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replaced --approx-ext with --sr 

--sr disables Z-drop and may come with other heurstics
This commit is contained in:
Heng Li 2017-09-20 10:51:18 -04:00
parent 4979e66ff0
commit 7a9b4db874
5 changed files with 12 additions and 10 deletions
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10
align.c
View File

@ -136,6 +136,7 @@ static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) //
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *mat, int w, int flag, ksw_extz_t *ez) static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *mat, int w, int flag, ksw_extz_t *ez)
{ {
int zdrop = opt->zdrop;
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) { if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i; int i;
fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, flag, opt->zdrop); fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, flag, opt->zdrop);
@ -144,16 +145,17 @@ 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_APPROX_EXT) { if (opt->flag & MM_F_SR) {
zdrop = (qlen < tlen? qlen : tlen) * opt->a; // zdrop disabled
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;
} }
if (opt->flag & MM_F_SPLICE) if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, opt->zdrop, flag, ez); ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, flag, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2) else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez); ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, flag, ez);
else else
ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, opt->zdrop, flag, ez); ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, flag, ez);
} }
static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x) static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x)

4
main.c
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@ -36,7 +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 }, { "sr", 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' },
@ -114,7 +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 == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 'V') { else if (c == 'V') {
puts(MM_VERSION); puts(MM_VERSION);
return 0; return 0;

2
map.c
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@ -75,7 +75,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->min_dp_max = 200; mo->min_dp_max = 200;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) { } else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11; io->is_hpc = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_APPROX_EXT; mo->flag |= MM_F_SR;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1; mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 100; mo->max_gap = 100;
mo->pri_ratio = 0.5f; mo->pri_ratio = 0.5f;

2
minimap.h
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@ -17,7 +17,7 @@
#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_APPROX_EXT 0x1000 #define MM_F_SR 0x1000
#define MM_IDX_MAGIC "MMI\2" #define MM_IDX_MAGIC "MMI\2"

4
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "17 September 2017" "minimap2-2.2 (r409)" "Bioinformatics tools" .TH minimap2 1 "20 September 2017" "minimap2-2.2 (r420)" "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
@ -338,7 +338,7 @@ tag ignores introns to demote hits to pseudogenes.
Short single-end reads without splicing Short single-end reads without splicing
.RB ( -k21 .RB ( -k21
.B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000 -n2 -m20 -s40 -g100 -K50m .B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000 -n2 -m20 -s40 -g100 -K50m
.BR --approx-ext ). .BR --sr ).
.RE .RE
.SS Miscellaneous options .SS Miscellaneous options
.TP 10 .TP 10