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wtdbg.c
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wtdbg.c
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/*
*
* Copyright (c) 2011, Jue Ruan <[email protected]>
*
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "wtdbg.h"
#include "wtdbg-graph.h"
#include <getopt.h>
#include <regex.h>
#ifndef VERSION
#define VERSION 0.0
#endif
#ifndef RELEASE
#define RELEASE 19830203
#endif
static struct option prog_opts[] = {
{"cpu", 1, 0, 't'},
{"input", 1, 0, 'i'},
{"err-free-seq", 1, 0, 'I'},
{"force", 0, 0, 'f'},
{"prefix", 1, 0, 'o'},
{"preset", 1, 0, 'x'},
{"kmer-fsize", 1, 0, 'k'},
{"kmer-psize", 1, 0, 'p'},
{"kmer-depth-max", 1, 0, 'K'},
{"kmer-depth-min", 1, 0, 'E'},
{"genome-size", 1, 0, 'g'},
{"rdcov-cutoff", 1, 0, 'X'},
{"rdname-filter", 1, 0, 3007},
{"rdname-includeonly", 1, 0, 3008},
{"rdcov-filter", 1, 0, 2009},
//{"kmer-depth-min-filter", 0, 0, 'F'},
{"kmer-subsampling", 1, 0, 'S'},
{"kbm-parts", 1, 0, 1035},
{"dp-max-gap", 1, 0, 2005},
{"dp-max-var", 1, 0, 2006},
{"dp-penalty-gap", 1, 0, 2007},
{"dp-penalty-var", 1, 0, 2008},
{"aln-min-length", 1, 0, 'l'},
{"aln-min-match", 1, 0, 'm'},
{"aln-min-similarity", 1, 0, 's'},
{"aln-max-var", 1, 0, 2004},
{"realign", 0, 0, 'R'},
{"realn-kmer-psize", 1, 0, 3001},
{"realn-kmer-subsampling", 1, 0, 3002},
{"realn-min-length", 1, 0, 3003},
{"realn-min-match", 1, 0, 3004},
{"realn-min-similarity", 1, 0, 3005},
{"realn-max-var", 1, 0, 3006},
//{"corr-mode", 1, 0, 2010},
//{"corr-min", 1, 0, 2012},
//{"corr-max", 1, 0, 2013},
//{"corr-cov", 1, 0, 2014},
//{"corr-block-size", 1, 0, 2015},
//{"corr-block-step", 1, 0, 2016},
{"keep-multiple-alignment-parts", 1, 0, 2011},
{"verbose", 0, 0, 'v'},
{"quiet", 0, 0, 'q'},
{"version", 0, 0, 'V'},
{"help", 0, 0, 1000}, // detailed document
{"tidy-reads", 1, 0, 'L'},
{"tidy-name", 0, 0, 1001},
{"err-free-nodes", 0, 0, 1002},
{"limit-input", 1, 0, 1003},
{"node-len", 1, 0, 1004},
{"node-ovl", 1, 0, 1005},
{"node-drop", 1, 0, 1006},
{"edge-min", 1, 0, 'e'},
{"edge-max-span", 1, 0, 3009},
{"node-min", 1, 0, 1007},
{"node-max", 1, 0, 1008},
{"ttr-cutoff-depth", 1, 0, 1009},
{"ttr-cutoff-ratio", 1, 0, 1010},
{"dump-seqs", 1, 0, 1036},
{"dump-kbm", 1, 0, 1011},
{"load-seqs", 1, 0, 2002},
{"load-kbm", 1, 0, 1012},
{"load-alignments", 1, 0, 1013},
{"load-nodes", 1, 0, 2000},
{"load-clips", 1, 0, 2001},
{"aln-strand", 1, 0, 1014},
{"bubble-step", 1, 0, 1015},
{"tip-step", 1, 0, 1016},
{"ctg-min-length", 1, 0, 1017},
{"ctg-min-nodes", 1, 0, 1018},
{"minimal-output", 0, 0, 1019},
{"bin-complexity-cutoff", 1, 0, 1020},
{"aln-dovetail", 1, 0, 1021},
{"no-local-graph-analysis", 0, 0, 1022},
{"no-read-length-sort", 0, 0, 1023},
{"keep-isolated-nodes", 0, 0, 1024},
{"no-read-clip", 0, 0, 1025},
{"no-chainning-clip", 0, 0, 1026},
{"aln-bestn", 1, 0, 1027},
{"aln-maxhit", 1, 0, 1028},
{"aln-kmer-sampling", 1, 0, 1029},
{"aln-noskip", 0, 0, 'A'},
{"node-matched-bins", 1, 0, 1031},
{"rescue-low-cov-edges", 0, 0, 1032},
{"drop-low-cov-edges", 0, 0, 1033},
{"mem-stingy", 0, 0, 1034},
{0, 0, 0, 0}
};
int usage(int level){
printf(
"WTDBG: De novo assembler for long noisy sequences\n"
"Author: Jue Ruan <[email protected]>\n"
"Version: %s (%s)\n"
"Usage: wtdbg2 [options] -i <reads.fa> -o <prefix> [reads.fa ...]\n"
"Options:\n"
" -i <string> Long reads sequences file (REQUIRED; can be multiple), []\n"
" -o <string> Prefix of output files (REQUIRED), []\n"
" -t <int> Number of threads, 0 for all cores, [4]\n"
" -f Force to overwrite output files\n"
" -x <string> Presets, comma delimited, []\n"
" preset1/rsII/rs: -p 21 -S 4 -s 0.05 -L 5000\n"
" preset2: -p 0 -k 15 -AS 2 -s 0.05 -L 5000\n"
" preset3: -p 19 -AS 2 -s 0.05 -L 5000\n"
" sequel/sq\n"
" nanopore/ont:\n"
" (genome size < 1G: preset2) -p 0 -k 15 -AS 2 -s 0.05 -L 5000\n"
" (genome size >= 1G: preset3) -p 19 -AS 2 -s 0.05 -L 5000\n"
" preset4/corrected/ccs: -p 21 -k 0 -AS 4 -K 0.05 -s 0.5\n"
" -g <number> Approximate genome size (k/m/g suffix allowed) [0]\n"
" -X <float> Choose the best <float> depth from input reads(effective with -g) [50.0]\n"
" -L <int> Choose the longest subread and drop reads shorter than <int> (5000 recommended for PacBio) [0]\n"
" Negative integer indicate tidying read names too, e.g. -5000.\n"
" -k <int> Kmer fsize, 0 <= k <= 23, [0]\n"
" -p <int> Kmer psize, 0 <= p <= 23, [21]\n"
" k + p <= 25, seed is <k-mer>+<p-homopolymer-compressed>\n"
" -K <float> Filter high frequency kmers, maybe repetitive, [1000.05]\n"
" >= 1000 and indexing >= (1 - 0.05) * total_kmers_count\n"
" -S <float> Subsampling kmers, 1/(<-S>) kmers are indexed, [4.00]\n"
" -S is very useful in saving memeory and speeding up\n"
" please note that subsampling kmers will have less matched length\n"
" -l <float> Min length of alignment, [2048]\n"
" -m <float> Min matched length by kmer matching, [200]\n"
" -R Enable realignment mode\n"
" -A Keep contained reads during alignment\n"
" -s <float> Min similarity, calculated by kmer matched length / aligned length, [0.05]\n"
" -e <int> Min read depth of a valid edge, [3]\n"
" -q Quiet\n"
" -v Verbose (can be multiple)\n"
" -V Print version information and then exit\n"
" --help Show more options\n"
, TOSTR(VERSION), TOSTR(RELEASE)
);
if(level > 0){
printf(
" ** more options **\n"
" --cpu <int>\n"
" See -t 0, default: all cores\n"
" --input <string> +\n"
" See -i\n"
//" --err-free-seq <string> +\n"
//" See -I. Error-free sequences will be firstly token for nodes, if --err-free-nodes is specified, only select nodes from those sequences\n"
" --force\n"
" See -f\n"
" --prefix <string>\n"
" See -o\n"
" --preset <string>\n"
" See -x\n"
" --kmer-fsize <int>\n"
" See -k 0\n"
" --kmer-psize <int>\n"
" See -p 21\n"
" --kmer-depth-max <float>\n"
" See -K 1000.05\n"
" -E, --kmer-depth-min <int>\n"
" Min kmer frequency, [2]\n"
//" --kmer-depth-min-filter\n"
//" See -F\n"
//" `wtdbg` uses a 4 Gbytes array to counting the occurence (0-3) of kmers in the way of counting-bloom-filter. It will reduce memory space largely\n"
//" Orphaned kmers won't appear in building kbm-index\n"
" --kmer-subsampling <float>\n"
" See -S 4.0\n"
" --kbm-parts <int>\n"
" Split total reads into multiple parts, index one part by one to save memory, [1]\n"
" --aln-kmer-sampling <int>\n"
" Select no more than n seeds in a query bin, default: 256\n"
" --dp-max-gap <int>\n"
" Max number of bin(256bp) in one gap, [4]\n"
" --dp-max-var <int>\n"
" Max number of bin(256bp) in one deviation, [4]\n"
" --dp-penalty-gap <int>\n"
" Penalty for BIN gap, [-7]\n"
" --dp-penalty-var <int>\n"
" Penalty for BIN deviation, [-21]\n"
" --aln-min-length <int>\n"
" See -l 2048\n"
" --aln-min-match <int>\n"
" See -m 200. Here the num of matches counting basepair of the matched kmer's regions\n"
" --aln-min-similarity <float>\n"
" See -s 0.05\n"
" --aln-max-var <float>\n"
" Max length variation of two aligned fragments, default: 0.25\n"
" --aln-dovetail <int>\n"
" Retain dovetail overlaps only, the max overhang size is <--aln-dovetail>, the value should be times of 256, -1 to disable filtering, default: 256\n"
" --aln-strand <int>\n"
" 1: forward, 2: reverse, 3: both. Please don't change the deault vaule 3, unless you exactly know what you are doing\n"
" --aln-maxhit <int>\n"
" Max n hits for each read in build graph, default: 1000\n"
" --aln-bestn <int>\n"
" Use best n hits for each read in build graph, 0: keep all, default: 500\n"
" <prefix>.alignments always store all alignments\n"
" -R, --realign\n"
" Enable re-alignment, see --realn-kmer-psize=15, --realn-kmer-subsampling=1, --realn-min-length=2048, --realn-min-match=200, --realn-min-similarity=0.1, --realn-max-var=0.25\n"
" --realn-kmer-psize <int>\n"
" Set kmer-psize in realignment, (kmer-ksize always eq 0), default:15\n"
" --realn-kmer-subsampling <int>\n"
" Set kmer-subsampling in realignment, default:1\n"
" --realn-min-length <int>\n"
" Set aln-min-length in realignment, default: 2048\n"
" --realn-min-match <int>\n"
" Set aln-min-match in realignment, default: 200\n"
" --realn-min-similarity <float>\n"
" Set aln-min-similarity in realignment, default: 0.1\n"
" --realn-max-var <float>\n"
" Set aln-max-var in realignment, default: 0.25\n"
" -A, --aln-noskip\n"
" Even a read was contained in previous alignment, still align it against other reads\n"
//" --corr-mode <float>\n"
//" Default: 0.0. If set > 0 and set --g <genome_size>, will turn on correct-align mode.\n"
//" Wtdbg will select <genome_size> * <corr-mode> bases from reads of middle length, and align them aginst all reads.\n"
//" Then, wtdbg will correct them using POACNS, and query corrected sequences against all reads again\n"
//" In correct-align mode, --aln-bestn = unlimited, --no-read-clip, --no-chaining-clip. Will support those features in future\n"
//" --corr-min <int>\n"
//" --corr-max <int>\n"
//" For each read to be corrected, uses at least <corr-min> alignments, and at most <corr-max> alignments\n"
//" Default: --corr_min = 5, --corr-max = 10\n"
//" --corr-cov <float>\n"
//" Default: 0.75. When aligning reads to be corrected, the alignments should cover at least <corr-cov> of read length\n"
//" --corr-block-size <int>\n"
//" Default: 2048. MUST be times of 256bp. Used in POACNS\n"
//" --corr-block-step <int>\n"
//" Default: 1536. MUST be times of 256bp. Used in POACNS\n"
" --keep-multiple-alignment-parts\n"
" By default, wtdbg will keep only the best alignment between two reads after chainning. This option will disable it, and keep multiple\n"
" --verbose +\n"
" See -v. -vvvv will display the most detailed information\n"
" --quiet\n"
" See -q\n"
" --limit-input <int>\n"
" Limit the input sequences to at most <int> M bp. Usually for test\n"
" -L <int>, --tidy-reads <int>\n"
" Default: 0. Pick longest subreads if possible. Filter reads less than <--tidy-reads>. Please add --tidy-name or set --tidy-reads to nagetive value\n"
" if want to rename reads. Set to 0 bp to disable tidy. Suggested value is 5000 for pacbio RSII reads\n"
" --tidy-name\n"
" Rename reads into 'S%%010d' format. The first read is named as S0000000001\n"
" --rdname-filter <string>\n"
" A file contains lines of reads name to be discarded in loading. If you want to filter reads by yourself, please also set -X 0\n"
" --rdname-includeonly <string>\n"
" Reverse manner with --rdname-filter\n"
//" --keep-name\n"
//" Keep orignal read names even with --tidy-reads, '-L 5000 --keep-name' equals '-L -5000'\n"
" -g <number>, --genome-size <number>\n"
" Provide genome size, e.g. 100.4m, 2.3g. In this version, it is used with -X/--rdcov-cutoff in selecting reads just after readed all.\n"
" -X <float>, --rdcov-cutoff <float>\n"
" Default: 50.0. Retaining 50.0 folds of genome coverage, combined with -g and --rdcov-filter.\n"
" --rdcov-filter [0|1]\n"
" Default 0. Strategy 0: retaining longest reads. Strategy 1: retaining medain length reads. \n"
" --err-free-nodes\n"
" Select nodes from error-free-sequences only. E.g. you have contigs assembled from NGS-WGS reads, and long noisy reads.\n"
" You can type '--err-free-seq your_ctg.fa --input your_long_reads.fa --err-free-nodes' to perform assembly somehow act as long-reads scaffolding\n"
" --node-len <int>\n"
" The default value is 1024, which is times of KBM_BIN_SIZE(always equals 256 bp). It specifies the length of intervals (or call nodes after selecting).\n"
" kbm indexs sequences into BINs of 256 bp in size, so that many parameter should be times of 256 bp. There are: --node-len, --node-ovl, --aln-min-length, --aln-dovetail ."
" Other parameters are counted in BINs, --dp-max-gap, --dp-max-var .\n"
" --node-matched-bins <int>\n"
" Min matched bins in a node, default:1\n"
" --node-ovl <int>\n"
" Default: 256. Max overlap size between two adjacent intervals in any read. It is used in selecting best nodes representing reads in graph\n"
" --node-drop <float>\n"
" Default: 0.25. Will discard an node when has more this ratio intervals are conflicted with previous generated node\n"
" -e <int>, --edge-min=<int>\n"
" Default: 3. The minimal depth of a valid edge is set to 3. In another word, Valid edges must be supported by at least 3 reads\n"
" When the sequence depth is low, have a try with --edge-min 2. Or very high, try --edge-min 4\n"
" --edge-max-span <int>\n"
" Default: 1024 BINs. Program will build edges of length no large than 1024\n"
" --drop-low-cov-edges\n"
" Don't attempt to rescue low coverage edges\n"
" --node-min <int>\n"
" Min depth of an interval to be selected as valid node. Defaultly, this value is automaticly the same with --edge-min.\n"
" --node-max <int>\n"
" Nodes with too high depth will be regarded as repetitive, and be masked. Default: 200, more than 200 reads contain this node\n"
" --ttr-cutoff-depth <int>, 0\n"
" --ttr-cutoff-ratio <float>, 0.5\n"
" Tiny Tandom Repeat. A node located inside ttr will bring noisy in graph, should be masked. The pattern of such nodes is:\n"
" depth >= <--ttr-cutoff-depth>, and none of their edges have depth greater than depth * <--ttr-cutoff-ratio 0.5>\n"
" set --ttr-cutoff-depth 0 to disable ttr masking\n"
" --dump-kbm <string>\n"
" Dump kbm index into file for loaded by `kbm` or `wtdbg`\n"
" --dump-seqs <string>\n"
" Dump kbm index (only sequences, no k-mer index) into file for loaded by `kbm` or `wtdbg`\n"
" Please note: normally load it with --load-kbm, not with --load-seqs\n"
" --load-kbm <string>\n"
" Instead of reading sequences and building kbm index, which is time-consumed, loading kbm-index from already dumped file.\n"
" Please note that, once kbm-index is mmaped by kbm -R <kbm-index> start, will just get the shared memory in minute time.\n"
" See `kbm` -R <your_seqs.kbmidx> [start | stop]\n"
" --load-seqs <string>\n"
" Similar with --load-kbm, but only use the sequences in kbmidx, and rebuild index in process's RAM.\n"
" --load-alignments <string> +\n"
" `wtdbg` output reads' alignments into <--prefix>.alignments, program can load them to fastly build assembly graph. Or you can offer\n"
" other source of alignments to `wtdbg`. When --load-alignment, will only reading long sequences but skip building kbm index\n"
" You can type --load-alignments <file> more than once to load alignments from many files\n"
" --load-clips <string>\n"
" Combined with --load-nodes. Load reads clips. You can find it in `wtdbg`'s <--prefix>.clps\n"
" --load-nodes <sting>\n"
" Load dumped nodes from previous execution for fast construct the assembly graph, should be combined with --load-clips. You can find it in `wtdbg`'s <--prefix>.1.nodes\n"
" --bubble-step <int>\n"
" Max step to search a bubble, meaning the max step from the starting node to the ending node. Default: 40\n"
" --tip-step <int>\n"
" Max step to search a tip, 10\n"
" --ctg-min-length <int>\n"
" Min length of contigs to be output, 5000\n"
" --ctg-min-nodes <int>\n"
" Min num of nodes in a contig to be ouput, 3\n"
" --minimal-output\n"
" Will generate as less output files (<--prefix>.*) as it can\n"
" --bin-complexity-cutoff <int>\n"
" Used in filtering BINs. If a BIN has less indexed valid kmers than <--bin-complexity-cutoff 2>, masks it.\n"
" --no-local-graph-analysis\n"
" Before building edges, for each node, local-graph-analysis reads all related reads and according nodes, and builds a local graph to judge whether to mask it\n"
" The analysis aims to find repetitive nodes\n"
" --no-read-length-sort\n"
" Defaultly, `wtdbg` sorts input sequences by length DSC. The order of reads affects the generating of nodes in selecting important intervals\n"
" --keep-isolated-nodes\n"
" In graph clean, `wtdbg` normally masks isolated (orphaned) nodes\n"
" --no-read-clip\n"
" Defaultly, `wtdbg` clips a input sequence by analyzing its overlaps to remove high error endings, rolling-circle repeats (see PacBio CCS), and chimera.\n"
" When building edges, clipped region won't contribute. However, `wtdbg` will use them in the final linking of unitigs\n"
" --no-chainning-clip\n"
" Defaultly, performs alignments chainning in read clipping\n"
" ** If '--aln-bestn 0 --no-read-clip', alignments will be parsed directly, and less RAM spent on recording alignments\n"
"\n"
);
}
return (level < 0)? 1 : 0;
}
static inline int64_t mm_parse_num(const char *str)
{
double x;
char *p;
x = strtod(str, &p);
if (*p == 'G' || *p == 'g') x *= 1e9;
else if (*p == 'M' || *p == 'm') x *= 1e6;
else if (*p == 'K' || *p == 'k') x *= 1e3;
return (int64_t)(x + .499);
}
int main(int argc, char **argv){
Graph *g;
KBMPar *par, *rpar;
KBM *kbm;
FileReader *fr;
BioSequence *seqs[2], *seq;
chash *rdtaghash[2];
cplist *pbs, *ngs, *pws;
FILE *evtlog;
char *prefix, *rdtag_filter[2], *dump_seqs, *load_seqs, *dump_kbm, *load_kbm, *load_nodes, *load_clips;
char regtag[14];
int len, tag_size, asyn_read, preset;
u8i tot_bp, cnt, bub, tip, rep, yarn, max_bp, max_idx_bp, nfix, opt_flags;
uint32_t i, j, k;
int c, opt_idx, ncpu, only_fix, realign, node_cov, max_node_cov, exp_node_cov, min_bins, edge_cov, edge_span, store_low_cov_edge, reglen, regovl, bub_step, tip_step, rep_step;
int frgtip_len, ttr_n_cov;
int quiet, tidy_reads, filter_rd_strategy, tidy_rdtag, less_out, tip_like, cut_tip, rep_filter, out_alns, cnn_filter, log_rep, rep_detach, del_iso, rdclip, chainning, uniq_hit, bestn, rescue_low_edges;
int min_ctg_len, min_ctg_nds, max_trace_end, max_overhang, overwrite, node_order, fast_mode, corr_min, corr_max, corr_bsize, corr_bstep, mem_stingy, num_index;
double genome_size, genome_depx;
float node_drop, node_mrg, ttr_e_cov, fval, cut_low_edges, corr_mode, corr_cov;
pbs = init_cplist(4);
ngs = init_cplist(4);
pws = init_cplist(4);
asyn_read = 1;
ncpu = 4;
mem_stingy = 0;
tidy_reads = 0;
tidy_rdtag = -1;
preset = 0;
genome_size = 0;
genome_depx = 50.0;
num_index = 1;
filter_rd_strategy = 0;
fast_mode = 0;
// no longer supports corr-mode
corr_mode = 0;
corr_min = 5;
corr_max = 10;
corr_cov = 0.75;
corr_bsize = 2048;
corr_bstep = 2048 - 512;
// -------
max_bp = 0;
max_idx_bp = 0LLU * 1000 * 1000 * 1000; // unlimited
rdtag_filter[0] = NULL;
rdtag_filter[1] = NULL;
rdtaghash[0] = NULL;
rdtaghash[1] = NULL;
reglen = 1024;
regovl = 256;
node_drop = 0.25;
node_mrg = 0.9;
only_fix = 0;
node_cov = 0; // will equal edge_cov, if no --node-cov
max_node_cov = 200;
exp_node_cov = 40;
min_bins = 1;
edge_cov = 0; // will be set to 3, if no genome_size available and no -e
edge_span = 1024;
rdclip = 1;
chainning = 1;
uniq_hit = 1;
bestn = 500;
ttr_n_cov = 0;
ttr_e_cov = 0.5;
dump_seqs = NULL;
load_seqs = NULL;
dump_kbm = NULL;
load_kbm = NULL;
load_clips = NULL;
load_nodes = NULL;
store_low_cov_edge = 1;
cut_low_edges = 0.0;
rescue_low_edges = 1;
bub_step = 40;
tip_step = 10;
rep_step = 0;
max_trace_end = 5;
frgtip_len = 50000;
prefix = NULL;
overwrite = 0;
less_out = 0;
quiet = 0;
rep_filter = 1;
tip_like = 0;
cut_tip = 1;
cnn_filter = 1;
log_rep = 1;
rep_detach = 0;
del_iso = 1;
max_overhang = 256;
min_ctg_len = 5000;
min_ctg_nds = 3;
node_order = 0;
out_alns = 1;
par = init_kbmpar();
par->ksize = 0;
par->psize = 21;
par->kmer_mod = KBM_N_HASH * 4;
par->kmin = 2;
par->max_bgap = 4;
par->max_bvar = 4;
par->self_aln = 1; // won't perform B->A when existing A->B
par->rd_len_order = 1;
par->min_aln = 2048 / KBM_BIN_SIZE;
par->min_mat = 200;
par->min_sim = 0.05;
par->aln_var = 0.25;
realign = 0;
rpar = init_kbmpar();
rpar->ksize = 0;
rpar->psize = 15;
rpar->kmer_mod = KBM_N_HASH;
rpar->kmin = 1;
rpar->max_bgap = 4;
rpar->max_bvar = 4;
rpar->self_aln = 0; // won't perform B->A when existing A->B
rpar->rd_len_order = 0;
rpar->min_aln = 2048 / KBM_BIN_SIZE;
rpar->min_mat = 200;
rpar->min_sim = 0.1;
rpar->aln_var = 0.25;
opt_flags = 0;
while((c = getopt_long(argc, argv, "ht:i:fo:x:E:k:p:K:S:l:m:s:RvqVe:L:Ag:X:", prog_opts, &opt_idx)) != -1){
switch(c){
case 't': ncpu = atoi(optarg); break;
case 'i': push_cplist(pbs, optarg); break;
//case 'I': push_cplist(ngs, optarg); par->rd_len_order = 0; break;
case 'f': overwrite = 1; break;
case 'o': prefix = optarg; break;
case 'x':
{
char *ptr, *beg;
beg = optarg;
do {
ptr = index(beg, ',');
if(ptr) *ptr = 0;
if(KBM_LOG){
fprintf(KBM_LOGF, " -- Preset: '%s' --", beg); fflush(KBM_LOGF);
}
if(strcasecmp(beg, "preset1") == 0 || strcasecmp(beg, "rs") == 0 || strcasecmp(beg, "rsII") == 0){
preset = 1;
} else if(strcasecmp(beg, "preset2") == 0){
preset = 2;
} else if(strcasecmp(beg, "preset3") == 0){
preset = 3;
} else if(strcasecmp(beg, "sq") == 0 || strcasecmp(beg, "sequel") == 0){
preset = -1;
} else if(strcasecmp(beg, "ont") == 0 || strcasecmp(beg, "nanopore") == 0){
preset = -1;
} else if(strcasecmp(beg, "preset4") == 0 || strcasecmp(beg, "ccs") == 0 || strcasecmp(beg, "corrected") == 0){
preset = 4;
} else {
fprintf(stderr, " ** ERROR: cannot recognize '%s' in '-x %s'\n", beg, optarg);
exit(1);
}
if(KBM_LOG){
fprintf(KBM_LOGF, "\n"); fflush(KBM_LOGF);
}
if(ptr){
*ptr = ',';
beg = ptr + 1;
} else {
break;
}
} while(1);
}
break;
case 'k': par->ksize = atoi(optarg); opt_flags |= (1 << 1); break;
case 'p': par->psize = atoi(optarg); opt_flags |= (1 << 0); break;
case 'K': fval = atof(optarg); par->kmax = fval; par->ktop = fval - par->kmax; opt_flags |= (1 << 6); break;
case 'E': par->kmin = atoi(optarg); break;
case 'S': par->kmer_mod = UInt(atof(optarg) * KBM_N_HASH); opt_flags |= (1 << 2);break;
case 'g': genome_size = mm_parse_num(optarg); break;
case 'X': genome_depx = atof(optarg); break;
case 3007: rdtag_filter[0] = optarg; break;
case 3008: rdtag_filter[1] = optarg; break;
case 2009: filter_rd_strategy = atoi(optarg); break;
case 2005: par->max_bgap = atoi(optarg); break;
case 2006: par->max_bvar = atoi(optarg); break;
case 2007: par->pgap = atoi(optarg); break;
case 2008: par->pvar = atoi(optarg); break;
case 'l': par->min_aln = atoi(optarg) / KBM_BIN_SIZE; break;
case 'm': par->min_mat = atoi(optarg); break;
case 2004: par->aln_var = atof(optarg); break;
case 's': par->min_sim = atof(optarg); opt_flags |= (1 << 3); break;
//case 2010: corr_mode = atof(optarg); break;
//case 2012: corr_min = atoi(optarg); break;
//case 2013: corr_max = atoi(optarg); break;
//case 2014: corr_cov = atof(optarg); break;
//case 2015: corr_bsize = atoi(optarg); break;
//case 2016: corr_bstep = atoi(optarg); break;
case 2011: uniq_hit = 0; break;
case 'v': KBM_LOG ++; break;
case 'q': quiet = 1; break;
case 'h': return usage(0);
case 1000: return usage(1);
case 'L': tidy_reads = atoi(optarg); opt_flags |= (1 << 4); break;
case 1001: tidy_rdtag = 1; break;
case 1002: only_fix = 1; break;
case 1003: max_bp = atol(optarg); break;
case 1035: num_index = atoi(optarg); break;
case 1004: reglen = atoi(optarg); break;
case 1005: regovl = atoi(optarg); break;
case 1006: node_drop = atof(optarg); break;
case 'e': edge_cov = atoi(optarg); break;
case 3009: edge_span = atoi(optarg); break;
case 1007: node_cov = atoi(optarg); break;
case 1008: max_node_cov = atoi(optarg); break;
case 1009: ttr_n_cov = atoi(optarg); break;
case 1010: ttr_e_cov = atof(optarg); break;
case 1036: dump_seqs = optarg; break;
case 2002: load_seqs = optarg; break;
case 1011: dump_kbm = optarg; break;
case 1012: load_kbm = optarg; break;
case 2000: load_nodes = optarg; break;
case 2001: load_clips = optarg; break;
case 1013: push_cplist(pws, optarg); break;
case 1014: par->strand_mask = atoi(optarg); break;
case 1015: bub_step = atoi(optarg); break;
case 1016: tip_step = atoi(optarg); break;
case 1017: min_ctg_len = atoi(optarg); break;
case 1018: min_ctg_nds = atoi(optarg); break;
case 1019: less_out = 1; break;
case 1020: par->min_bin_degree = atoi(optarg); break;
case 1021: max_overhang = atoi(optarg); break;
case 1022: cnn_filter = 0; break;
case 1023: par->rd_len_order = 0; break;
case 1024: del_iso = 0; break;
case 1025: rdclip = 0; break;
case 1026: chainning = 0; break;
case 1027: bestn = atoi(optarg); break;
case 1028: par->max_hit = atoi(optarg); break;
case 1029: par->ksampling = atoi(optarg); break;
case 'R': realign = 1; break;
case 3001: rpar->psize = atoi(optarg); break;
case 3002: rpar->kmer_mod = UInt(atof(optarg) * KBM_N_HASH); break;
case 3003: rpar->min_aln = atoi(optarg) / KBM_BIN_SIZE; break;
case 3004: rpar->min_mat = atoi(optarg); break;
case 3005: rpar->min_sim = atof(optarg); break;
case 3006: rpar->aln_var = atof(optarg); break;
case 'A': par->skip_contained = 0; opt_flags |= (1 << 5); break;
case 1031: min_bins = atoi(optarg); break;
case 1032: rescue_low_edges = 1; break;
case 1033: rescue_low_edges = 0; break;
case 'V': fprintf(stdout, "wtdbg2 %s\n", TOSTR(VERSION)); return 0;
case 1034: mem_stingy = 1; break;
default: return usage(-1);
}
}
if(optind == 1) return usage(-1);
if(optind < argc){
fprintf(stderr, "WARNING: unused command-line arguments. For multiple input files, please apply multiple -i.\n");
fprintf(stderr, "WARNING: try to recognize and add to input files list\n");
for(c=optind;c<argc;c++){
if(file_exists(argv[c])){
fprintf(stderr, " * \"%s\" exists, added.\n", argv[c]);
push_cplist(pbs, argv[c]);
}
}
}
if(prefix == NULL) {
fprintf(stderr, "ERROR: please specify the output prefix with -o\n");
return 1;
}
if(load_seqs == NULL && load_kbm == NULL && pbs->size + ngs->size == 0) {
fprintf(stderr, "ERROR: please specify the input with -i/--load-seqs/--load-kbm\n");
return 1;
}
if((reglen % KBM_BIN_SIZE)){
reglen = ((reglen + KBM_BIN_SIZE - 1) / KBM_BIN_SIZE) * KBM_BIN_SIZE;
fprintf(stderr, " ** Adjust -j to %d\n", reglen);
}
if(!overwrite && file_exists(prefix)){
fprintf(stderr, "File exists! '%s'\n\n", prefix);
return usage(-1);
}
if(max_idx_bp == 0) max_idx_bp = 0xFFFFFFFFFFFFFFFFLLU;
if(preset == -1){
if(genome_size && genome_size < 1000000000LLU){
preset = 2;
} else {
preset = 3;
}
}
switch(preset){
case 1:
if(!(opt_flags & (1 << 1))) par->ksize = 0;
if(!(opt_flags & (1 << 0))) par->psize = 21;
if(!(opt_flags & (1 << 2))) par->kmer_mod = 4 * KBM_N_HASH;
if(!(opt_flags & (1 << 3))) par->min_sim = 0.05;
if(!(opt_flags & (1 << 5))) par->skip_contained = 1;
if(!(opt_flags & (1 << 4))) tidy_reads = 5000;
break;
case 2:
if(!(opt_flags & (1 << 1))) par->ksize = 15;
if(!(opt_flags & (1 << 0))) par->psize = 0;
if(!(opt_flags & (1 << 2))) par->kmer_mod = 2 * KBM_N_HASH;
if(!(opt_flags & (1 << 3))) par->min_sim = 0.05;
if(!(opt_flags & (1 << 5))) par->skip_contained = 0;
if(!(opt_flags & (1 << 4))) tidy_reads = 5000;
break;
case 3:
if(!(opt_flags & (1 << 1))) par->ksize = 0;
if(!(opt_flags & (1 << 0))) par->psize = 19;
if(!(opt_flags & (1 << 2))) par->kmer_mod = 2 * KBM_N_HASH;
if(!(opt_flags & (1 << 3))) par->min_sim = 0.05;
if(!(opt_flags & (1 << 5))) par->skip_contained = 0;
if(!(opt_flags & (1 << 4))) tidy_reads = 5000;
break;
case 4:
if(!(opt_flags & (1 << 1))) par->ksize = 0;
if(!(opt_flags & (1 << 0))) par->psize = 21;
if(!(opt_flags & (1 << 2))) par->kmer_mod = 4 * KBM_N_HASH;
if(!(opt_flags & (1 << 3))) par->min_sim = 0.5;
if(!(opt_flags & (1 << 5))) par->skip_contained = 0;
if(!(opt_flags & (1 << 6))){ par->kmax = 0; par->ktop = 0.05; }
//if(!(opt_flags & (1 << 4))) tidy_reads = 5000;
break;
}
if(par->ksize + par->psize > KBM_MAX_KSIZE){
fprintf(stderr, " -- Invalid kmer size %d+%d=%d > %d in %s -- %s:%d --\n", par->ksize, par->psize, par->ksize + par->psize, KBM_MAX_KSIZE, __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
return 1;
}
if(quiet){
int devnull;
devnull = open("/dev/null", O_WRONLY);
dup2(devnull, STDERR_FILENO);
}
if(tidy_rdtag == -1){
if(tidy_reads >= 0){
tidy_rdtag = 0;
} else {
tidy_rdtag = 1;
}
}
if(tidy_reads < 0) tidy_reads = - tidy_reads;
max_bp *= 1000000;
BEG_STAT_PROC_INFO(stderr, argc, argv);
if(ncpu <= 0 && _sig_proc_deamon) ncpu = _sig_proc_deamon->ncpu;
if(ncpu <= 0){
fprintf(stderr, " -- Invalid cpu number '%d' in %s -- %s:%d --\n", ncpu, __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
return 1;
}
if(load_kbm){
fprintf(KBM_LOGF, "[%s] loading kbm index from %s\n", date(), load_kbm);
if((kbm = mem_find_obj_file(&kbm_obj_desc, load_kbm, NULL, NULL, NULL, NULL, 0)) == NULL){
fprintf(KBM_LOGF, " -- cannot find mmap object %s --\n", load_kbm);
fprintf(KBM_LOGF, " -- try read from file --\n");
kbm = mem_read_obj_file(&kbm_obj_desc, load_kbm, NULL, NULL, NULL, NULL);
}
nfix = 0;
tot_bp = 0;
for(i=0;i<kbm->reads->size;i++) tot_bp += kbm->reads->buffer[i].bincnt * KBM_BIN_SIZE;
fprintf(KBM_LOGF, "[%s] Done. %u sequences, %llu bp, parameter('-S %d')\n", date(), (u4i)kbm->reads->size, tot_bp, kbm->par->kmer_mod / KBM_N_HASH);
{
// check KBMPar
if((opt_flags >> 0) & 0x01){
if(kbm->par->psize != par->psize){
fprintf(KBM_LOGF, " ** -p is different, %d != %d\n", kbm->par->psize, par->psize); exit(1);
}
} else {
par->psize = kbm->par->psize;
}
if((opt_flags >> 1) & 0x01){
if(kbm->par->ksize != par->ksize){
fprintf(KBM_LOGF, " ** -k is different, %d != %d\n", kbm->par->ksize, par->ksize); exit(1);
}
} else {
par->ksize = kbm->par->ksize;
}
if((opt_flags >> 2) & 0x01){
if(kbm->par->kmer_mod != par->kmer_mod){
fprintf(KBM_LOGF, " ** -S is different, %d != %d\n", kbm->par->kmer_mod / KBM_N_HASH, par->kmer_mod / KBM_N_HASH); exit(1);
}
} else {
par->kmer_mod = kbm->par->kmer_mod;
}
if((opt_flags >> 3) & 0x01){
if(kbm->par->rd_len_order != par->rd_len_order){
fprintf(KBM_LOGF, " ** par->rd_len_order is different, %d != %d\n", kbm->par->rd_len_order, par->rd_len_order); exit(1);
}
} else {
par->rd_len_order = kbm->par->rd_len_order;
}
}
} else if(load_seqs){
fprintf(KBM_LOGF, "[%s] loading kbm index from %s\n", date(), load_seqs);
if((kbm = mem_find_obj_file(&kbm_obj_desc, load_seqs, NULL, NULL, NULL, NULL, 0)) == NULL){
fprintf(KBM_LOGF, " -- cannot find mmap object %s --\n", load_seqs);
fprintf(KBM_LOGF, " -- try read from file --\n");
kbm = mem_read_obj_file(&kbm_obj_desc, load_seqs, NULL, NULL, NULL, NULL);
}
kbm = clone_seqs_kbm(kbm, par);
nfix = 0;
tot_bp = 0;
for(i=0;i<kbm->reads->size;i++) tot_bp += kbm->reads->buffer[i].bincnt * KBM_BIN_SIZE;
fprintf(KBM_LOGF, "[%s] Done. %u sequences, %llu bp\n", date(), (u4i)kbm->reads->size, tot_bp);
} else {
kbm = init_kbm(par);
for(i=0;i<2;i++){
if(rdtag_filter[i]){
rdtaghash[i] = init_chash(1023);
fr = open_filereader(rdtag_filter[i], 0);
while(readline_filereader(fr)){
char *str = strdup(fr->line->string);
put_chash(rdtaghash[i], str);
}
close_filereader(fr);
tidy_reads = 0;
} else {
rdtaghash[i] = NULL;
}
}
fprintf(KBM_LOGF, "[%s] loading reads\n", date());
tot_bp = 0;
nfix = 0;
seqs[0] = init_biosequence();
seqs[1] = init_biosequence();
regex_t reg;
regmatch_t mats[3];
int z;
z = regcomp(®, "^(.+?)/[0-9]+_[0-9]+$", REG_EXTENDED);
if(z){
regerror(z, ®, regtag, 13);
fprintf(stderr, " -- REGCOMP: %s --\n", regtag); fflush(stderr);
return 1;
}
for(j=0;j<2;j++){
if(j == 0){
if(ngs->size == 0){
continue;
} else {
fr = open_all_filereader(ngs->size, ngs->buffer, asyn_read);
}
} else {
if(pbs->size == 0){
continue;
} else {
fr = open_all_filereader(pbs->size, pbs->buffer, asyn_read);
}
}
k = 0;
reset_biosequence(seqs[0]);
reset_biosequence(seqs[1]);
while(1){
int has = readseq_filereader(fr, seqs[k]);
if(tidy_reads){
if(has){
if((z = regexec(®, seqs[k]->tag->string, 3, mats, 0)) == 0){
trunc_string(seqs[k]->tag, mats[1].rm_eo);
} else if(z != REG_NOMATCH){
regerror(z, ®, regtag, 13);
fprintf(stderr, " -- REGEXEC: %s --\n", regtag); fflush(stderr);
}
//fprintf(stderr, "1: %s len=%d\n", seqs[k]->tag->string, seqs[k]->seq->size); fflush(stderr);
//fprintf(stderr, "2: %s len=%d\n", seqs[!k]->tag->string, seqs[!k]->seq->size); fflush(stderr);
if(seqs[k]->tag->size == seqs[!k]->tag->size && strcmp(seqs[k]->tag->string, seqs[!k]->tag->string) == 0){
if(seqs[k]->seq->size > seqs[!k]->seq->size){
k = !k;
}
continue;
} else {
seq = seqs[!k];
k = !k;
}
} else {
seq = seqs[!k];
}
if(seq->seq->size < tidy_reads){
if(has) continue;
else break;
}
if(tidy_rdtag){
sprintf(regtag, "S%010llu", (u8i)kbm->reads->size);
clear_string(seq->tag);
append_string(seq->tag, regtag, 11);
}
} else {
if(has == 0) break;
seq = seqs[k];
if(rdtaghash[0]){
if(exists_chash(rdtaghash[0], seq->tag->string)){
continue;
}
}
if(rdtaghash[1]){
if(!exists_chash(rdtaghash[1], seq->tag->string)){
continue;
}
}
}
tag_size = seq->tag->size;
for(i=0;(int)i<seq->seq->size;i+=WT_MAX_RDLEN){
len = num_min(seq->seq->size - i, WT_MAX_RDLEN);
if(i){
append_string(seq->tag, "_V", 2);
add_int_string(seq->tag, i / WT_MAX_RDLEN);
}
if(!KBM_LOG && (kbm->reads->size % 10000) == 0){ fprintf(KBM_LOGF, "\r%u", (u4i)kbm->reads->size); fflush(KBM_LOGF); }
//fprintf(stderr, " -- %s len=%d in %s -- %s:%d --\n", seq->tag->string, seq->seq->size, __FUNCTION__, __FILE__, __LINE__); fflush(stderr);
if(kbm->reads->size >= WT_MAX_RD){
fprintf(stderr, " -- Read Number Out of Range: %u --\n", (u4i)kbm->reads->size); fflush(stderr);
break;
}
push_kbm(kbm, seq->tag->string, seq->tag->size, seq->seq->string + i, len);
if(i){ seq->tag->size = tag_size; seq->tag->string[tag_size] = '\0'; }
if(j == 0) nfix ++;
}
tot_bp += seq->seq->size;
if(max_bp && tot_bp >= max_bp){ break; }
if(has == 0) break;
if(kbm->reads->size >= WT_MAX_RD){
fprintf(stderr, " -- Read Number Out of Range: %u --\n", (u4i)kbm->reads->size); fflush(stderr);
break;
}
}
close_filereader(fr);
for(i=0;i<2;i++){
if(rdtaghash[i]){
char **str;
reset_iter_chash(rdtaghash[i]);
while((str = ref_iter_chash(rdtaghash[i]))){
free(*str);
}
free_chash(rdtaghash[i]);
}
}
}
regfree(®);
free_biosequence(seqs[0]);
free_biosequence(seqs[1]);
if(!KBM_LOG){ fprintf(KBM_LOGF, "\r%u reads", (unsigned)kbm->reads->size); fflush(KBM_LOGF); }
{
if(par->rd_len_order && genome_size > 0 && genome_depx > 0){
cnt = genome_size * genome_depx;
if(cnt < tot_bp){
fprintf(KBM_LOGF, "\n[%s] filtering from %u reads (>=%u bp), %llu bp. Try selecting %llu bp", date(), (unsigned)kbm->reads->size, tidy_reads, tot_bp, cnt); fflush(KBM_LOGF);
tot_bp = filter_reads_kbm(kbm, cnt, filter_rd_strategy);
}
}
ready_kbm(kbm);
fprintf(KBM_LOGF, "\n[%s] Done, %u reads (>=%u bp), %llu bp, %u bins\n", date(), (unsigned)kbm->reads->size, tidy_reads, tot_bp, (u4i)kbm->bins->size); fflush(KBM_LOGF);
if(dump_seqs){
FILE *dump;
fprintf(KBM_LOGF, "[%s] dump kbm-index (only seqs) to %s ...", date(), dump_seqs); fflush(KBM_LOGF);
dump = open_file_for_write(dump_seqs, NULL, 1);
mem_dump_obj_file(kbm, 1, &kbm_obj_desc, 1, 0, dump);
fclose(dump);
fprintf(KBM_LOGF, " Done\n"); fflush(KBM_LOGF);
}
}
}
print_proc_stat_info(0);
if(edge_cov <= 0){
if(genome_size > 0){
float dep;
dep = tot_bp / genome_size;
if(dep <= 40){
edge_cov = 2;
} else if(dep >= 80){
edge_cov = 4;
} else {
edge_cov = 3;
}
} else {
edge_cov = 3;
}
fprintf(KBM_LOGF, "[%s] Set --edge-cov to %d\n", date(), edge_cov); fflush(KBM_LOGF);
}
//if(genome_size <= 0 && corr_mode > 0){
//fprintf(KBM_LOGF, "[%s] MUST set -g <?> with --corr-mode %f\n", date(), corr_mode); fflush(KBM_LOGF);
//return 1;
//}
if(node_cov == 0) node_cov = edge_cov;
fprintf(KBM_LOGF, "KEY PARAMETERS: -k %d -p %d -K %f %s-S %f -s %f -g %llu -X %f -e %d -L %d\n",
par->ksize, par->psize, par->kmax + par->ktop, par->skip_contained? "" : "-A ", ((double)par->kmer_mod) / KBM_N_HASH, par->min_sim, (u8i)genome_size, genome_depx, edge_cov, tidy_reads);
g = init_graph(kbm);
{
g->rpar = realign? rpar : NULL;
g->genome_size = genome_size;
g->num_index = num_index;
//g->corr_mode = (corr_mode > 0 && genome_size > 0)? 1 : 0;
//g->corr_gcov = corr_mode;
//g->corr_min = corr_min;
//g->corr_max = corr_max;
//g->corr_cov = corr_cov;
//g->corr_bsize = corr_bsize;
//g->corr_bstep = corr_bstep;
g->node_order = node_order;
g->mem_stingy = mem_stingy;
g->reglen = reglen / KBM_BIN_SIZE;
g->regovl = regovl / KBM_BIN_SIZE;
g->max_overhang = max_overhang / KBM_BIN_SIZE;
g->node_max_conflict = node_drop;
g->node_merge_cutoff = node_mrg;
g->min_node_cov = node_cov;
g->max_node_cov_sg = node_cov;
g->max_node_cov = max_node_cov;
g->exp_node_cov = exp_node_cov;
g->min_node_mats = min_bins;
g->min_edge_cov = edge_cov;
g->max_edge_span = edge_span;
g->max_sg_end = max_trace_end;
g->store_low_cov_edge = store_low_cov_edge;
g->bub_step = bub_step;
g->tip_step = tip_step;
g->rep_step = rep_step;
g->min_ctg_len = min_ctg_len;
g->min_ctg_nds = min_ctg_nds;
g->n_fix = nfix;
g->only_fix = only_fix;
g->rep_filter = rep_filter;
g->rep_detach = rep_detach;
g->cut_tip = cut_tip;
g->chainning_hits = chainning;
g->uniq_hit = uniq_hit;
g->bestn = bestn;
g->minimal_output = less_out;
}
g->par = par;
if(log_rep && !less_out){
evtlog = open_file_for_write(prefix, ".events", 1);
} else evtlog = NULL;
if(load_nodes && load_clips){
fprintf(KBM_LOGF, "[%s] loading nodes from %s ... ", date(), load_nodes); fflush(KBM_LOGF);
FileReader *clp = open_filereader(load_clips, asyn_read);
FileReader *nds = open_filereader(load_nodes, asyn_read);
load_nodes_graph(g, clp, nds);
close_filereader(clp);
close_filereader(nds);
fprintf(KBM_LOGF, " %llu nodes\n", (u8i)g->nodes->size);