tripoa.h

/*
 * 
 * Copyright (c) 2018, Jue Ruan <ruanjue@gmail.com>
 *
 *
 * 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/>.
 */

#ifndef TRI_PO_MSA_CNS_RJ_H
#define TRI_PO_MSA_CNS_RJ_H

#include "poacns.h"
#include "ksw.h"

typedef struct {
	SeqBank *seqs;
	u2v *rbegs, *rends;
	u4i longest_idx, seqmax;
	int8_t matrix[16];
	int fail_skip;
	u1i ksize; // 11
	float kdup; // 0.1
	float keqs; // 0.2
	uuhash *khash;
	u1v *qry, *ref;
	u2i winlen, winmin;
	u2v *regs[2];
	POG *pogs[3];
	u4v *kidxs;
	f4v *kords;
	BaseBank *cns;
	int is_tripog, refmode;
	int shuffle; // 0: no shuffling, 1: by kmer, 2, random
} TriPOG;

//static inline TriPOG* init_tripog(u4i seqmax, int refmode, int winlen, int winmin, int fail_skip, int M, int X, int I, int D, int W, int use_sse, int rW, u4i min_cnt, float min_freq){
static inline TriPOG* init_tripog(u4i seqmax, int shuffle, int winlen, int winmin, int fail_skip, POGPar *par){
	TriPOG *tp;
	u4i i;
	tp = malloc(sizeof(TriPOG));
	tp->seqs = init_seqbank();
	tp->rbegs = init_u2v(32);
	tp->rends = init_u2v(32);
	tp->seqmax = seqmax;
	tp->longest_idx = 0;
	tp->ksize = 11;
	tp->kdup = 0.1;
	tp->keqs = 0.2;
	tp->khash = init_uuhash(13);
	tp->ref  = init_u1v(winlen);
	tp->qry  = init_u1v(1024);
	tp->regs[0] = init_u2v(32);
	tp->regs[1] = init_u2v(32);
	tp->refmode = par->refmode;
	tp->fail_skip = fail_skip;
	tp->winlen = winlen;
	tp->winmin = winmin;
	tp->pogs[0] = init_pog(*par);
#if 0
	if(winlen > 0){
		tp->winlen = winlen;
		tp->winmin = winmin;
		tp->pogs[0] = init_pog(refmode, M, X, I, D, 0, 0, use_sse, 0, min_cnt, min_freq);
	} else {
		tp->winlen = 0;
		tp->winmin = 0;
		tp->pogs[0] = init_pog(refmode, M, X, I, D, W, - winlen, use_sse, rW, min_cnt, min_freq);
	}
#endif
	tp->pogs[1] = init_pog(*par);
	tp->pogs[1]->par->W_score = 0;
	tp->pogs[2] = init_pog(*par);
	tp->pogs[2]->par->W_score = 0;
	//tp->pogs[1] = init_pog(refmode, M, X, I, D, W, 0, use_sse, rW, min_cnt, min_freq);
	//tp->pogs[2] = init_pog(refmode, M, X, I, D, W, 0, use_sse, rW, min_cnt, min_freq);
	//tp->pogs[1]->near_dialog = 1;
	//tp->pogs[2]->near_dialog = 1;
	tp->kidxs = init_u4v(32);
	tp->kords = init_f4v(32);
	tp->cns = init_basebank();
	for(i=0;i<16;i++){
		tp->matrix[i] = ((i / 4) == (i % 4))? par->M : par->X;
	}
	tp->is_tripog = 0;
	tp->shuffle = shuffle;
	return tp;
}

static inline void free_tripog(TriPOG *tp){
	free_seqbank(tp->seqs);
	free_u2v(tp->rbegs);
	free_u2v(tp->rends);
	free_uuhash(tp->khash);
	free_u1v(tp->qry);
	free_u1v(tp->ref);
	free_u2v(tp->regs[0]);
	free_u2v(tp->regs[1]);
	free_pog(tp->pogs[0]);
	free_pog(tp->pogs[1]);
	free_pog(tp->pogs[2]);
	free_u4v(tp->kidxs);
	free_f4v(tp->kords);
	free_basebank(tp->cns);
	free(tp);
}

static inline void beg_tripog(TriPOG *tp){
	clear_seqbank(tp->seqs);
	clear_u2v(tp->rbegs);
	clear_u2v(tp->rends);
	tp->longest_idx = 0;
	tp->is_tripog = 0;
}

static inline void push_tripog(TriPOG *tp, char *seq, u4i len, u2i refbeg, u2i refend){
	if(!tp->shuffle && tp->seqs->nseq >= tp->seqmax) return;
	push_seqbank(tp->seqs, NULL, 0, seq, len);
	push_u2v(tp->rbegs, refbeg);
	push_u2v(tp->rends, refend);
	if(tp->seqs->rdlens->buffer[tp->longest_idx] < len){
		tp->longest_idx = tp->seqs->nseq - 1;
	}
}

static inline void fwdbitpush_tripog(TriPOG *tp, u8i *bits, u8i off, u4i len, u2i refbeg, u2i refend){
	if(!tp->shuffle && tp->seqs->nseq >= tp->seqmax) return;
	fwdbitpush_seqbank(tp->seqs, NULL, 0, bits, off, len);
	push_u2v(tp->rbegs, refbeg);
	push_u2v(tp->rends, refend);
	if(tp->seqs->rdlens->buffer[tp->longest_idx] < len){
		tp->longest_idx = tp->seqs->nseq - 1;
	}
}

static inline void revbitpush_tripog(TriPOG *tp, u8i *bits, u8i off, u4i len, u2i refbeg, u2i refend){
	if(!tp->shuffle && tp->seqs->nseq >= tp->seqmax) return;
	revbitpush_seqbank(tp->seqs, NULL, 0, bits, off, len);
	push_u2v(tp->rbegs, refbeg);
	push_u2v(tp->rends, refend);
	if(tp->seqs->rdlens->buffer[tp->longest_idx] < len){
		tp->longest_idx = tp->seqs->nseq - 1;
	}
}

static inline void direct_run_tripog(TriPOG *tp){
	POG *g;
	u4i ridx;
	clear_basebank(tp->cns);
	if(tp->refmode){
	} else {
		tp->pogs[0]->par->W = tp->pogs[1]->par->W;
		tp->pogs[0]->par->rW = tp->pogs[1]->par->rW;
		tp->pogs[0]->par->W_score = tp->pogs[1]->par->W * tp->pogs[1]->par->M * 8;
	}
	g = tp->pogs[0];
	beg_pog(g);
	for(ridx=0;ridx<tp->seqs->nseq;ridx++){
		fwdbitpush_pog_core(g, tp->seqs->rdseqs->bits, tp->seqs->rdoffs->buffer[ridx], tp->seqs->rdlens->buffer[ridx], tp->rbegs->buffer[ridx], tp->rends->buffer[ridx]);
	}
	end_pog(g);
	if(g->cns->size == 0){
		fast_fwdbits2basebank(tp->cns, tp->seqs->rdseqs->bits, tp->seqs->rdoffs->buffer[tp->longest_idx], tp->seqs->rdlens->buffer[tp->longest_idx]);
	} else {
		fast_fwdbits2basebank(tp->cns, g->cns->bits, 0, g->cns->size);
	}
	if(tp->refmode){
	} else {
		tp->pogs[0]->par->W = 0;
		tp->pogs[0]->par->rW = 0;
		tp->pogs[0]->par->W_score = 0;
	}
}

static inline void shuffle_reads_by_kmers_tripog(TriPOG *tp){
	SeqBank *sb;
	uuhash *khash;
	u4v *kidxs;
	f4v *kords;
	u2v *rbegs, *rends;
	uuhash_t *u;
	u8i roff;
	u4i ridx, i, ksize, kmer, kmask, rlen, khit, mincnt;
	double logv;
	int exists;
	sb = tp->seqs;
	if(sb->nseq == 0) return;
	khash = tp->khash;
	kidxs = tp->kidxs;
	kords = tp->kords;
	rbegs = tp->rbegs;
	rends = tp->rends;
	ksize = tp->ksize;
	clear_u4v(kidxs);
	clear_f4v(kords);
	clear_uuhash(khash);
	kmask = MAX_U4 >> ((16 - ksize) << 1);
	mincnt = tp->refmode? 1 : 2;
	for(ridx=0;ridx<sb->nseq;ridx++){
		rlen = sb->rdlens->buffer[ridx];
		kmer = 0;
		roff = sb->rdoffs->buffer[ridx];
		for(i=0;i<rlen;i++){
			kmer = ((kmer << 2) | get_basebank(sb->rdseqs, roff + i)) & kmask;
			if(i + 1 < ksize) continue;
			u = prepare_uuhash(khash, kmer, &exists);
			if(exists){
				if(((u->val >> 16) & 0x7FFFU) == ridx + 1){
					u->val |= 1U << 31;
				} else {
					u->val = (u->val & 0x8000FFFFU) | ((ridx + 1) << 16);
				}
				u->val ++;
			} else {
				u->key = kmer;
				u->val = (0U << 31) | ((ridx + 1) << 16) | 1;
			}
		}
		if(tp->refmode) break;
	}
	logv = log(1.2);
	for(ridx=0;ridx<sb->nseq;ridx++){
		rlen = sb->rdlens->buffer[ridx];
		kmer = 0;
		roff = sb->rdoffs->buffer[ridx];
		khit = 0;
		for(i=0;i<rlen;i++){
			kmer = ((kmer << 2) | get_basebank(sb->rdseqs, roff + i)) & kmask;
			if(i + 1 < ksize) continue;
			u = get_uuhash(khash, kmer);
			if(u && (u->val & 0x80000000U) == 0 && (u->val & 0xFFFFU) >= mincnt){
				khit ++;
			}
		}
		if(tp->refmode){
			if(ridx == 0){
				push_f4v(kords, 3e+38F);
			} else {
				push_f4v(kords, ((double)khit) * logv / log(num_max(rlen, sb->rdlens->buffer[0])));
			}
		} else {
			push_f4v(kords, ((double)khit) * logv / log(rlen));
		}
		push_u4v(kidxs, ridx);
	}
	sort_array(kidxs->buffer, kidxs->size, u4i, num_cmpgt(kords->buffer[b], kords->buffer[a]));
	if(cns_debug > 1){
		for(i=0;i<kidxs->size;i++){
			fprintf(stderr, "SHUFFLE[%u] %u\t%u\t%0.4f\n", i, kidxs->buffer[i], sb->rdlens->buffer[kidxs->buffer[i]], kords->buffer[kidxs->buffer[i]]);
		}
	}
	for(i=0;i<kidxs->size;i++){
		push_u8v(sb->rdoffs, sb->rdoffs->buffer[kidxs->buffer[i]]);
		push_u4v(sb->rdlens, sb->rdlens->buffer[kidxs->buffer[i]]);
		push_u2v(rbegs, rbegs->buffer[kidxs->buffer[i]]);
		push_u2v(rends, rends->buffer[kidxs->buffer[i]]);
	}
	remove_array_u8v(sb->rdoffs, 0, kidxs->size);
	remove_array_u4v(sb->rdlens, 0, kidxs->size);
	remove_array_u2v(rbegs, 0, kidxs->size);
	remove_array_u2v(rends, 0, kidxs->size);
	if(tp->seqmax && sb->nseq > tp->seqmax){
		if(cns_debug > 1){
			fprintf(stderr, "SEQMAX: %u -> %u\n", sb->nseq, tp->seqmax);
		}
		sb->nseq = tp->seqmax;
		sb->rdoffs->size = tp->seqmax;
		sb->rdlens->size = tp->seqmax;
		rbegs->size = tp->seqmax;
		rends->size = tp->seqmax;
	}
}

static inline void subsample_reads_tripog(TriPOG *tp){
	SeqBank *sb;
	u4v *kidxs;
	u2v *rbegs, *rends;
	f4v *kords;
	u4i ridx, i;
	f4i cutoff;
	sb = tp->seqs;
	if(sb->nseq == 0 || sb->nseq <= tp->seqmax) return;
	kidxs = tp->kidxs;
	kords = tp->kords;
	rbegs = tp->rbegs;
	rends = tp->rends;
	clear_u4v(kidxs);
	clear_f4v(kords);
	if(tp->refmode){
		push_u4v(kidxs, 0);
		push_f4v(kords, 200.0);
		ridx = 1;
	} else {
		ridx = 0;
	}
	for(;ridx<sb->nseq;ridx++){
		push_u4v(kidxs, ridx);
		push_f4v(kords, 100.0 * drand48());
	}
	sort_array(kidxs->buffer, kidxs->size, u4i, num_cmpgt(kords->buffer[b], kords->buffer[a]));
	cutoff = kords->buffer[kidxs->buffer[tp->seqmax - 1]];
	clear_u4v(kidxs);
	for(i=0;i<kords->size;i++){
		if(kords->buffer[i] >= cutoff){
			push_u4v(kidxs, i);
		}
	}
	if(cns_debug > 1){
		fprintf(stderr, "RANDOM CUTOFF = %f\n", cutoff);
		for(i=0;i<kidxs->size;i++){
			fprintf(stderr, "SHUFFLE[%u] %u\t%0.4f\n", i, kidxs->buffer[i], kords->buffer[kidxs->buffer[i]]);
		}
	}
	for(i=0;i<kidxs->size;i++){
		push_u8v(sb->rdoffs, sb->rdoffs->buffer[kidxs->buffer[i]]);
		push_u4v(sb->rdlens, sb->rdlens->buffer[kidxs->buffer[i]]);
		push_u2v(rbegs, rbegs->buffer[kidxs->buffer[i]]);
		push_u2v(rends, rends->buffer[kidxs->buffer[i]]);
	}
	remove_array_u8v(sb->rdoffs, 0, kords->size);
	remove_array_u4v(sb->rdlens, 0, kords->size);
	remove_array_u2v(rbegs, 0, kords->size);
	remove_array_u2v(rends, 0, kords->size);
	if(cns_debug > 1){
		fprintf(stderr, "SEQMAX: %u -> %u\n", sb->nseq, tp->seqmax);
	}
	sb->nseq = tp->seqmax;
}

static inline void end_tripog(TriPOG *tp){
	POG *g;
	kswr_t R;
	u4i ridx, rlen, b, e, failed;
	switch(tp->shuffle){
		case 1: shuffle_reads_by_kmers_tripog(tp); break;
		case 2: subsample_reads_tripog(tp); break;
	}
	if(tp->winlen == 0){
		return direct_run_tripog(tp);
	}
	tp->longest_idx = 0;
	for(ridx=1;ridx<tp->seqs->nseq;ridx++){
		if(tp->seqs->rdlens->buffer[ridx] > tp->seqs->rdlens->buffer[tp->longest_idx]){
			tp->longest_idx = ridx;
		}
	}
	if(tp->seqs->nseq < 2){
		return direct_run_tripog(tp);
	}
	rlen = tp->seqs->rdlens->buffer[0];
	if(rlen < 2 * tp->winlen){
		return direct_run_tripog(tp);
	}
	clear_u2v(tp->regs[0]);
	clear_u2v(tp->regs[1]);
	// selecting unique window
	{
		uuhash_t *u;
		u4i i, j, hit, nb, kmer, kcnt, kdup, keqs, ktot, kmask, roff;
		reset_iter_uuhash(tp->khash);
		while((u = ref_iter_uuhash(tp->khash))){
			u->val &= 0xFFFFU;
		}
		kmask = MAX_U4 >> ((16 - tp->ksize) << 1);
		for(ridx=0;ridx<1;ridx++){
			rlen = tp->seqs->rdlens->buffer[ridx];
			kmer = 0;
			roff = tp->seqs->rdoffs->buffer[ridx];
			for(i=0;i<rlen;i++){
				kmer = ((kmer << 2) | get_basebank(tp->seqs->rdseqs, roff + i)) & kmask;
				if(i + 1 < tp->ksize) continue;
				u = get_uuhash(tp->khash, kmer);
				u->val += 1U << 16;
			}
		}
		nb = ((rlen - tp->winlen) * 2 / 3 / tp->winlen / 2) * 2;
		b = (rlen - tp->winlen) / 2;
		hit = 0;
		roff = tp->seqs->rdoffs->buffer[0];
		for(j=0;j<nb;){
			e = b + tp->winlen;
			kmer = 0;
			kdup = 0;
			keqs = 0;
			ktot = e - b + 1 - tp->ksize;
			for(i=b;i<e;i++){
				kmer = ((kmer << 2) | get_basebank(tp->seqs->rdseqs, roff + i)) & kmask;
				if(i + 1 - b < tp->ksize) continue;
				kcnt = getval_uuhash(tp->khash, kmer);
				if((kcnt >> 16) > 1){
					kdup ++;
				} else if((kcnt & 0xFFFFU) > 1){
					keqs ++;
				}
			}
			if(cns_debug > 1){
				fprintf(stderr, "Selecting anchor[%4d,%4d]: ktot=%d keqs=%d kdup=%d\n", b, e, ktot, keqs, kdup);
			}
			if(kdup < UInt(tp->kdup * ktot) && keqs >= UInt(tp->keqs * ktot)){
				hit = 1;
				break;
			}
			j ++;
			if(j & 0x01){
				b = (rlen - tp->winlen) / 2 + tp->winlen * ((j + 1) >> 1);
			} else {
				b = (rlen - tp->winlen) / 2 - tp->winlen * ((j + 1) >> 1);
			}
		}
		if(hit == 0){
			return direct_run_tripog(tp);
		}
	}
	push_u2v(tp->regs[0], b);
	push_u2v(tp->regs[1], e);
	failed = 0;
	for(ridx=1;ridx<tp->seqs->nseq;ridx++){
		clear_and_encap_u1v(tp->qry, tp->winlen);
		bitseq_basebank(tp->seqs->rdseqs, tp->seqs->rdoffs->buffer[0] + b, tp->winlen, tp->qry->buffer);
		rlen = tp->seqs->rdlens->buffer[ridx];
		clear_and_encap_u1v(tp->ref, rlen);
		bitseq_basebank(tp->seqs->rdseqs, tp->seqs->rdoffs->buffer[ridx], rlen, tp->ref->buffer);
		R = ksw_align(tp->winlen, tp->qry->buffer, rlen, tp->ref->buffer, 4, tp->matrix, - (tp->pogs[0]->par->I + tp->pogs[0]->par->D)/2, 1, KSW_XSTART, NULL);
		if(R.qb <= -1 || R.tb <= -1 || R.qe <= -1 || R.te <= -1){
			if(cns_debug > 1){
				fprintf(stderr, "FAILED_ALIGN: READ%u [%d,%d=%d][%d,%d=%d]\n", ridx, R.qb, R.qe, R.qe - R.qb, R.tb, R.te, R.te - R.tb);
			}
			if(tp->fail_skip){
				push_u2v(tp->regs[0], MAX_U2);
				push_u2v(tp->regs[1], MAX_U2);
				failed ++;
				continue;
			} else {
				return direct_run_tripog(tp);
			}
		}
		if(R.qe + 1 - R.qb < tp->winmin || R.te + 1 - R.tb < tp->winmin){
			if(cns_debug > 1){
				fprintf(stderr, "FAILED_ALIGN: READ%u [%d,%d=%d][%d,%d=%d]\n", ridx, R.qb, R.qe, R.qe - R.qb, R.tb, R.te, R.te - R.tb);
			}
			if(tp->fail_skip){
				push_u2v(tp->regs[0], MAX_U2);
				push_u2v(tp->regs[1], MAX_U2);
				failed ++;
				continue;
			} else {
				return direct_run_tripog(tp);
			}
		}
		push_u2v(tp->regs[0], R.tb);
		push_u2v(tp->regs[1], R.te + 1);
	}
	if(failed * 2 >= tp->seqs->nseq){
		return direct_run_tripog(tp);
	}
	// building cns for fast aligned regions
	g = tp->pogs[0];
	g->par->alnmode = POG_ALNMODE_GLOBAL;
	beg_pog(g);
	for(ridx=0;ridx<tp->seqs->nseq;ridx++){
		if(tp->regs[0]->buffer[ridx] == MAX_U2) continue;
		fwdbitpush_pog(g, tp->seqs->rdseqs->bits, tp->seqs->rdoffs->buffer[ridx] + tp->regs[0]->buffer[ridx], tp->regs[1]->buffer[ridx] - tp->regs[0]->buffer[ridx]);
	}
	if(0){
		print_seqs_pog(g, "p0.fa", NULL);
	}
	end_pog(g);
	g->par->alnmode = POG_ALNMODE_OVERLAP;
	// finding a best break point
	{
		u2v *rs;
		u1i *s;
		u2i i, idx, bst, bsi, cnt;
		rs = init_u2v(256);
		bst = 0;
		bsi = MAX_U2;
		s = g->msa->buffer + g->msa_len * g->seqs->nseq;
		for(idx=0;idx<g->msa_len;idx++){
			if(s[idx] == 4) continue;
			cnt = 0;
			for(ridx=0;ridx<g->seqs->nseq;ridx++){
				if(g->msa->buffer[g->msa_len * ridx + idx] == s[idx]) cnt ++;
			}
			if(cnt > bst){
				bst = cnt;
				bsi = idx;
				clear_u2v(rs);
				push_u2v(rs, idx);
			} else if(cnt == bst){
				push_u2v(rs, idx);
			}
		}
		if(rs->size){
			bsi = rs->buffer[rs->size / 2];
		}
		free_u2v(rs);
		if(bsi == MAX_U2){
			return direct_run_tripog(tp);
		}
		if(cns_debug > 1){
			fprintf(stderr, "BREAKPOINT[MSA]: %u/%u\n", bsi, g->msa_len);
		}
		// transform coordinate
		i = 0;
		for(ridx=0;ridx<tp->seqs->nseq;ridx++){
			if(tp->regs[0]->buffer[ridx] == MAX_U2) continue;
			cnt = 0;
			s = g->msa->buffer + g->msa_len * i;
			for(idx=0;idx<bsi;idx++){
				if(s[idx] != 4) cnt ++;
			}
			tp->regs[0]->buffer[ridx] = tp->regs[0]->buffer[ridx] + cnt;
			tp->regs[1]->buffer[ridx] = tp->regs[0]->buffer[ridx];
			if(cns_debug > 1){
				fprintf(stderr, "BREAKPOINT[%u:%u]: %u/%u\n", i, ridx, tp->regs[0]->buffer[ridx], tp->seqs->rdlens->buffer[ridx]);
			}
			i ++;
		}
	}
	// forward cns to seqs' ends
	g = tp->pogs[2];
	beg_pog(g);
	for(ridx=0;ridx<tp->seqs->nseq;ridx++){
		if(tp->regs[0]->buffer[ridx] == MAX_U2) continue;
		fwdbitpush_pog(g, tp->seqs->rdseqs->bits, tp->seqs->rdoffs->buffer[ridx] + tp->regs[1]->buffer[ridx], tp->seqs->rdlens->buffer[ridx] - tp->regs[1]->buffer[ridx]);
	}
	if(0){
		print_seqs_pog(g, "p2.fa", NULL);
	}
	end_pog(g);
	if(g->cns->size == 0){
		return direct_run_tripog(tp);
	}
	// backward cns to seqs' begs
	g = tp->pogs[1];
	beg_pog(g);
	for(ridx=0;ridx<tp->seqs->nseq;ridx++){
		if(tp->regs[0]->buffer[ridx] == MAX_U2) continue;
		revbitpush_pog(g, tp->seqs->rdseqs->bits, tp->seqs->rdoffs->buffer[ridx], tp->regs[0]->buffer[ridx]);
	}
	if(0){
		print_seqs_pog(g, "p1.fa", NULL);
	}
	end_pog(g);
	if(g->cns->size == 0){
		return direct_run_tripog(tp);
	}
	// merge two parts
	clear_basebank(tp->cns);
	fast_revbits2basebank(tp->cns, tp->pogs[1]->cns->bits, 0, tp->pogs[1]->cns->size);
	fast_fwdbits2basebank(tp->cns, tp->pogs[2]->cns->bits, 0, tp->pogs[2]->cns->size);
	tp->is_tripog = 1;
}

#endif