TP
-.BI --q-occ-frac \ FLOAT
-Discard a query minimizer if its occurrence is higher than
-.I FLOAT
-fraction of query minimizers and than the reference occurrence threshold
-[0.01]. Set 0 to disable. Available since r1105.
-.TP
-.BI -e \ INT
-Sample a high-frequency minimizer every
-.I INT
-basepairs [500].
-.TP
-.BI -g \ NUM
-Stop chain enlongation if there are no minimizers within
-.IR NUM -bp
-[10k].
-.TP
-.BI -r \ NUM1 [, NUM2 ]
-Bandwidth for chaining and base alignment [500,20k].
-.I NUM1
-is used for initial chaining and alignment extension;
-.I NUM2
-for RMQ-based re-chaining and closing gaps in alignments.
-.TP
-.BI -n \ INT
-Discard chains consisting of
-.RI < INT
-number of minimizers [3]
-.TP
-.BI -m \ INT
-Discard chains with chaining score
-.RI < INT
-[40]. Chaining score equals the approximate number of matching bases minus a
-concave gap penalty. It is computed with dynamic programming.
-.TP
-.B -D
-If query sequence name/length are identical to the target name/length, ignore
-diagonal anchors. This option also reduces DP-based extension along the
-diagonal.
-.TP
-.B -P
-Retain all chains and don't attempt to set primary chains. Options
-.B -p
-and
-.B -N
-have no effect when this option is in use.
-.TP
-.BR --dual = yes | no
-If
-.BR no ,
-skip query-target pairs wherein the query name is lexicographically greater
-than the target name [yes]
-.TP
-.B -X
-Equivalent to
-.RB ' -DP
-.BR --dual = no
-.BR --no-long-join '.
-Primarily used for all-vs-all read overlapping.
-.TP
-.BI -p \ FLOAT
-Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
-Between two chains overlaping over half of the shorter chain (controlled by
-.BR -M ),
-the chain with a lower score is secondary to the chain with a higher score.
-If the ratio of the scores is below
-.IR FLOAT ,
-the secondary chain will not be outputted or extended with DP alignment later.
-This option has no effect when
-.B -X
-is applied.
-.TP
-.BI -N \ INT
-Output at most
-.I INT
-secondary alignments [5]. This option has no effect when
-.B -X
-is applied.
-.TP
-.BI -G \ NUM
-Maximum gap on the reference (effective with
-.BR -xsplice / --splice ).
-This option also changes the chaining and alignment band width to
-.IR NUM .
-Increasing this option slows down spliced alignment. [200k]
-.TP
-.BI -F \ NUM
-Maximum fragment length (aka insert size; effective with
-.BR -xsr / --frag = yes )
-[800]
-.TP
-.BI -M \ FLOAT
-Mark as secondary a chain that overlaps with a better chain by
-.I FLOAT
-or more of the shorter chain [0.5]
-.TP
-.BR --rmq = no | yes
-Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
-for aligning contigs through long INDELs.
-.TP
-.BI --rmq-inner \ NUM
-Apply full dynamic programming for anchors within distance
-.I NUM
-[1000].
-.TP
-.B --hard-mask-level
-Honor option
-.B -M
-and disable a heurstic to save unmapped subsequences and disables
-.BR --mask-len .
-.TP
-.BI --mask-len \ NUM
-Keep an alignment if dropping it leaves an unaligned region on query longer than
-.IR INT
-[inf]. Effective without
-.BR --hard-mask-level .
-.TP
-.BI --max-chain-skip \ INT
-A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming
-for chaining. The time complexity is quadratic in the number of seeds. This
-option makes minimap2 exits the inner loop if it repeatedly sees seeds already
-on chains. Set
-.I INT
-to a large number to switch off this heurstics.
-.TP
-.BI --max-chain-iter \ INT
-Check up to
-.I INT
-partial chains during chaining [5000]. This is a heuristic to avoid quadratic
-time complexity in the worst case.
-.TP
-.BI --chain-gap-scale \ FLOAT
-Scale of gap cost during chaining [1.0]
-.TP
-.B --no-long-join
-Disable the long gap patching heuristic. When this option is applied, the
-maximum alignment gap is mostly controlled by
-.BR -r .
-.TP
-.B --splice
-Enable the splice alignment mode.
-.TP
-.BR --sr [= no | dna | rna ]
-Enable short-read alignment heuristics [no]. If this option is used with no argument,
-.RB ` dna '
-is set. In the DNA short-read mode, minimap2 applies a second round of chaining
-with a higher minimizer occurrence threshold if no good chain is found. In
-addition, minimap2 attempts to patch gaps between seeds with ungapped
-alignment.
-.TP
-.BI --split-prefix \ STR
-Prefix to create temporary files. Typically used for a multi-part index.
-.TP
-.BR --frag = no | yes
-Whether to enable the fragment mode [no]
-.TP
-.B --for-only
-Only map to the forward strand of the reference sequences. For paired-end
-reads in the forward-reverse orientation, the first read is mapped to forward
-strand of the reference and the second read to the reverse stand.
-.TP
-.B --rev-only
-Only map to the reverse complement strand of the reference sequences.
-.TP
-.BR --heap-sort = no | yes
-If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
-faster for short reads, but slower for long reads. [no]
-.TP
-.B --no-hash-name
-Produce the same alignment for identical sequences regardless of their sequence names.
-.SS Alignment options
-.TP 10
-.BI -A \ INT
-Matching score [2]
-.TP
-.BI -B \ INT
-Mismatching penalty [4]
-.TP
-.BI -b \ INT
-Mismatching penalty for transitions [same as
-.BR -B ].
-.TP
-.BI -O \ INT1[,INT2]
-Gap open penalty [4,24]. If
-.I INT2
-is not specified, it is set to
-.IR INT1 .
-.TP
-.BI -E \ INT1[,INT2]
-Gap extension penalty [2,1]. A gap of length
-.I k
-costs
-.RI min{ O1 + k * E1 , O2 + k * E2 }.
-In the splice mode, the second gap penalties are not used.
-.TP
-.BI -J \ INT
-Splice model [1]. 0 for the original minimap2 splice model that always penalizes non-GT-AG splicing;
-1 for the miniprot model that considers non-GT-AG. Option
-.B -C
-has no effect with the default
-.BR -J1 .
-.TP
-.BR -j \ FILE
-Junctions used to extend alignment towards ends of reads [].
-.I FILE
-can be gene annotations in the BED12 format (aka 12-column BED), or intron
-positions in 5-column BED with the strand column required. BED12 file can be
-converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'. This option is
-intended for short RNA-seq reads, while
-.B --junc-bed
-for long noisy RNA-seq reads.
-.TP
-.BI -C \ INT
-Cost for a non-canonical GT-AG splicing (effective with
-.B --splice
-.BR -J0 )
-[0].
-.TP
-.BI -z \ INT1[,INT2]
-Truncate an alignment if the running alignment score drops too quickly along
-the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the
-drop of score is above
-.IR INT2 ,
-minimap2 will reverse complement the query in the related region and align
-again to test small inversions. Minimap2 truncates alignment if there is an
-inversion or the drop of score is greater than
-.IR INT1 .
-Decrease
-.I INT2
-to find small inversions at the cost of performance and false positives.
-Increase
-.I INT1
-to improves the contiguity of alignment at the cost of poor alignment in the
-middle.
-.TP
-.BI -s \ INT
-Minimal peak DP alignment score to output [40]. The peak score is computed from
-the final CIGAR. It is the score of the max scoring segment in the alignment
-and may be different from the total alignment score.
-.TP
-.BI -u \ CHAR
-How to find canonical splicing sites GT-AG -
-.BR f :
-transcript strand;
-.BR b :
-both strands;
-.BR n :
-no attempt to match GT-AG [n]
-.TP
-.BI --end-bonus \ INT
-Score bonus when alignment extends to the end of the query sequence [0].
-.TP
-.BI --score-N \ INT
-Penalty of a mismatch involving ambiguous bases [1].
-.TP
-.BR --pairing = strong | weak | no
-How to pair paired-end reads [strong].
-.RB ` no '
-for aligning the two ends in a pair independently with no `properly paired' set.
-.RB ` weak '
-for aligning the two ends independently and then pairing the hits.
-.RB ` strong '
-for jointly aligning and pairing the two ends.
-.TP
-.BR --splice-flank = yes | no
-Assume the next base to a
-.B GT
-donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
-base to a
-.B AG
-acceptor tends to be C/T [no].
-This trend is evolutionarily conservative, all the way to S. cerevisiae
-(PMID:18688272). Specifying this option generally leads to higher junction
-accuracy by several percents, so it is applied by default with
-.BR --splice .
-However, the SIRV control does not honor this trend
-(only ~60%). This option reduces accuracy. If you are benchmarking minimap2
-on SIRV data, please add
-.B --splice-flank=no
-to the command line.
-.TP
-.BR --spsc \ FILE
-Splice scores []. Each line consists of five fields: 1) contig, 2) offset, 3) `+' or `-', 4) `D' or `A', and 5) score,
-where offset is the number of bases before a splice junction, `D' indicates the
-line corresponds to a donor site and `A' for an acceptor site.
-A positive score suggests the junction is preferred and a negative score
-suggests the junction is not preferred.
-.TP
-.BR --spsc0 \ INT
-Penalty for positions not in
-.I FILE
-specified by
-.B --spsc
-[5]. Effective with
-.B --spsc
-but not
-.BR --junc-bed .
-.TP
-.BR --spsc-scale \ FLOAT
-Scale splice scores in
-.B --spsc
-by
-.IR FLOAT
-rounded to the nearest integer [0.7].
-.TP
-.BR --junc-bed \ FILE
-Junctions to prefer during base alignment [].
-Same format as
-.BR -j .
-It is
-.I NOT
-recommended to apply this option to short RNA-seq reads. This would increase
-run time with little improvement to junction accuracy.
-.TP
-.BR --junc-bonus \ INT
-Score bonus for a splice donor or acceptor found in annotation [9]. Effective with
-.B --junc-bed
-but not
-.BR --spsc .
-.TP
-.BR --jump-min-match \ INT
-Minimum matching length to create a jump [3]. Equivalent to
-.B STAR
-.BR --alignSJDBoverhangMin .
-.TP
-.BI --end-seed-pen \ INT
-Drop a terminal anchor if
-.IR s <log( g )+ INT ,
-where
-.I s
-is the local alignment score around the anchor and
-.I g
-the length of the terminal gap in the chain. This option is only effective
-with
-.BR --splice .
-It helps to avoid tiny terminal exons. [6]
-.TP
-.B --no-end-flt
-Don't filter seeds towards the ends of chains before performing base-level
-alignment.
-.TP
-.BI --cap-sw-mem \ NUM
-Skip alignment if the DP matrix size is above
-.IR NUM .
-Set 0 to disable [100m].
-.TP
-.BI --cap-kalloc \ NUM
-Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
-.IR NUM .
-Set 0 to disable [500m].
-.SS Input/output options
-.TP 10
-.B -a
-Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
-by default.
-.TP
-.BI -o \ FILE
-Output alignments to
-.I FILE
-[stdout].
-.TP
-.B -Q
-Ignore base quality in the input file.
-.TP
-.B -L
-Write CIGAR with >65535 operators at the CG tag. Older tools are unable to
-convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM
-compatible with older tools. Newer tools recognizes this tag and reconstruct
-the real CIGAR in memory.
-.TP
-.BI -R \ STR
-SAM read group line in a format like
-.B @RG\\\\tID:foo\\\\tSM:bar
-[].
-.TP
-.B -y
-Copy input FASTA/Q comments to output.
-.TP
-.B -c
-Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
-.TP
-.BR --cs [= short | long ]
-Output the
-.B cs
-tag.
-If no argument is given,
-.RB ` short '
-is set. [none]
-.TP
-.B --MD
-Output the MD tag (see the SAM spec).
-.TP
-.B --eqx
-Output =/X CIGAR operators for sequence match/mismatch.
-.TP
-.B -Y
-In SAM output, use soft clipping for supplementary alignments.
-.TP
-.B --secondary-seq
-In SAM output, show query sequences for secondary alignments.
-.TP
-.B --write-junc
-Output splice junctions in 6-column BED: contig name, start, end,
-read name, score and strand. Score is the sum of donor and acceptor scores,
-where GT gets 3, GC gets 2 and AT gets 1 at donor sites,
-while AG gets 3 and AC gets 1 at acceptor sites.
-Alignments with mapping quality below 10 are ignored.
-.TP
-.BI --pass1 \ FILE
-Junctions BED file outputted by
-.B --write-junc
-[]. Rows with scores lower than 5 are ignored. When both
-.B -j
-and
-.B --pass1
-are present, junctions in
-.B -j
-are preferred over in
-.BR --pass1
-when there is ambiguity.
-.TP
-.BI --seed \ INT
-Integer seed for randomizing equally best hits. Minimap2 hashes
-.I INT
-and read name when choosing between equally best hits. [11]
-.TP
-.BI -t \ INT
-Number of threads [3]. Minimap2 uses at most three threads when indexing target
-sequences, and uses up to
-.IR INT +1
-threads when mapping (the extra thread is for I/O, which is frequently idle and
-takes little CPU time).
-.TP
-.B -2
-Use two I/O threads during mapping. By default, minimap2 uses one I/O thread.
-When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O
-thread may become the bottleneck. Apply this option to use one thread for input
-and another thread for output, at the cost of increased peak RAM.
-.TP
-.BI -K \ NUM
-Number of bases loaded into memory to process in a mini-batch [500M].
-Similar to option
-.BR -I ,
-K/M/G/k/m/g suffix is accepted. A large
-.I NUM
-helps load balancing in the multi-threading mode, at the cost of increased
-memory.
-.TP
-.BR --secondary = yes | no
-Whether to output secondary alignments [yes]
-.TP
-.BI --max-qlen \ NUM
-Filter out query sequences longer than
-.IR NUM .
-.TP
-.B --paf-no-hit
-In PAF, output unmapped queries; the strand and the reference name fields are
-set to `*'. Warning: some paftools.js commands may not work with such output
-for the moment.
-.TP
-.B --sam-hit-only
-In SAM, don't output unmapped reads.
-.TP
-.B --version
-Print version number to stdout
-.SS Preset options
-.TP 10
-.BI -x \ STR
-Preset []. This option applies multiple options at the same time. It should be
-applied before other options because options applied later will overwrite the
-values set by
-.BR -x .
-Available
-.I STR
-are:
-.RS
-.TP 10
-.B map-ont
-Align noisy long reads of ~10% error rate to a reference genome. This is the
-default mode.
-.TP
-.B lr:hq
-Align accurate long reads (error rate <1%) to a reference genome
-.RB ( -k19
-.B -w19 -U50,500
-.BR -g10k ).
-This was recommended by ONT developers for recent Nanopore reads
-produced with chemistry v14 that can reach ~99% in accuracy.
-It was shown to work better for accurate Nanopore reads
-than
-.BR map-hifi .
-.TP
-.B map-hifi
-Align PacBio high-fidelity (HiFi) reads to a reference genome
-.RB ( -xlr:hq
-.B -A1 -B4 -O6,26 -E2,1
-.BR -s200 ).
-It differs from
-.B lr:hq
-only in scoring. It has not been tested whether
-.B lr:hq
-would work better for PacBio HiFi reads.
-.TP
-.B map-pb
-Align older PacBio continuous long (CLR) reads to a reference genome
-.RB ( -Hk19 ).
-Note that this data type is effectively deprecated by HiFi.
-Unless you work on very old data, you probably want to use
-.B map-hifi
-or
-.BR lr:hq .
-.TP
-.B map-iclr
-Align Illumina Complete Long Reads (ICLR) to a reference genome
-.RB ( -k19
-.B -B6 -b4
-.BR -O10,50 ).
-This was recommended by Illumina developers.
-.TP
-.B asm5
-Long assembly to reference mapping
-.RB ( -k19
-.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
-.BR -N50 ).
-Typically, the alignment will not extend to regions with 5% or higher sequence
-divergence. Use this preset if the average divergence is not much higher than 0.1%.
-.TP
-.B asm10
-Long assembly to reference mapping
-.RB ( -k19
-.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
-.BR -N50 ).
-Use this if the average divergence is around 1%.
-.TP
-.B asm20
-Long assembly to reference mapping
-.RB ( -k19
-.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
-.BR -N50 ).
-Use this if the average divergence is around several percent.
-.TP
-.B splice
-Long-read spliced alignment
-.RB ( -k15
-.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
-.BR --splice-flank=yes ).
-In the splice mode, 1) long deletions are taken as introns and represented as
-the
-.RB ` N '
-CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
-costs are different during chaining; 4) the computation of the
-.RB ` ms '
-tag ignores introns to demote hits to pseudogenes.
-.TP
-.B splice:hq
-Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
-.RB ( -xsplice
-.B -C5 -O6,24
-.BR -B4 ).
-.TP
-.B splice:sr
-Spliced alignment for short RNA-seq reads
-.RB ( -xsplice:hq
-.B --frag=yes -m25 -s40 -2K100m --heap-sort=yes --pairing=weak --sr=rna --min-dp-len=20
-.BR --secondary=no ).
-.TP
-.B sr
-Short-read alignment without splicing
-.RB ( -k21
-.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m25
-.B -s40 -g100 -2K50m --heap-sort=yes
-.BR --secondary=no ).
-.TP
-.B ava-pb
-PacBio CLR all-vs-all overlap mapping
-.RB ( -Hk19
-.B -Xw5 -e0
-.BR -m100 ).
-.TP
-.B ava-ont
-Oxford Nanopore all-vs-all overlap mapping
-.RB ( -k15
-.B -Xw5 -e0 -m100
-.BR -r2k ).
-.RE
-.SS Miscellaneous options
-.TP 10
-.B --no-kalloc
-Use the libc default allocator instead of the kalloc thread-local allocator.
-This debugging option is mostly used with Valgrind to detect invalid memory
-accesses. Minimap2 runs slower with this option, especially in the
-multi-threading mode.
-.TP
-.B --print-qname
-Print query names to stderr, mostly to see which query is crashing minimap2.
-.TP
-.B --print-seeds
-Print seed positions to stderr, for debugging only.
-.SH OUTPUT FORMAT
-.PP
-Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
-default. PAF is a TAB-delimited text format with each line consisting of at
-least 12 fields as are described in the following table:
-.TS
-center box;
-cb | cb | cb
-r | c | l .
-Col	Type	Description
-_
-1	string	Query sequence name
-2	int	Query sequence length
-3	int	Query start coordinate (0-based)
-4	int	Query end coordinate (0-based)
-5	char	`+' if query/target on the same strand; `-' if opposite
-6	string	Target sequence name
-7	int	Target sequence length
-8	int	Target start coordinate on the original strand
-9	int	Target end coordinate on the original strand
-10	int	Number of matching bases in the mapping
-11	int	Number bases, including gaps, in the mapping
-12	int	Mapping quality (0-255 with 255 for missing)
-.TE
-
-.PP
-When alignment is available, column 11 gives the total number of sequence
-matches, mismatches and gaps in the alignment; column 10 divided by column 11
-gives the BLAST-like alignment identity. When alignment is unavailable,
-these two columns are approximate. PAF may optionally have additional fields in
-the SAM-like typed key-value format. Minimap2 may output the following tags:
-.TS
-center box;
-cb | cb | cb
-r | c | l .
-Tag	Type	Description
-_
-tp	A	Type of aln: P/primary, S/secondary and I,i/inversion
-cm	i	Number of minimizers on the chain
-s1	i	Chaining score
-s2	i	Chaining score of the best secondary chain
-NM	i	Total number of mismatches and gaps in the alignment
-MD	Z	To generate the ref sequence in the alignment
-AS	i	DP alignment score
-SA	Z	List of other supplementary alignments (with approximate CIGAR strings)
-ms	i	DP score of the max scoring segment in the alignment
-nn	i	Number of ambiguous bases in the alignment
-ts	A	Transcript strand (splice mode only)
-cg	Z	CIGAR string (only in PAF)
-cs	Z	Difference string
-dv	f	Approximate per-base sequence divergence
-de	f	Gap-compressed per-base sequence divergence
-rl	i	Length of query regions harboring repetitive seeds
-zd	i	Alignment broken due to Z-drop; bit 1: left broken; bit 2: right broken
-.TE
-
-.PP
-The
-.B cs
-tag encodes difference sequences in the short form or the entire query
-.I AND
-reference sequences in the long form. It consists of a series of operations:
-.TS
-center box;
-cb | cb |cb
-r | l | l .
-Op	Regex	Description
-_
- =	[ACGTN]+	Identical sequence (long form)
- :	[0-9]+	Identical sequence length
- *	[acgtn][acgtn]	Substitution: ref to query
- +	[acgtn]+	Insertion to the reference
- -	[acgtn]+	Deletion from the reference
- ~	[acgtn]{2}[0-9]+[acgtn]{2}	Intron length and splice signal
-.TE
-
-.SH LIMITATIONS
-.TP 2
-*
-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.
-.TP
-*
-Minimap2 requires SSE2 or NEON instructions to compile. It is possible to add
-non-SSE2/NEON support, but it would make minimap2 slower by several times.
-.SH SEE ALSO
-.PP
-miniasm(1), minimap(1), bwa(1).