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minimap2
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Heng Li 2019-12-23 17:33:56 -05:00
parent 367aed4271 081df6ac7d
commit a79cb3e991
2 changed files with 7 additions and 5 deletions
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2
example.c
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@ -35,6 +35,8 @@ int main(int argc, char *argv[])
while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
gzrewind(f);
kseq_rewind(ks);
while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
mm_reg1_t *reg;
int j, i, n_reg;

10
main.c
View File

@ -323,11 +323,11 @@ int main(int argc, char *argv[])
fprintf(fp_help, " --version show version number\n");
fprintf(fp_help, " Preset:\n");
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
fprintf(fp_help, " - map-pb/map-ont: PacBio/Nanopore vs reference mapping\n");
fprintf(fp_help, " - ava-pb/ava-ont: PacBio/Nanopore read overlap\n");
fprintf(fp_help, " - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - splice: long-read spliced alignment\n");
fprintf(fp_help, " - sr: genomic short-read mapping\n");
fprintf(fp_help, " - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
fprintf(fp_help, " - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
fprintf(fp_help, " - sr - genomic short-read mapping\n");
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of these and other advanced command-line options.\n");
return fp_help == stdout? 0 : 1;
}