r151: documentations
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Heng Li
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12
main.c
12
main.c
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@ -10,7 +10,7 @@
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#include "minimap.h"
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#include "mmpriv.h"
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#define MM_VERSION "2.0-r150-pre"
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#define MM_VERSION "2.0-r151-pre"
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void liftrlimit()
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{
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@ -70,7 +70,7 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_mapopt_init(&opt);
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while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
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while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
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if (c == 'w') w = atoi(optarg);
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else if (c == 'k') k = atoi(optarg);
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else if (c == 'H') is_hpc = 1;
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@ -85,7 +85,7 @@ int main(int argc, char *argv[])
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else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
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else if (c == 'M') opt.mask_level = atof(optarg);
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else if (c == 'c') opt.flag |= MM_F_CIGAR;
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else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
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else if (c == 'T') opt.sdust_thres = atoi(optarg);
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else if (c == 'n') opt.min_cnt = atoi(optarg);
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@ -145,12 +145,12 @@ int main(int argc, char *argv[])
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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, " -X 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, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
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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, " ava10k: -Hk19 -w5 -Xp0 -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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fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
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fprintf(stderr, " Alignment:\n");
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@ -166,7 +166,7 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
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// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
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fprintf(stderr, " -V show version number\n");
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fprintf(stderr, "\nSee minimap2.1 for detailed description of the command-line options.\n");
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fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
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return 1;
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}
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22
minimap2.1
22
minimap2.1
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@ -142,7 +142,7 @@ 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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.B -X
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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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@ -160,7 +160,9 @@ the secondary chain will not be outputted or extended with DP alignment later.
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.BI -N \ INT
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Output at most
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.I INT
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secondary alignments [5]
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secondary alignments [5]. This option has no effect when
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.B -X
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is applied.
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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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@ -179,7 +181,7 @@ 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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PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -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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@ -224,14 +226,24 @@ by default.
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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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Number of threads [3]. Minimap2 uses at most three threads when indexing target
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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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.SS Miscellaneous options
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.TP 10
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.B --no-kalloc
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Use the libc default allocator instead of the kalloc thread-local allocator.
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This debugging option is mostly used with Valgrind to detect invalid memory
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accesses. Minimap2 runs slower with this option, especially in the
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multi-threading mode.
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.TP
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.B --print-qname
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Print query names to stderr, mostly to see which query is crashing minimap2.
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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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