finished the first draft of manpage
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Heng Li
parent
a9f089f0aa
commit
2338e887d9
2
chain.c
2
chain.c
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@ -50,7 +50,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
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dd = dr > dq? dr - dq : dq - dr;
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if (dd > bw) continue;
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sc = dq > q_span && dr > q_span? q_span : dq < dr? dq : dr;
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sc = f[j] + sc - (dd? ilog2_32(dd) : 0);
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sc = f[j] + sc - (dd? ilog2_32(dd) : 0); // TODO: consider to also penalize the shortest distance
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if (sc > max_f) max_f = sc, max_j = j;
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}
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if (max_j >= 0) f[i] = max_f, p[i] = max_j;
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8
main.c
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main.c
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@ -135,14 +135,14 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -d FILE dump index to FILE []\n");
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fprintf(stderr, " Mapping:\n");
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fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
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fprintf(stderr, " -g INT split a mapping if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
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fprintf(stderr, " -r INT bandwidth [%d]\n", opt.bw);
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fprintf(stderr, " -n INT minimal number of minimizers [%d]\n", opt.min_cnt);
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fprintf(stderr, " -g INT stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
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fprintf(stderr, " -r INT bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
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fprintf(stderr, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
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fprintf(stderr, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
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// fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
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fprintf(stderr, " -S skip self and dual mappings (for the all-vs-all mode)\n");
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fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
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fprintf(stderr, " -D FLOAT min fraction of seed matches [%g]\n", opt.min_seedcov_ratio);
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fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
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fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 -D.05 (PacBio/ONT all-vs-all read mapping)\n");
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fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
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151
minimap2.1
151
minimap2.1
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@ -8,6 +8,13 @@ minimap2 - mapping and alignment between collections of DNA sequences
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* Indexing the target sequences (optional):
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.RS 4
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minimap2
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.RB [ -x
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.IR preset ]
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.B -d
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.I target.mmi
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.I target.fa
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.br
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minimap2
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.RB [ -H ]
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.RB [ -k
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.IR kmer ]
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@ -74,18 +81,15 @@ SAM format.
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.TP 10
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.BI -k \ INT
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Minimizer k-mer length [17]
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.TP
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.BI -w \ INT
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Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
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in a window of w consecutive k-mers.
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.TP
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.B -H
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Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
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contracting homopolymer runs to a single base. An HPC minimizer is a minimizer
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on the HPC sequence.
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.TP
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.BI -I \ NUM
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Load at most
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@ -100,7 +104,6 @@ multiple times to map it against each batch of target sequences.
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.I NUM
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may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
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multi-part index.
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.TP
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.BI -d \ FILE
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Save the minimizer index of
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@ -116,8 +119,125 @@ to
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Ignore top
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.I FLOAT
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fraction of most frequent minimizers [0.0002]
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.TP
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.BI -g \ INT
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Stop chain enlongation if there are no minimizers in
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.IR INT -bp
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[10000].
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.TP
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.BI -r \ INT
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Bandwidth used in chaining and DP-based alignment [1000]. This option
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approximately controls the maximum gap size.
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.TP
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.BI -n \ INT
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Discard chains consisting of
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.RI < INT
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number of minimizers [3]
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.TP
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.BI -m \ INT
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Discard chains with chaining score
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.RI < INT
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[40]. Chaining score equals the approximate number of matching bases (exact if
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not using
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.BR -H )
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minus base-2 logarithm gap penalty. It is computed with dynamic programming.
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.TP
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.B -S
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Perform all-vs-all mapping. In this mode, if the query sequence name is
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lexicographically larger than the target sequence name, the hits between them
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will be suppressed; if the query sequence name is the same as the target name,
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diagonal minimizer hits will also be suppressed.
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.TP
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.BI -p \ FLOAT
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Minimal secondary-to-primary score ratio to output secondary mappings [2].
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Between two chains overlaping over half of the shorter chain (controled by
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.BR --mask-level ),
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the chain with a lower score is secondary to the chain with a higher score.
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If the ratio of the scores is below
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.IR FLOAT ,
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the secondary chain will not be outputted or extended with DP alignment later.
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The default value suppresses all secondary chains.
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.TP
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.BI -D \ FLOAT
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Discard a chain if the fraction of matching bases over the length of
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query/target sequences in the chain is
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.RI < FLOAT
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[0].
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.TP
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.BI -x \ STR
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Preset []. This option applies multiple options at the same time. It should be
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applied before other options because options applied later will overwrite the
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values set by
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.BR -x .
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Available
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.I STR
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are:
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.RS
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.TP 8
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.B ava10k
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PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -Sw5 -p0 -m100 -D.05)
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.TP
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.B map10k
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PacBio/Oxford Nanopore read to reference mapping (-Hk19)
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.TP
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.B asm1m
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Long assembly to reference mapping (-k19 -w19)
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.RE
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.SS Alignment options
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.TP 10
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.BI -A \ INT
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Matching score [1]
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.TP
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.BI -B \ INT
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Mismatching penalty [2]
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.TP
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.BI -O \ INT
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Gap open penalty [2]
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.TP
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.BI -E \ INT
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Gap extension penalty [1]. A gap of length
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.I l
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costs
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.RI {-O}+{-E}* l .
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.TP
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.BI -z \ INT
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Break an alignment if the running score drops too quickly along the diagonal of
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the DP matrix (diagonal X-drop, or Z-drop) [200]. Increasing the value improves
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the contiguity of the alignment at the cost of poor alignment in the middle
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(e.g. caused by a long inversion).
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.TP
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.BI -s \ INT
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Minimal peak DP alignment score to output [40]. The peak score is computed from
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the final CIGAR. It is the score of the max scoring segment in the alignment
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and may be different from the total alignment score.
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.SS Input/output options
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.TP 10
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.B -b
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Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
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by default.
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.TP
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.B -c
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Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
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.TP
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.BI -t \ INT
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Number of threads [3]. Minimap2 uses at most three threads when collecting
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minimizers on target sequences, and uses up to
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.IR INT +1
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threads when mapping (the extra thread is for I/O, which is frequently idle and
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takes little CPU time).
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.TP
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.B -V
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Print version number to stdout
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.SH OUTPUT FORMAT
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.PP
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Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
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default. PAF is a TAB-delimited text format with each line consisting of at
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least 12 fields as are described in the following table:
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.TS
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center box;
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@ -139,6 +259,29 @@ _
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12 int Mapping quality (0-255 with 255 for missing)
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.TE
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.PP
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When alignment is available, column 11 gives the total number of sequence
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matches, mismatches and gaps in the alignment; column 10 divided by column 11
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gives the BLAST-like alignment identity. When alignment is unavailable,
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these two columns are approximate. PAF may optionally have additional fields in
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the SAM-like typed key-value format. Minimap2 may output the following tags:
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.TS
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center box;
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cb | cb | cb
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r | c | l .
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Tag Type Description
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_
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cm i Number of minimizers on the chain
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s1 i Chaining score
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s2 i Chaining score of the best secondary chain
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NM i Total number of mismatches and gaps in the alignment
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AS i DP alignment score
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ms i DP score of the max scoring segment in the alignment
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nn i Number of ambiguous bases in the alignment
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cg Z CIGAR string (only in PAF)
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.TE
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.SH SEE ALSO
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.PP
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miniasm(1), minimap(1), bwa(1).
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