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Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option

This commit is contained in:
Heng Li 2022-03-06 18:21:49 -05:00
parent 5d250d35de 34caf50d46
commit 49c397d16e
1 changed files with 8 additions and 2 deletions
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10
fastmap.c
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@ -156,7 +156,7 @@ 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:F:")) >= 0) {
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:F:z:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg;
@ -199,6 +199,7 @@ int main_mem(int argc, char *argv[])
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->max_XA_hits_alt = strtol(p+1, &p, 10);
}
else if (c == 'z') opt->XA_drop_ratio = atof(optarg);
else if (c == 'Q') {
opt0.mapQ_coef_len = 1;
opt->mapQ_coef_len = atoi(optarg);
@ -303,7 +304,12 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -h INT[,INT] if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
fprintf(stderr, " -h INT[,INT] if there are <INT hits with score >%.2f%% of the max score, output all in XA [%d,%d]\n",
opt->XA_drop_ratio * 100.0,
opt->max_XA_hits, opt->max_XA_hits_alt);
fprintf(stderr, " A second value may be given for alternate sequences.\n");
fprintf(stderr, " -z FLOAT The fraction of the max score to use with -h [%f].\n", opt->XA_drop_ratio);
fprintf(stderr, " specify the mean, standard deviation (10%% of the mean if absent), max\n");
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -V output the reference FASTA header in the XR tag\n");