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process_circ.cpp
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process_circ.cpp
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#include <vector>
#include <cstring>
#include <algorithm>
#include <utility>
#include <cstdlib>
#include "process_circ.h"
#include "gene_annotation.h"
#include "hash_table.h"
#include "fastq_parser.h"
#include "match_read.h"
#include "chain.h"
#include "extend.h"
#include "utils.h"
#include "genome.h"
#define BINSIZE 5000
#define MAXHTLISTSIZE 0
#define TOPCHAIN 10
typedef pair<uint32_t, int> pu32i;
void set_mm(chain_t &ch, uint32_t qspos, int rlen, int dir, MatchedMate &mm);
ProcessCirc::ProcessCirc(int last_round_num, int ws) : extension(0, EDIT_ALIGNMENT) {
Logger::instance().info.set_prefix("[INFO] + ");
sprintf(fq_file1, "%s_%d_remain_R1.fastq", outputFilename, last_round_num);
sprintf(fq_file2, "%s_%d_remain_R2.fastq", outputFilename, last_round_num);
double cpu_time = get_cpu_time();
double real_time = get_real_time();
if (internalSort) {
Logger::instance().info("Sorting remaining read mappings internally... \n");
sort_fq_internal(fq_file1);
sort_fq_internal(fq_file2);
} else {
Logger::instance().info("Sorting remaining read mappings using GNU sort... \n");
int ret1 = sort_fq(fq_file1);
int ret2 = sort_fq(fq_file2);
// if (ret1 and ret2)
// fprintf(stdout, "OK\n");
}
double final_cpu_time = get_cpu_time();
double final_real_time = get_real_time();
Logger::instance().info("Completed! (CPU time: %.2lfs; Real time: %.2lfs)\n",
final_cpu_time - cpu_time, final_real_time - real_time);
fflush(stdout);
sprintf(fq_file1, "%s_%d_remain_R1.fastq.srt", outputFilename, last_round_num);
sprintf(fq_file2, "%s_%d_remain_R2.fastq.srt", outputFilename, last_round_num);
report_file = NULL;
candid_file = NULL;
window_size = ws;
step = 3;
pre_contig = -1;
pre_chr = "-";
RegionalHashTable *rht;
for (int i = 0; i < MAXHTLISTSIZE; ++i) {
rht = new RegionalHashTable(ws, 0, 0);
ind2ht.insert(make_pair(i, rht));
removables.insert(i);
gid2ind.insert(make_pair(INF - i, i));
gids.push_back(INF - i);
}
int max_kmer_cnt = (maxReadLength - window_size) / step + 1;
bc1.chains = (chain_t *) malloc(maxChainLen * sizeof(chain_t));
for (int i = 0; i < maxChainLen; i++)
bc1.chains[i].frags = (fragment_t *) malloc(max_kmer_cnt * sizeof(fragment_t));
bc2.chains = (chain_t *) malloc(maxChainLen * sizeof(chain_t));
for (int i = 0; i < maxChainLen; i++)
bc2.chains[i].frags = (fragment_t *) malloc(max_kmer_cnt * sizeof(fragment_t));
// circ_type.push_back("SingleTranscriptomeCircRNA");
// circ_type.push_back("MultiTranscriptomeCircRNA");
// circ_type.push_back("NovelCircRNA");
circ_type.push_back("STC");
circ_type.push_back("MTC");
circ_type.push_back("NC");
}
ProcessCirc::~ProcessCirc(void) {
check_removables(MAXUB);
close_file(report_file);
close_file(candid_file);
for (int i = 0; i < maxChainLen; i++)
free(bc1.chains[i].frags);
for (int i = 0; i < maxChainLen; i++)
free(bc2.chains[i].frags);
free(bc1.chains);
free(bc2.chains);
// Remove intermediate files
if (finalCleaning) {
char command[FILE_NAME_MAX_LEN + 100];
sprintf(command, "rm %s*_remain_R*.fastq{,.srt}", outputFilename);
system(command);
}
}
bool record_ptr_compare(Record *r, Record *o) {
if (r->mr->contig_num != o->mr->contig_num)
return r->mr->contig_num < o->mr->contig_num;
if (r->mr->chr_r1 != o->mr->chr_r1)
return r->mr->chr_r1 < o->mr->chr_r1;
return r->mr->spos_r1 < o->mr->spos_r1;
}
void ProcessCirc::sort_fq_internal(char *fqname) {
Logger::instance().debug("Filename: %s\n", fqname);
fflush(stdout);
char *sorted_file = (char *) malloc(FILE_NAME_MAX_LEN);
char *wmode = (char *) malloc(FILE_NAME_MAX_LEN);
sprintf(sorted_file, "%s.srt", fqname);
sprintf(wmode, "%c", 'w');
FASTQParser fq_parser;
fq_parser.init();
fq_parser.reset(fqname);
vector <RecordStr> all_records;
Record *current_record;
while ((current_record = fq_parser.get_next_read(0)) != NULL) {
all_records.push_back(RecordStr(current_record));
}
sort(all_records.begin(), all_records.end());
FILE *sorted_fout = open_file(sorted_file, wmode);
char sep = '\n';
MatchedRead *mr;
char comment[400];
char r1_dir, r2_dir;
for (unsigned int i = 0; i < all_records.size(); ++i) {
mr = &(all_records[i].mr);
r1_dir = (mr->r1_forward) ? '+' : '-';
r2_dir = (mr->r2_forward) ? '+' : '-';
sprintf(comment, " %" PRId64 " %d %s %u %u %d %u %u %c %d %s %u %u %d %u %u %c %d %d %d %d %d",
mr->genome_spos, mr->type,
mr->chr_r1.c_str(), mr->spos_r1, mr->epos_r1, mr->mlen_r1,
mr->qspos_r1, mr->qepos_r1, r1_dir, mr->ed_r1,
mr->chr_r2.c_str(), mr->spos_r2, mr->epos_r2, mr->mlen_r2,
mr->qspos_r2, mr->qepos_r2, r2_dir, mr->ed_r2,
mr->tlen, mr->junc_num, mr->gm_compatible, mr->contig_num);
fprintf(sorted_fout, "@%s%s%c%s%c%s%c%s\n", all_records[i].rname.c_str(), comment, sep,
all_records[i].seq.c_str(), sep, all_records[i].comment.c_str(), sep, all_records[i].qual.c_str());
}
close_file(sorted_fout);
free(sorted_file);
free(wmode);
}
int ProcessCirc::sort_fq(char *fqname) {
Logger::instance().debug("Filename: %s\n", fqname);
fflush(stdout);
if (!system(NULL)) {
fprintf(stdout, "Error: Unable to run system call.\n");
exit(EXIT_FAILURE);
}
char command[FILE_NAME_MAX_LEN + 500];
sprintf(command, "cat %s | paste - - - - | sort --parallel=%d -S 8G -k2,2n | tr \"\t\" \"\n\" > %s.srt", fqname,
threadCount, fqname);
int ret = system(command);
return ret;
}
void ProcessCirc::do_process(void) {
/**********************/
/**Loading Hash Table**/
/**********************/
double cputime_start = get_cpu_time();
double realtime_start = get_real_time();
double cputime_curr;
double realtime_curr;
vector <ContigLen> orig_contig_len;
genome_packer.load_index_info(orig_contig_len);
char index_file[FILE_NAME_MAX_LEN];
strcpy(index_file, genome_packer.get_index_fname().c_str());
initCommon();
THREAD_COUNT = threadCount;
for (int i = 0; i < 255; i++)
THREAD_ID[i] = i;
if (!checkHashTable(index_file))
return;
if (!initLoadingCompressedGenomeMeta(index_file))
return;
kmer = WINDOW_SIZE + checkSumLength;
genome_seeder.init(LOADCONTIGSTRINMEM);
/**********************/
/**Finised Loading HT**/
/**********************/
/*******************/
/**GTF Parser Init**/
/*******************/
if (stage == 1) {
Logger::instance().info("Loading GTF file...\n");
gtf_parser.init(gtfFilename, orig_contig_len);
if (!gtf_parser.load_gtf()) {
fprintf(stdout, "Error in reading GTF file.\n");
exit(1);
}
cputime_curr = get_cpu_time();
realtime_curr = get_real_time();
Logger::instance().info("Completed! (CPU time: %.2lfs; Real time: %.2lfs)\n", cputime_curr - cputime_start,
realtime_curr - realtime_start);
cputime_start = cputime_curr;
realtime_start = realtime_curr;
}
/*******************/
/**Finished GTF PI**/
/*******************/
double fq_cputime_start = cputime_start;
double fq_realtime_start = realtime_start;
bool is_pe = pairedEnd;
FASTQParser fq_parser1;
fq_parser1.init();
fq_parser1.reset(fq_file1);
Record *current_record1 = NULL;
FASTQParser fq_parser2;
fq_parser2.init();
Record *current_record2 = NULL;
if (is_pe) {
fq_parser2.reset(fq_file2);
}
open_candid_file();
int line = 0;
//while ( (current_record1 = fq_parser1.get_next()) != NULL ) { // go line by line on fastq file
while (true) {
current_record1 = fq_parser1.get_next_read(0);
if (current_record1 == NULL)
break;
if (is_pe)
current_record2 = fq_parser2.get_next_read(0);
line++;
vafprintf(2, stderr, "Line: %d\n", line);
if (line % LINELOG == 0) {
cputime_curr = get_cpu_time();
realtime_curr = get_real_time();
// fprintf(stdout, "[P] %d reads in %.2lf CPU sec (%.2lf real sec)\t Look ups: %u\n", line, cputime_curr - cputime_start, realtime_curr - realtime_start, lookup_cnt);
// fflush(stdout);
cputime_start = cputime_curr;
realtime_start = realtime_curr;
lookup_cnt = 0;
}
while (pre_contig != current_record1->mr->contig_num) {
load_genome();
refresh_hash_table_list();
}
//if (pre_chr != current_record1->mr->chr_r1)
// refresh_hash_table_list();
//pre_chr = current_record1->mr->chr_r1;
if (is_pe)
call_circ(current_record1, current_record2);
}
refresh_hash_table_list();
report_events();
cputime_curr = get_cpu_time();
realtime_curr = get_real_time();
Logger::instance().info.set_prefix("[INFO] ");
Logger::instance().info("CircRNA detection Completed! (CPU time: %.2lfs; Real time: %.2lfs)\n",
cputime_curr - fq_cputime_start, realtime_curr - fq_realtime_start);
finalizeLoadingCompressedGenome();
genome_seeder.finalize();
}
// PE
void ProcessCirc::call_circ(Record *current_record1, Record *current_record2) {
fullmap_seq = NULL;
remain_seq = NULL;
r1_seq = NULL;
r2_seq = NULL;
fullmap_seq_len = 0;
remain_seq_len = 0;
r1_seq_len = 0;
r2_seq_len = 0;
MatchedRead mr = *(current_record1->mr);
vafprintf(2, stderr, "%s\n%s\n", current_record1->seq, current_record2->seq);
vafprintf(2, stderr, "%s\t%s\t%u\t%u\t%d\t%u\t%u\t%d\t%s\t%u\t%u\t%d\t%u\t%u\t%d\t%d\t%d\t%d\t%d\n",
current_record1->rname,
mr.chr_r1.c_str(), mr.spos_r1, mr.epos_r1, mr.mlen_r1, mr.qspos_r1, mr.qepos_r1, mr.ed_r1,
mr.chr_r2.c_str(), mr.spos_r2, mr.epos_r2, mr.mlen_r2, mr.qspos_r2, mr.qepos_r2, mr.ed_r2,
mr.tlen, mr.junc_num, mr.gm_compatible, mr.type);
if (mr.type == CHIBSJ) {
call_circ_single_split(current_record1, current_record2);
} else if (mr.type == CHI2BSJ) {
call_circ_double_split(current_record1, current_record2);
}
}
void ProcessCirc::call_circ_single_split(Record *current_record1, Record *current_record2) {
MatchedRead mr = *(current_record1->mr);
bool r1_partial = mr.mlen_r1 < mr.mlen_r2;
remain_seq = (r1_partial) ? ((mr.r1_forward) ? current_record1->seq : current_record1->rcseq) :
((mr.r2_forward) ? current_record2->seq : current_record2->rcseq);
fullmap_seq = (!r1_partial) ? ((mr.r1_forward) ? current_record1->seq : current_record1->rcseq) :
((mr.r2_forward) ? current_record2->seq : current_record2->rcseq);
remain_seq_len = (r1_partial) ? current_record1->seq_len : current_record2->seq_len;
fullmap_seq_len = (!r1_partial) ? current_record1->seq_len : current_record2->seq_len;
// convert to position on contig
gtf_parser.chrloc2conloc(mr.chr_r1, mr.spos_r1, mr.epos_r1);
gtf_parser.chrloc2conloc(mr.chr_r2, mr.spos_r2, mr.epos_r2);
// fill MatchedMate
MatchedMate mm_r1(mr, 1, current_record1->seq_len, r1_partial);
MatchedMate mm_r2(mr, 2, current_record2->seq_len, !r1_partial);
//if (r1_partial)
// remove_side_introns(mm_r1, current_record1->seq_len);
//else
// remove_side_introns(mm_r2, current_record2->seq_len);
uint32_t qspos = (r1_partial) ? (((mm_r1.qspos - 1) > (current_record1->seq_len - mm_r1.qepos)) ? (1) :
(mm_r1.qepos + 1)) : (((mm_r2.qspos - 1) > (current_record2->seq_len - mm_r2.qepos)) ? (1) :
(mm_r2.qepos + 1));
uint32_t qepos = (r1_partial) ? (((mm_r1.qspos - 1) > (current_record1->seq_len - mm_r1.qepos)) ? (mm_r1.qspos - 1)
: (current_record1->seq_len))
: (((mm_r2.qspos - 1) > (current_record2->seq_len - mm_r2.qepos)) ? (mm_r2.qspos - 1)
: (current_record2->seq_len));
int whole_seq_len = (r1_partial) ? current_record1->seq_len : current_record2->seq_len;
int remain_len = qepos - qspos + 1;
if (qepos < qspos or remain_len < window_size) { // it was fully mapped
return;
}
const IntervalInfo<GeneInfo> *gene_info = gtf_parser.get_gene_overlap(mm_r1.spos, false);
bool found = (gene_info != NULL);
if (!found) {
vafprintf(2, stderr, "Gene not found!\n");
return;
}
vafprintf(2, stderr, "# Gene overlaps: %d\n", gene_info->seg_list.size());
ConShift con_shift;
check_removables(mm_r1.spos);
RegionalHashTable *regional_ht;
CircRes best_cr;
best_cr.type = NF;
for (unsigned int i = 0; i < gene_info->seg_list.size(); ++i) {
uint32_t gene_len = gene_info->seg_list[i].end - gene_info->seg_list[i].start + 1;
regional_ht = get_hash_table_smart(gene_info->seg_list[i]);
vafprintf(2, stderr, "R%d partial: [%d-%d]\n", (int) (!r1_partial) + 1, qspos, qepos);
vafprintf(2, stderr, "%s\n", remain_seq);
chaining(qspos, qepos, regional_ht, remain_seq, gene_len, gene_info->seg_list[i].start, bc1);
if (bc1.best_chain_count <= 0)
continue;
// find rspos and repos for the best chain
bool forward = (r1_partial) ? (mr.r1_forward) : (mr.r2_forward);
int dir = (forward) ? 1 : -1;
for (int j = 0; j < minM(bc1.best_chain_count, TOPCHAIN); ++j) {
// fprintf(stderr, "Trying chain #%d\n\n\n", j);
MatchedMate partial_mm;
find_exact_coord(mm_r1, mm_r2, partial_mm, dir, qspos, remain_seq, remain_len, whole_seq_len,
bc1.chains[j]);
if (partial_mm.type == CONCRD) {
con_shift = gtf_parser.get_shift(contigNum, mm_r1.spos);
vafprintf(2, stderr, "Coordinates: [%d-%d]\n", partial_mm.spos - con_shift.shift,
partial_mm.epos - con_shift.shift);
CircRes cr;
// fprintf(stderr, "%s\t", current_record1->rname);
int type = check_split_map(mm_r1, mm_r2, partial_mm, r1_partial, cr);
print_split_mapping(current_record1->rname, mm_r1, mm_r2, partial_mm, con_shift);
// fprintf(stderr, "\n");
fprintf(candid_file, "%d\n", type);
if (type < CR) {
best_cr.type = type;
return;
}
if (type >= CR and type <= MCR and type < best_cr.type) {
best_cr.chr = con_shift.contig;
best_cr.rname = current_record1->rname;
best_cr.spos = cr.spos - con_shift.shift;
best_cr.epos = cr.epos - con_shift.shift;
best_cr.type = type;
best_cr.start_signal = cr.start_signal;
best_cr.end_signal = cr.end_signal;
best_cr.start_bp_ref = cr.start_bp_ref;
best_cr.end_bp_ref = cr.end_bp_ref;
if (type == CR) {
circ_res.push_back(best_cr);
return;
}
}
}
}
}
if (best_cr.type >= CR and best_cr.type <= MCR)
circ_res.push_back(best_cr);
}
void ProcessCirc::call_circ_double_split(Record *current_record1, Record *current_record2) {
MatchedRead mr = *(current_record1->mr);
vafprintf(2, stderr, "Double split read...\n");
char *r1_remain_seq = (mr.r1_forward) ? current_record1->seq : current_record1->rcseq;
char *r2_remain_seq = (mr.r2_forward) ? current_record2->seq : current_record2->rcseq;
r1_seq = r1_remain_seq;
r2_seq = r2_remain_seq;
r1_seq_len = current_record1->seq_len;
r2_seq_len = current_record2->seq_len;
uint32_t r1_qspos = ((mr.qspos_r1 - 1) > (current_record1->seq_len - mr.qepos_r1)) ? (1) : (mr.qepos_r1 + 1);
uint32_t r2_qspos = ((mr.qspos_r2 - 1) > (current_record2->seq_len - mr.qepos_r2)) ? (1) : (mr.qepos_r2 + 1);
uint32_t r1_qepos = ((mr.qspos_r1 - 1) > (current_record1->seq_len - mr.qepos_r1)) ? (mr.qspos_r1 - 1)
: (current_record1->seq_len);
uint32_t r2_qepos = ((mr.qspos_r2 - 1) > (current_record2->seq_len - mr.qepos_r2)) ? (mr.qspos_r2 - 1)
: (current_record2->seq_len);
int r1_remain_len = r1_qepos - r1_qspos + 1;
int r2_remain_len = r2_qepos - r2_qspos + 1;
// it was fully mapped
if (r1_remain_len < window_size and r2_remain_len < window_size) {
return;
}
// single split
if (r1_remain_len < window_size or r2_remain_len < window_size) {
call_circ_single_split(current_record1, current_record2);
}
// convert to position on contig
gtf_parser.chrloc2conloc(mr.chr_r1, mr.spos_r1, mr.epos_r1);
gtf_parser.chrloc2conloc(mr.chr_r2, mr.spos_r2, mr.epos_r2);
const IntervalInfo<GeneInfo> *gene_info = gtf_parser.get_gene_overlap(mr.spos_r1, false);
bool found = (gene_info != NULL);
if (!found) {
vafprintf(2, stderr, "Gene not found!\n");
return;
}
vafprintf(2, stderr, "# Gene overlaps: %d\n", gene_info->seg_list.size());
// fill MatchedMate
MatchedMate mm_r1(mr, 1, current_record1->seq_len, true);
MatchedMate mm_r2(mr, 2, current_record2->seq_len, true);
ConShift con_shift;
check_removables(mr.spos_r1);
RegionalHashTable *regional_ht;
CircRes best_cr;
best_cr.type = NF;
for (unsigned int i = 0; i < gene_info->seg_list.size(); ++i) {
uint32_t gene_len = gene_info->seg_list[i].end - gene_info->seg_list[i].start + 1;
regional_ht = get_hash_table_smart(gene_info->seg_list[i]);
vafprintf(2, stderr, "R1 partial: [%d-%d]\nremain: %s\n", r1_qspos, r1_qepos, r1_remain_seq);
chaining(r1_qspos, r1_qepos, regional_ht, r1_remain_seq, gene_len, gene_info->seg_list[i].start, bc1);
vafprintf(2, stderr, "R2 partial: [%d-%d]\nremain: %s\n", r2_qspos, r2_qepos, r2_remain_seq);
chaining(r2_qspos, r2_qepos, regional_ht, r2_remain_seq, gene_len, gene_info->seg_list[i].start, bc2);
if (bc1.best_chain_count <= 0 and bc2.best_chain_count <= 0) {
// fprintf(stderr, "LostRead: Not chained!\n");
continue;
}
if (bc1.best_chain_count <= 0 or bc2.best_chain_count <= 0) {
// fprintf(stderr, "Doing one single split check instead of double!\n");
call_circ_single_split(current_record1, current_record2);
continue;
}
for (int j = 0; j < minM(bc1.best_chain_count, TOPCHAIN); ++j) {
for (int k = 0; k < minM(bc2.best_chain_count, TOPCHAIN); ++k) {
// find rspos and repos for the best chain
MatchedMate r1_partial_mm;
MatchedMate r2_partial_mm;
set_mm(bc1.chains[j], r1_qspos, r1_remain_len, mm_r1.dir, r1_partial_mm);
set_mm(bc2.chains[k], r2_qspos, r2_remain_len, mm_r2.dir, r2_partial_mm);
overlap_to_spos(mm_r1);
overlap_to_spos(mm_r2);
overlap_to_spos(r1_partial_mm);
overlap_to_spos(r2_partial_mm);
vector <uint32_t> common_tid;
// if (! same_transcript(mm_r1.exons_spos, mm_r2.exons_spos, r1_partial_mm.exons_spos, r2_partial_mm.exons_spos, common_tid))
// continue;
vector <MatchedMate> segments;
segments.push_back(mm_r1);
segments.push_back(mm_r2);
segments.push_back(r1_partial_mm);
segments.push_back(r2_partial_mm);
if (!same_transcript(segments, 4, common_tid))
continue;
bool success = false;
if (bc1.chains[j].frags[0].rpos <= bc2.chains[k].frags[0].rpos) {
success = extension.extend_both_mates(bc1.chains[j], bc2.chains[k], common_tid, r1_remain_seq,
r2_remain_seq, r1_qspos, r2_qspos, r1_qepos, r2_qepos,
r1_partial_mm, r2_partial_mm);
} else {
success = extension.extend_both_mates(bc2.chains[k], bc1.chains[j], common_tid, r2_remain_seq,
r1_remain_seq, r2_qspos, r1_qspos, r2_qepos, r1_qepos,
r2_partial_mm, r1_partial_mm);
}
if (!success) {
// fprintf(stderr, "LostRead: Not extended!\n");
continue;
}
if (r1_partial_mm.type == CONCRD and r2_partial_mm.type == CONCRD) {
con_shift = gtf_parser.get_shift(contigNum, mm_r1.spos);
vafprintf(2, stderr, "R1 Partial Coordinates: [%d-%d]\n", r1_partial_mm.spos - con_shift.shift,
r1_partial_mm.epos - con_shift.shift);
vafprintf(2, stderr, "R2 Partial Coordinates: [%d-%d]\n", r2_partial_mm.spos - con_shift.shift,
r2_partial_mm.epos - con_shift.shift);
CircRes cr;
int type = check_split_map(mm_r1, mm_r2, r1_partial_mm, r2_partial_mm, cr);
print_split_mapping(current_record1->rname, mm_r1, mm_r2, r1_partial_mm, r2_partial_mm, con_shift);
fprintf(candid_file, "%d\n", type);
if (type < CR) {
best_cr.type = type;
return;
}
if (type >= CR and type <= MCR and type < best_cr.type) {
best_cr.chr = con_shift.contig;
best_cr.rname = current_record1->rname;
best_cr.spos = cr.spos - con_shift.shift;
best_cr.epos = cr.epos - con_shift.shift;
best_cr.type = type;
best_cr.start_signal = cr.start_signal;
best_cr.end_signal = cr.end_signal;
best_cr.start_bp_ref = cr.start_bp_ref;
best_cr.end_bp_ref = cr.end_bp_ref;
if (type == CR) {
circ_res.push_back(best_cr);
return;
}
}
}
}
}
}
if (best_cr.type >= CR and best_cr.type <= MCR) {
circ_res.push_back(best_cr);
} else {
call_circ_single_split(current_record1, current_record2);
}
}
void ProcessCirc::binning(uint32_t qspos, uint32_t qepos, RegionalHashTable *regional_ht, char *remain_seq,
uint32_t gene_len) {
int bin_num = gene_len / BINSIZE + 1;
int bins[bin_num];
int max_id = 0;
memset(bins, 0, bin_num * sizeof(int));
for (uint32_t i = qspos - 1; i <= qepos - window_size; i += step) {
GIMatchedKmer *gl = regional_ht->find_hash(regional_ht->hash_val(remain_seq + i));
if (gl == NULL) {
vafprintf(2, stderr, "Hash val not found!!!\n");
}
vafprintf(2, stderr, "Occ: %d\n", gl->frag_count);
for (uint32_t j = 0; j < gl->frag_count; j++) {
int bin_id = gl->frags[j].info / BINSIZE;
bins[bin_id]++;
if (bins[bin_id] > bins[max_id])
max_id = bin_id;
vafprintf(2, stderr, "%d - %d\t", gl->frags[j].info, bins[bin_id]);
}
vafprintf(2, stderr, "\n");
}
vafprintf(2, stderr, "Biggest bin: bin[%d][%d - %d] = %d\n", max_id, max_id * BINSIZE, (max_id + 1) * BINSIZE - 1,
bins[max_id]);
}
void ProcessCirc::chaining(uint32_t qspos, uint32_t qepos, RegionalHashTable *regional_ht, char *remain_seq,
uint32_t gene_len, uint32_t shift, chain_list &bc) {
int seq_len = qepos - qspos + 1;
if (seq_len < window_size) {
bc.best_chain_count = 0;
return;
}
int kmer_cnt = (seq_len - window_size) / step + 1;
GIMatchedKmer fl[kmer_cnt + 1];
int l = 0;
for (uint32_t i = qspos - 1; i <= qepos - window_size; i += step) {
GIMatchedKmer *gl = regional_ht->find_hash(regional_ht->hash_val(remain_seq + i));
if (gl == NULL) { // has N inside kmer
vafprintf(2, stderr, "Hash val not found!!!\n");
continue;
}
fl[l] = *gl;
fl[l].qpos = i;
//vafprintf(2, stderr, "Occ: %d\n", fl[l].frag_count);
//for (int j = 0; j < gl->frag_count; j++) {
// vafprintf(2, stderr, "%d - %d\t", gl->frags[j].info, fl[l].frags[j].info);
//}
//vafprintf(2, stderr, "\n");
if (fl[l].frag_count > seedLim)
fl[l].frag_count = 0;
l++;
}
kmer_cnt = l;
chain_seeds_sorted_kbest2(qepos, fl, bc, window_size, kmer_cnt, shift);
vafprintf(1, stderr, "Chaining score:%.4f,\t len: %lu\n", bc.chains[0].score, (unsigned long) bc.best_chain_count);
int allowed_missed_kmers = (qepos - qspos + 1) / 20 * 3 + 1;
vafprintf(2, stderr, "Allowed missing kmers: %d\n", allowed_missed_kmers);
int missing;
int least_miss = INF;
for (int j = 0; j < bc.best_chain_count; j++) {
missing = kmer_cnt - bc.chains[j].chain_len;
vafprintf(2, stderr, "Actual missing: %d\n", missing);
if (missing > least_miss) {
// this one does not count
bc.best_chain_count = j;
break;
}
least_miss = missing;
for (uint32_t i = 0; i < bc.chains[j].chain_len; i++) {
vafprintf(1, stderr, "#%d\tfrag[%d]: %lu\t%d\t%d\n", j, i, bc.chains[j].frags[i].rpos - shift,
bc.chains[j].frags[i].qpos, bc.chains[j].frags[i].len);
}
}
}
bool ProcessCirc::find_exact_coord(MatchedMate &mm_r1, MatchedMate &mm_r2, MatchedMate &partial_mm,
int dir, uint32_t qspos, char *rseq, int rlen, int whole_len, chain_t &bc) {
set_mm(bc, qspos, rlen, dir, partial_mm);
--qspos; // convert to 0-based
overlap_to_spos(mm_r1);
overlap_to_spos(mm_r2);
overlap_to_spos(partial_mm);
vector <uint32_t> common_tid;
// bool success = same_transcript(mm_r1.exons_spos, mm_r2.exons_spos, partial_mm.exons_spos, common_tid);
vector <MatchedMate> segments;
segments.push_back(mm_r1);
segments.push_back(mm_r2);
segments.push_back(partial_mm);
bool success = same_transcript(segments, 3, common_tid);
if (!success) {
// fprintf(stderr, "No common transcript!\n");
return false;
}
partial_mm.middle_ed = extension.calc_middle_ed(bc, maxEd, rseq, rlen);
if (partial_mm.middle_ed > maxEd)
return false;
bool extend = true;
partial_mm.is_concord = false;
if (bc.chain_len <= 0) {
partial_mm.type = ORPHAN;
partial_mm.matched_len = 0;
return false;
}
bool lok;
bool rok;
int err = partial_mm.middle_ed;
if (extend) {
partial_mm.matched_len = rlen;
lok = extension.extend_chain_left(common_tid, bc, rseq + qspos, qspos, MINLB, partial_mm, err);
if (qspos == 0) {
rok = extension.extend_chain_right(common_tid, bc, rseq, rlen, MAXUB, partial_mm, err);
} else {
rok = extension.extend_chain_right(common_tid, bc, rseq, whole_len, MAXUB, partial_mm, err);
}
update_match_mate_info(lok, rok, err, partial_mm);
}
return partial_mm.type == CONCRD;
}
void ProcessCirc::refresh_hash_table_list(void) {
for (auto it = ind2ht.begin(); it != ind2ht.end(); ++it) {
delete it->second;
//removables.insert(it->first);
}
removables.clear();
gids.clear();
gid2ind.clear();
ind2ht.clear();
}
void ProcessCirc::check_removables(uint32_t rspos) {
for (auto it = ind2ht.begin(); it != ind2ht.end(); ++it) {
if (rspos > it->second->gene_epos) {
removables.insert(it->first);
// fprintf(stderr, "Removed gid: %d --removables size: %d\n", gids[it->first], removables.size());
}
}
}
RegionalHashTable *ProcessCirc::get_hash_table(const GeneInfo &gene_info) {
RegionalHashTable *regional_ht;
RegionalHashTable *new_ht;
int gene_len = gene_info.end - gene_info.start + 1;
char gene_seq[gene_len + 1];
gene_seq[gene_len] = '\0';
genome_seeder.pac2char_otf(gene_info.start, gene_len, gene_seq);
new_ht = new RegionalHashTable(window_size, gene_info.start, gene_info.end);
new_ht->create_table(gene_seq, 0, gene_len);
regional_ht = new_ht;
return regional_ht;
}
RegionalHashTable *ProcessCirc::get_hash_table_smart(const GeneInfo &gene_info) {
uint32_t gid, removable_ind;
RegionalHashTable *regional_ht;
RegionalHashTable *new_ht;
int gene_len = gene_info.end - gene_info.start + 1;
gid = gene_info.gene_id;
//fprintf(stderr, "Gene id: %d\n", gid);
if (gid2ind.find(gid) != gid2ind.end()) {
uint32_t ind = gid2ind[gid];
regional_ht = ind2ht[ind];
//fprintf(stderr, "Found gid: %d\t---Skipping HT create\n", gid);
} else {
char gene_seq[gene_len + 1];
gene_seq[gene_len] = '\0';
//genome_seeder.pac2char(gene_info.start, gene_len, gene_seq);
genome_seeder.pac2char_otf(gene_info.start, gene_len, gene_seq);
if (removables.size() == 0) {
new_ht = new RegionalHashTable(window_size, gene_info.start, gene_info.end);
uint32_t new_ind = ind2ht.size();
ind2ht.insert(make_pair(new_ind, new_ht));
gid2ind.insert(make_pair(gid, new_ind));
gids.push_back(gid);
new_ht->create_table(gene_seq, 0, gene_len);
regional_ht = new_ht;
//fprintf(stderr, "Allocated new HT gid: %d, %s [%u-%u]\n", gid, mr.chr_r1.c_str(), mr.spos_r1, mr.spos_r2);
} else {
removable_ind = *(removables.cbegin());
removables.erase(removables.cbegin());
gid2ind.erase(gids[removable_ind]);
gid2ind.insert(make_pair(gid, removable_ind));
//fprintf(stderr, "Removed gid: %d\tTotal: %d\n", gids[removable_ind], gid2ind.size());
gids[removable_ind] = gid;
regional_ht = ind2ht[removable_ind];
regional_ht->gene_spos = gene_info.start;
regional_ht->gene_epos = gene_info.end;
regional_ht->create_table(gene_seq, 0, gene_len);
}
//fprintf(stderr, "Added gid: %d\tTotal: %d\n", gid, gid2ind.size());
//fprintf(stderr, "----------------------------------------------------------\n");
//fprintf(stderr, "Map Info \n");
//for (auto it = ind2ht.begin(); it != ind2ht.end(); ++it) {
// fprintf(stderr, "ind: %d,\tgid: %d\n", it->first, gids[it->first]);
//}
//fprintf(stderr, "----------------------------------------------------------\n");
}
return regional_ht;
}
// for non-overlapping split mates
int ProcessCirc::check_split_map(MatchedMate &mm_r1, MatchedMate &mm_r2, MatchedMate &partial_mm, bool r1_partial,
CircRes &cr) {
int valid = NF;
int split_read_ed = 0;
if (r1_partial) {
split_read_ed = mm_r1.right_ed + mm_r1.left_ed + mm_r1.middle_ed +
partial_mm.right_ed + partial_mm.left_ed + partial_mm.middle_ed;
if (mm_r1.qspos < partial_mm.qspos)
valid = final_check(mm_r2, mm_r1, partial_mm, cr);
else
valid = final_check(mm_r2, partial_mm, mm_r1, cr);
} else {
split_read_ed = mm_r2.right_ed + mm_r2.left_ed + mm_r2.middle_ed +
partial_mm.right_ed + partial_mm.left_ed + partial_mm.middle_ed;
if (mm_r2.qspos < partial_mm.qspos)
valid = final_check(mm_r1, mm_r2, partial_mm, cr);
else
valid = final_check(mm_r1, partial_mm, mm_r2, cr);
}
if (split_read_ed > maxEd) {
//fprintf(stderr, "non-overlapping edit distance exceeded! ed: %d\n", split_read_ed);
valid = UD;
}
return valid;
}
// for overlapping split mates
int ProcessCirc::check_split_map(MatchedMate &mm_r1_1, MatchedMate &mm_r2_1, MatchedMate &mm_r1_2, MatchedMate &mm_r2_2,
CircRes &cr) {
int r1_ed = mm_r1_1.right_ed + mm_r1_1.left_ed + mm_r1_1.middle_ed +
mm_r1_2.right_ed + mm_r1_2.left_ed + mm_r1_2.middle_ed;
int r2_ed = mm_r2_1.right_ed + mm_r2_1.left_ed + mm_r2_1.middle_ed +
mm_r2_2.right_ed + mm_r2_2.left_ed + mm_r2_2.middle_ed;
if (r1_ed > maxEd or r2_ed > maxEd) {
//fprintf(stderr, "overlapping edit distance exceeded! ed1: %d, ed2: %d\n", r1_ed, r2_ed);
return UD;
}
MatchedMate mm_r1_l = (mm_r1_1.spos <= mm_r1_2.spos) ? mm_r1_1 : mm_r1_2;
MatchedMate mm_r1_r = (mm_r1_1.spos <= mm_r1_2.spos) ? mm_r1_2 : mm_r1_1;
MatchedMate mm_r2_l = (mm_r2_1.spos <= mm_r2_2.spos) ? mm_r2_1 : mm_r2_2;
MatchedMate mm_r2_r = (mm_r2_1.spos <= mm_r2_2.spos) ? mm_r2_2 : mm_r2_1;
bool r1_regular_bsj = (mm_r1_l.qspos < mm_r1_r.qspos);
bool r2_regular_bsj = (mm_r2_l.qspos < mm_r2_r.qspos);
string ssignal_final;
string esignal_final;
string ssignal1;
string esignal1;
string ssignal2;
string esignal2;
// RF or FR check
if (r1_regular_bsj and r2_regular_bsj) {
if (mm_r1_l.dir == 1) {
if (mm_r1_r.spos <= mm_r2_l.spos)
return FR;
else if (mm_r1_l.epos >= mm_r2_r.epos)
return RF;
}
if (mm_r1_l.dir == -1) {
if (mm_r2_r.spos <= mm_r1_l.spos)
return FR;
else if (mm_r2_l.epos >= mm_r1_r.epos)
return RF;
}
}
// single BSJ on R2
else if (r1_regular_bsj and !r2_regular_bsj) {
MatchedMate full_mm = mm_r1_l;
if (!full_mm.merge_to_right(mm_r1_r))
return UD;
remain_seq = r2_seq;
remain_seq_len = r2_seq_len;
return final_check(full_mm, mm_r2_l, mm_r2_r, cr);
}
// single BSJ on R1
else if (!r1_regular_bsj and r2_regular_bsj) {
MatchedMate full_mm = mm_r2_l;
if (!full_mm.merge_to_right(mm_r2_r))
return UD;
remain_seq = r1_seq;
remain_seq_len = r1_seq_len;
return final_check(full_mm, mm_r1_l, mm_r1_r, cr);
}
// BSJ on the overlap
else if (!r1_regular_bsj and !r2_regular_bsj) {
if (mm_r1_l.spos == mm_r2_l.spos and mm_r1_r.epos == mm_r2_r.epos) {
overlap_to_spos(mm_r1_l);
overlap_to_epos(mm_r1_r);
// if (mm_r1_l.exons_spos == NULL or mm_r1_r.exons_epos == NULL) {
// cr.set_bp(mm_r1_l.spos - mm_r1_l.sclen_left, mm_r1_r.epos + mm_r1_r.sclen_right);
// return MCR;
// }
vector <pu32i> end_tids;
int diff;