From a3e7a575fb8b2a046f4f99ce3cb09f0418c179c5 Mon Sep 17 00:00:00 2001 From: Torsten Seemann Date: Mon, 4 Nov 2019 07:38:10 +1100 Subject: [PATCH 1/2] Add splice:hq to --help --- main.c | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/main.c b/main.c index 84a536b..a5633c2 100644 --- a/main.c +++ b/main.c @@ -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; } From 081df6ac7df97c43f2d45a1d62840a62bdf03683 Mon Sep 17 00:00:00 2001 From: xdudiagnoa <47234985+xdudiagnoa@users.noreply.github.com> Date: Mon, 16 Sep 2019 17:21:40 +0800 Subject: [PATCH 2/2] Fix example.c seq read logic for every idx should map all input seqs --- example.c | 2 ++ 1 file changed, 2 insertions(+) diff --git a/example.c b/example.c index 80e493c..ca1fdbe 100644 --- a/example.c +++ b/example.c @@ -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;