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reordering BWA-SW command-line prompt

This commit is contained in:
Heng Li 2011-11-23 23:36:08 -05:00
parent b17b6577ac
commit 9f84384ed2
2 changed files with 12 additions and 10 deletions
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2
bwtsw2.h
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@ -13,7 +13,7 @@
typedef struct {
int a, b, q, r, t, qr, bw;
int z, is, t_seeds, hard_clip;
int z, is, t_seeds, hard_clip, multi_2nd;
float mask_level, coef;
int n_threads, chunk_size;
} bsw2opt_t;

20
bwtsw2_main.c
View File

@ -17,7 +17,7 @@ int bwa_bwtsw2(int argc, char *argv[])
opt = bsw2_init_opt();
srand48(11);
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:")) >= 0) {
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:M")) >= 0) {
switch (c) {
case 'q': opt->q = atoi(optarg); break;
case 'r': opt->r = atoi(optarg); break;
@ -31,6 +31,7 @@ int bwa_bwtsw2(int argc, char *argv[])
case 'm': opt->mask_level = atof(optarg); break;
case 'c': opt->coef = atof(optarg); break;
case 'N': opt->t_seeds = atoi(optarg); break;
case 'M': opt->multi_2nd = 1; break;
case 'H': opt->hard_clip = 1; break;
case 'f': xreopen(optarg, "w", stdout); break;
}
@ -44,19 +45,20 @@ int bwa_bwtsw2(int argc, char *argv[])
fprintf(stderr, " -b INT mismatch penalty [%d]\n", opt->b);
fprintf(stderr, " -q INT gap open penalty [%d]\n", opt->q);
fprintf(stderr, " -r INT gap extension penalty [%d]\n", opt->r);
fprintf(stderr, "\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, "\n");
fprintf(stderr, " -w INT band width [%d]\n", opt->bw);
fprintf(stderr, " -m FLOAT mask level [%.2f]\n", opt->mask_level);
fprintf(stderr, "\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -f FILE file to output results to instead of stdout\n");
fprintf(stderr, " -H in SAM output, use hard clipping instead of soft clipping\n");
fprintf(stderr, " -M mark multi-part alignments as secondary\n");
fprintf(stderr, "\n");
fprintf(stderr, " -T INT score threshold divided by a [%d]\n", opt->t);
fprintf(stderr, " -s INT maximum seeding interval size [%d]\n", opt->is);
fprintf(stderr, " -z INT Z-best [%d]\n", opt->z);
fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
fprintf(stderr, " -H in SAM output, use hard clipping rather than soft\n");
fprintf(stderr, " -f FILE file to output results to instead of stdout\n\n");
fprintf(stderr, " -z INT Z-best [%d]\n", opt->z);
fprintf(stderr, " -s INT maximum seeding interval size [%d]\n", opt->is);
fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
fprintf(stderr, "\n");
fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
fprintf(stderr, " BACs, the default setting usually works well. For the current PacBio\n");
fprintf(stderr, " reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");