diff --git a/main.c b/main.c index a9928d9..a7a9d82 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.2-r517-dirty" +#define MM_VERSION "2.2-r518-dirty" #ifdef __linux__ #include @@ -231,7 +231,7 @@ int main(int argc, char *argv[]) fprintf(fp_help, " -c output CIGAR in PAF\n"); fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none]\n"); fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads); - fprintf(fp_help, " -K NUM minibatch size for mapping [200M]\n"); + fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n"); // fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose); fprintf(fp_help, " --version show version number\n"); fprintf(fp_help, " Preset:\n"); @@ -240,8 +240,8 @@ int main(int argc, char *argv[]) fprintf(fp_help, " map-ont: -k15 (Oxford Nanopore vs reference mapping)\n"); fprintf(fp_help, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n"); fprintf(fp_help, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n"); - 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, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)\n"); + fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 --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"); diff --git a/map.c b/map.c index c6c80af..284d48c 100644 --- a/map.c +++ b/map.c @@ -36,7 +36,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) opt->end_bonus = -1; opt->min_dp_max = opt->min_chain_score * opt->a; opt->min_ksw_len = 200; - opt->mini_batch_size = 200000000; + opt->mini_batch_size = 500000000; opt->pe_ori = 0; // FF opt->pe_bonus = 33; @@ -61,12 +61,10 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) io->is_hpc = 0, io->k = 15, io->w = 5; mo->flag |= MM_F_AVA | MM_F_NO_SELF; mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25; - mo->mini_batch_size = 500000000; } else if (strcmp(preset, "ava-pb") == 0) { io->is_hpc = 1, io->k = 19, io->w = 5; mo->flag |= MM_F_AVA | MM_F_NO_SELF; mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25; - mo->mini_batch_size = 500000000; } else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) { io->is_hpc = 1, io->k = 19; } else if (strcmp(preset, "map-ont") == 0) { diff --git a/minimap2.1 b/minimap2.1 index 2a96c91..b1a2837 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "20 September 2017" "minimap2-2.2 (r420)" "Bioinformatics tools" +.TH minimap2 1 "17 October 2017" "minimap2-2.2-dirty (r518)" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -263,18 +263,13 @@ thread may become the bottleneck. Apply this option to use one thread for input and another thread for output, at the cost of increased peak RAM. .TP .BI -K \ NUM -Number of bases loaded into memory to process in a mini-batch [200M]. +Number of bases loaded into memory to process in a mini-batch [500M]. Similar to option .BR -I , K/M/G/k/m/g suffix is accepted. A large .I NUM helps load balancing in the multi-threading mode, at the cost of increased -memory. Preset -.B ava-pb -and -.B ava-ont -use -.BR -K500m . +memory. .TP .B --version Print version number to stdout @@ -320,13 +315,13 @@ Up to 10% sequence divergence. .B ava-pb PacBio all-vs-all overlap mapping .RB ( -Hk19 -.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip +.B -w5 -Xp0 -m100 -g10000 --max-chain-skip .BR 25 ). .TP .B ava-ont Oxford Nanopore all-vs-all overlap mapping .RB ( -k15 -.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip +.B -w5 -Xp0 -m100 -g10000 --max-chain-skip .BR 25 ). Similarly, the major difference from .B ava-pb