From 0f7455cefa019dd6f09b11632bb4bdbf91abf5ba Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 14 Sep 2017 12:57:21 -0400 Subject: [PATCH] r365: documented the "sr" preset --- align.c | 2 +- main.c | 7 +++++-- minimap.h | 2 +- minimap2.1 | 8 +++++++- 4 files changed, 14 insertions(+), 5 deletions(-) diff --git a/align.c b/align.c index 1ed42e5..03f97d6 100644 --- a/align.c +++ b/align.c @@ -143,7 +143,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); fputc('\n', stderr); } - if (opt->flag & MM_F_SR) { + if (opt->flag & MM_F_APPROX_EXT) { flag |= KSW_EZ_APPROX_MAX; if (flag & KSW_EZ_EXTZ_ONLY) flag |= KSW_EZ_APPROX_DROP; } diff --git a/main.c b/main.c index 1f6b354..57fb5b5 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.1.1-r364-dirty" +#define MM_VERSION "2.1.1-r365-dirty" #ifdef __linux__ #include @@ -36,6 +36,7 @@ static struct option long_options[] = { { "splice", no_argument, 0, 0 }, { "cost-non-gt-ag", required_argument, 0, 0 }, { "no-sam-sq", no_argument, 0, 0 }, + { "approx-ext", no_argument, 0, 0 }, { "help", no_argument, 0, 'h' }, { "max-intron-len", required_argument, 0, 'G' }, { "version", no_argument, 0, 'V' }, @@ -113,6 +114,7 @@ int main(int argc, char *argv[]) else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq + else if (c == 0 && long_idx ==13) opt.flag |= MM_F_APPROX_EXT; // --approx-ext else if (c == 'V') { puts(MM_VERSION); return 0; @@ -163,7 +165,7 @@ int main(int argc, char *argv[]) } else if (strcmp(optarg, "short") == 0 || strcmp(optarg, "sr") == 0) { k = 21, w = 11, is_hpc = 0; minibatch_size = 50000000; - opt.flag |= MM_F_SR; + opt.flag |= MM_F_APPROX_EXT; opt.a = 2, opt.b = 8, opt.q = 12, opt.e = 2, opt.q2 = 32, opt.e2 = 1; opt.max_gap = 100; opt.pri_ratio = 0.5f; @@ -237,6 +239,7 @@ int main(int argc, char *argv[]) fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n"); fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n"); fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n"); + fprintf(fp_help, " sr: short single-end reads without splicing (see minimap2.1 for details)\n"); fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n"); return fp_help == stdout? 0 : 1; } diff --git a/minimap.h b/minimap.h index e0a28fd..4add2fe 100644 --- a/minimap.h +++ b/minimap.h @@ -19,7 +19,7 @@ #define MM_F_SPLICE_REV 0x200 #define MM_F_SPLICE_BOTH 0x400 #define MM_F_NO_SAM_SQ 0x800 -#define MM_F_SR 0x1000 +#define MM_F_APPROX_EXT 0x1000 #define MM_IDX_MAGIC "MMI\2" diff --git a/minimap2.1 b/minimap2.1 index 6cef237..3ce967f 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "6 September 2017" "minimap2-2.1.1-r341" "Bioinformatics tools" +.TH minimap2 1 "14 September 2017" "minimap2-2.1.1-r364-dirty" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -333,6 +333,12 @@ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the .RB ` ms ' tag ignores introns to demote hits to pseudogenes. +.TP +.B sr +Short single-end reads without splicing +.RB ( -k21 +.B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000 -n2 -m20 -s40 -g100 -K50m +.BR --approx-ext ). .RE .SS Miscellaneous options .TP 10