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Convert "properly read" constants to command line parameters #309

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Convert "properly read" constants to command line parameters #309

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8c15147
Convert "properly read" constants to command line parameters
Jan 29, 2021
de39326
Remove unused constants
Jan 29, 2021
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5 changes: 5 additions & 0 deletions bwamem.c
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Expand Up @@ -105,6 +105,11 @@ mem_opt_t *mem_opt_init()
o->min_chain_weight = 0;
o->max_chain_extend = 1<<30;
o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);

o->outlier_bound_mem = 2.0;
o->mapping_bound_mem = 3.0;
o->max_stddev_mem = 4.0;

bwa_fill_scmat(o->a, o->b, o->mat);
return o;
}
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4 changes: 4 additions & 0 deletions bwamem.h
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Expand Up @@ -81,6 +81,10 @@ typedef struct {
int max_matesw; // perform maximally max_matesw rounds of mate-SW for each end
int max_XA_hits, max_XA_hits_alt; // if there are max_hits or fewer, output them all
int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset

float outlier_bound_mem; // controls how to calculate low and high boundaries for computing mean and std.dev
float mapping_bound_mem; // controls how to calculate low and high boundaries for proper pairs. Low and high boundaries is calculated : F(Q1, Q2, Q3, mapping_bound_mem, max_stddev_mem) where Q2 is median insert size, Q1 and Q3 are lower and higher quartile (also see max_stddev_mem).
float max_stddev_mem; // controls how to calculate low and high boundaries for proper pairs. Low and high boundaries is calculated : F(Q1, Q2, Q3, mapping_bound_mem, max_stddev_mem) where Q2 is median insert size, Q1 and Q3 are lower and higher quartile (also see mapping_bound_mem).
} mem_opt_t;

typedef struct {
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15 changes: 6 additions & 9 deletions bwamem_pair.c
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Expand Up @@ -42,9 +42,6 @@
#define MIN_RATIO 0.8
#define MIN_DIR_CNT 10
#define MIN_DIR_RATIO 0.05
#define OUTLIER_BOUND 2.0
#define MAPPING_BOUND 3.0
#define MAX_STDDEV 4.0

static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
{
Expand Down Expand Up @@ -103,9 +100,9 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
p25 = q->a[(int)(.25 * q->n + .499)];
p50 = q->a[(int)(.50 * q->n + .499)];
p75 = q->a[(int)(.75 * q->n + .499)];
r->low = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
r->low = (int)(p25 - opt->outlier_bound_mem * (p75 - p25) + .499);
if (r->low < 1) r->low = 1;
r->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
r->high = (int)(p75 + opt->outlier_bound_mem * (p75 - p25) + .499);
fprintf(stderr, "[M::%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
fprintf(stderr, "[M::%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r->low, r->high);
for (i = x = 0, r->avg = 0; i < q->n; ++i)
Expand All @@ -117,10 +114,10 @@ void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *
r->std += (q->a[i] - r->avg) * (q->a[i] - r->avg);
r->std = sqrt(r->std / x);
fprintf(stderr, "[M::%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r->avg, r->std);
r->low = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
if (r->low > r->avg - MAX_STDDEV * r->std) r->low = (int)(r->avg - MAX_STDDEV * r->std + .499);
if (r->high < r->avg + MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
r->low = (int)(p25 - opt->mapping_bound_mem * (p75 - p25) + .499);
r->high = (int)(p75 + opt->mapping_bound_mem * (p75 - p25) + .499);
if (r->low > r->avg - opt->max_stddev_mem * r->std) r->low = (int)(r->avg - opt->max_stddev_mem * r->std + .499);
if (r->high < r->avg + opt->max_stddev_mem * r->std) r->high = (int)(r->avg + opt->max_stddev_mem * r->std + .499);
if (r->low < 1) r->low = 1;
fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
free(q->a);
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8 changes: 7 additions & 1 deletion fastmap.c
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Expand Up @@ -156,8 +156,11 @@ int main_mem(int argc, char *argv[])

aux.opt = opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:b:e:g:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'b') opt->outlier_bound_mem = atof(optarg);
else if (c == 'e') opt->mapping_bound_mem = atof(optarg);
else if (c == 'g') opt->max_stddev_mem = atof(optarg);
else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
Expand Down Expand Up @@ -267,6 +270,9 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
fprintf(stderr, "Algorithm options:\n\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -b FLOAT controls how to calculate low and high boundaries for computing mean and std.dev [%f]\n", opt->outlier_bound_mem);
fprintf(stderr, " -e FLOAT mapping bound mem. Controls how to calculate low and high boundaries for proper pairs. [%f]\n", opt->mapping_bound_mem);
fprintf(stderr, " -g FLOAT max stddev mem. Controls how to calculate low and high boundaries for proper pairs. [%f]\n", opt->max_stddev_mem);
fprintf(stderr, " -k INT minimum seed length [%d]\n", opt->min_seed_len);
fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w);
fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop);
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