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r365: documented the "sr" preset

This commit is contained in:
Heng Li 2017-09-14 12:57:21 -04:00
parent 4d3768bf26
commit 0f7455cefa
4 changed files with 14 additions and 5 deletions
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2
align.c
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@ -143,7 +143,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
fputc('\n', stderr); fputc('\n', stderr);
} }
if (opt->flag & MM_F_SR) { if (opt->flag & MM_F_APPROX_EXT) {
flag |= KSW_EZ_APPROX_MAX; flag |= KSW_EZ_APPROX_MAX;
if (flag & KSW_EZ_EXTZ_ONLY) flag |= KSW_EZ_APPROX_DROP; if (flag & KSW_EZ_EXTZ_ONLY) flag |= KSW_EZ_APPROX_DROP;
} }

7
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.1.1-r364-dirty" #define MM_VERSION "2.1.1-r365-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -36,6 +36,7 @@ static struct option long_options[] = {
{ "splice", no_argument, 0, 0 }, { "splice", no_argument, 0, 0 },
{ "cost-non-gt-ag", required_argument, 0, 0 }, { "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 }, { "no-sam-sq", no_argument, 0, 0 },
{ "approx-ext", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' }, { "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' }, { "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' }, { "version", no_argument, 0, 'V' },
@ -113,6 +114,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_APPROX_EXT; // --approx-ext
else if (c == 'V') { else if (c == 'V') {
puts(MM_VERSION); puts(MM_VERSION);
return 0; return 0;
@ -163,7 +165,7 @@ int main(int argc, char *argv[])
} else if (strcmp(optarg, "short") == 0 || strcmp(optarg, "sr") == 0) { } else if (strcmp(optarg, "short") == 0 || strcmp(optarg, "sr") == 0) {
k = 21, w = 11, is_hpc = 0; k = 21, w = 11, is_hpc = 0;
minibatch_size = 50000000; minibatch_size = 50000000;
opt.flag |= MM_F_SR; opt.flag |= MM_F_APPROX_EXT;
opt.a = 2, opt.b = 8, opt.q = 12, opt.e = 2, opt.q2 = 32, opt.e2 = 1; opt.a = 2, opt.b = 8, opt.q = 12, opt.e = 2, opt.q2 = 32, opt.e2 = 1;
opt.max_gap = 100; opt.max_gap = 100;
opt.pri_ratio = 0.5f; opt.pri_ratio = 0.5f;
@ -237,6 +239,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n"); fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n"); fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n"); fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n");
fprintf(fp_help, " sr: short single-end reads without splicing (see minimap2.1 for details)\n");
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n"); fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
return fp_help == stdout? 0 : 1; return fp_help == stdout? 0 : 1;
} }

2
minimap.h
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@ -19,7 +19,7 @@
#define MM_F_SPLICE_REV 0x200 #define MM_F_SPLICE_REV 0x200
#define MM_F_SPLICE_BOTH 0x400 #define MM_F_SPLICE_BOTH 0x400
#define MM_F_NO_SAM_SQ 0x800 #define MM_F_NO_SAM_SQ 0x800
#define MM_F_SR 0x1000 #define MM_F_APPROX_EXT 0x1000
#define MM_IDX_MAGIC "MMI\2" #define MM_IDX_MAGIC "MMI\2"

8
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "6 September 2017" "minimap2-2.1.1-r341" "Bioinformatics tools" .TH minimap2 1 "14 September 2017" "minimap2-2.1.1-r364-dirty" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@ -333,6 +333,12 @@ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the costs are different during chaining; 4) the computation of the
.RB ` ms ' .RB ` ms '
tag ignores introns to demote hits to pseudogenes. tag ignores introns to demote hits to pseudogenes.
.TP
.B sr
Short single-end reads without splicing
.RB ( -k21
.B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000 -n2 -m20 -s40 -g100 -K50m
.BR --approx-ext ).
.RE .RE
.SS Miscellaneous options .SS Miscellaneous options
.TP 10 .TP 10