1package "nucmer"
2description "nucmer generates nucleotide alignments between two mutli-FASTA input
3files. The out.delta output file lists the distance between insertions
4and deletions that produce maximal scoring alignments between each
5sequence. The show-* utilities know how to read this format.
6
7By default, nucmer uses anchor matches that are unique in in the
8reference but not necessarily unique in the query. See --mum and
9--maxmatch for different bevahiors."
10
11option("mum") {
12  description "Use anchor matches that are unique in both the reference and query"
13  off }
14option("maxmatch") {
15  description "Use all anchor matches regardless of their uniqueness"
16  off; conflict "mum" }
17option("b", "breaklen") {
18  description "Set the distance an alignment extension will attempt to extend poor scoring regions before giving up"
19  uint32; default 200 }
20option("c", "mincluster") {
21  description "Sets the minimum length of a cluster of matches"
22  uint32; default 65 }
23option("D", "diagdiff") {
24  description "Set the maximum diagonal difference between two adjacent anchors in a cluster"
25  uint32; default 5 }
26option("d", "diagfactor") {
27  description "Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length"
28  double; default 0.12 }
29option("noextend") {
30  description "Do not perform cluster extension step"
31  off }
32option("f", "forward") {
33  description "Use only the forward strand of the Query sequences"
34  off }
35option("g", "maxgap") {
36  description "Set the maximum gap between two adjacent matches in a cluster"
37  uint32; default 90 }
38option("l", "minmatch") {
39  description "Set the minimum length of a single exact match"
40  uint32; default 20 }
41option("L", "minalign") {
42  description "Minimum length of an alignment, after clustering and extension"
43  uint32; default 0 }
44option("nooptimize") {
45  description "No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence"
46  off }
47option("r", "reverse") {
48  description "Use only the reverse complement of the Query sequences"
49  off; conflict "forward" }
50option("nosimplify") {
51  description "Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats"
52  off }
53option("p", "prefix") {
54  description "Write output to PREFIX.delta"
55  string; typestr "PREFIX"; default "out" }
56option("delta") {
57  description "Output delta file to PATH (instead of PREFIX.delta)"
58  c_string; typestr "PATH"; conflict "prefix" }
59option("sam-short") {
60  description "Output SAM file to PATH, short format"
61  c_string; typestr "PATH"; conflict "prefix", "delta" }
62option("sam-long") {
63  description "Output SAM file to PATH, long format"
64  c_string; typestr "PATH"; conflict "prefix", "delta", "sam-short" }
65option("save") {
66  description "Save suffix array to files starting with PREFIX"
67  string; typestr "PREFIX" }
68option("load") {
69  description "Load suffix array from file starting with PREFIX"
70  string; typestr "PREFIX" }
71option("batch") {
72  description "Proceed by batch of chunks of BASES from the reference"
73  uint64; typestr "BASES"
74  conflict "save", "load" }
75option("t", "threads") {
76  description "Use NUM threads (# of cores)"
77  uint32; typestr "NUM" }
78
79# Hidden / experimental options
80option("banded") {
81  description "Enforce absolute banding of dynamic programming matrix based on diagdiff parameter"
82  off; hidden }
83option("large") {
84  description "Force the use of large offsets"
85  off; hidden }
86option("G", "genome") {
87  description "Map genome to genome (long query sequences)"
88  off; hidden }
89option("M", "max-chunk") {
90  description "Max chunk. Stop adding sequence for a thread if more than MAX already."
91  uint64; typestr "MAX"; default 50000; hidden }
92
93arg("ref") {
94  description "Reference sequence file"
95  c_string; typestr "path" }
96arg("qry") {
97  description "Query sequence file"
98  c_string; typestr "path"
99  multiple; }
100