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utils.cpp
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utils.cpp
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#include "utils.h"
#include "common.h"
#include "align.h"
#include "gene_annotation.h"
#include "match_read.h"
void get_mate_name(char *fq1, char *fq2) {
strcpy(fq2, fq1);
int i = strlen(fq1) - 1;
while (fq1[i--] != '.' and i >= 1);
if (fq1[i] == '1')
fq2[i] = '2';
else if (fq1[i] == '2')
fq2[i] = '1';
else {
fprintf(stderr, "Error: PE FASTQ names are not in the correct format\n");
exit(1);
}
}
void update_match_mate_info(bool lok, bool rok, int err, MatchedMate &mm) {
mm.left_ok = lok and (mm.sclen_left <= maxSc);
mm.right_ok = rok and (mm.sclen_right <= maxSc);
if (lok and rok and (err <= maxEd) and (mm.sclen_right <= maxSc) and (mm.sclen_left <= maxSc)) {
mm.is_concord = true;
mm.type = CONCRD;
} else if (lok or rok) {
mm.type = CANDID;
} else
mm.type = ORPHAN;
}
int estimate_middle_error(const chain_t &ch) {
int mid_err = 0;
for (uint32_t i = 0; i < ch.chain_len - 1; i++) {
if (ch.frags[i + 1].qpos > int32_t(ch.frags[i].qpos + ch.frags[i].len)) {
int diff = (ch.frags[i + 1].rpos - ch.frags[i].rpos) - (ch.frags[i + 1].qpos - ch.frags[i].qpos);
if (diff == 0)
mid_err++;
else if (diff > 0 and diff <= bandWidth)
mid_err += diff;
else if (diff < 0 and diff >= (-1 * bandWidth))
mid_err -= diff;
}
}
return mid_err;
}
// calculate tlen including sm.epos and lm.spos
int calc_tlen(const MatchedMate &sm, const MatchedMate &lm, int &intron_num) {
const IntervalInfo<UniqSeg> *this_region;
uint32_t tid;
int start_ind;
uint32_t start_table_ind;
uint32_t end_table_ind;
int tlen;
int min_tlen = INF;
int this_it_ind;
int in;
for (unsigned int i = 0; i < sm.exons_epos->seg_list.size(); i++) {
for (unsigned int j = 0; j < sm.exons_epos->seg_list[i].trans_id.size(); j++) {
tid = sm.exons_epos->seg_list[i].trans_id[j];
start_ind = gtf_parser.get_trans_start_ind(contigNum, tid);
start_table_ind = sm.exon_ind_epos - start_ind;
if (start_table_ind < 0) // assert
continue;
end_table_ind = lm.exon_ind_spos - start_ind;
// transcript does not contain lm exon
if (lm.exon_ind_spos < start_ind or
end_table_ind >= gtf_parser.trans2seg[contigNum][tid].size() or
gtf_parser.trans2seg[contigNum][tid][end_table_ind] == 0)
continue;
if (start_table_ind == end_table_ind) {
in = 0;
tlen = lm.spos - sm.epos + 1;
} else {
bool pre_zero = false;
in = 0;
tlen = sm.exons_epos->epos - sm.epos + 1;
this_it_ind = sm.exon_ind_epos;
for (uint32_t k = start_table_ind + 1; k < end_table_ind; k++) {
this_it_ind++;
if (gtf_parser.trans2seg[contigNum][tid][k] != 0) {
this_region = gtf_parser.get_interval(this_it_ind);
tlen += this_region->epos - this_region->spos + 1;
pre_zero = false;
} else {
if (!pre_zero)
in++;
pre_zero = true;
}
}
tlen += lm.spos - lm.exons_spos->spos + 1;
}
//fprintf(stdout, "tr[%d]: %s\ttlen: %d\tintrons: %d\n", tid, gtf_parser.transcript_ids[contigNum][tid].c_str(), tlen, in);
if (tlen < min_tlen) {
intron_num = in;
min_tlen = tlen;
}
}
}
return (min_tlen == INF) ? -1 : min_tlen + sm.matched_len - 1 + lm.matched_len - 1;
}
bool is_concord(const chain_t &a, uint32_t seq_len, MatchedMate &mr) {
if (a.chain_len < 2) {
mr.is_concord = false;
} else if ((a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - a.frags[0].qpos) >= seq_len) {
mr.is_concord = true;
mr.type = CONCRD;
mr.spos = a.frags[0].rpos;
mr.epos = a.frags[a.chain_len - 1].rpos + a.frags[a.chain_len - 1].len - 1;
mr.matched_len = a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - a.frags[0].qpos;
mr.qspos = a.frags[0].qpos;
mr.qepos = a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - 1;
} else {
mr.is_concord = false;
}
return mr.is_concord;
}
bool is_concord2(const chain_t &a, uint32_t seq_len, MatchedMate &mr) {
if (a.chain_len < 2) {
mr.is_concord = false;
} else if ((a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - a.frags[0].qpos) >= seq_len) {
mr.is_concord = true;
mr.type = CONCRD;
mr.spos = a.frags[0].rpos;
mr.epos = a.frags[a.chain_len - 1].rpos + a.frags[a.chain_len - 1].len - 1;
mr.matched_len = a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - a.frags[0].qpos;
mr.qspos = a.frags[0].qpos;
mr.qepos = a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len - 1;
} else {
mr.is_concord = false;
if (a.frags[0].qpos == 0 or a.frags[a.chain_len - 1].qpos + a.frags[a.chain_len - 1].len == seq_len) {
mr.type = CANDID;
}
}
return mr.is_concord;
}
// sm should start before lm
bool
concordant_explanation(const MatchedMate &sm, const MatchedMate &lm, MatchedRead &mr, const string &chr, uint32_t shift,
bool r1_sm, int pair_type) {
if (sm.spos > lm.spos)
return false;
int32_t tlen;
bool on_cdna;
on_cdna =
(sm.exons_spos != NULL) and (sm.exons_epos != NULL) and (lm.exons_spos != NULL) and (lm.exons_epos != NULL);
if (sm.exons_spos == NULL or lm.exons_spos == NULL) {
tlen = lm.spos - sm.epos - 1 + lm.matched_len + sm.matched_len;
if (tlen <= maxTlen)
mr.update(sm, lm, chr, shift, tlen, 0, false, CONGNM, r1_sm);
else if (tlen <= MAXDISCRDTLEN)
mr.update(sm, lm, chr, shift, tlen, 0, false, CONGNM, r1_sm);
} else {
//fprintf(stderr, "Left Mate [%u-%u] dir=%d, type=%d, Right Mate[%u-%u] dir=%d, type=%d\n", sm.spos, sm.epos, sm.dir, sm.type, lm.spos, lm.epos, lm.dir, lm.type);
// starts on same exon
for (unsigned int i = 0; i < sm.exons_spos->seg_list.size(); i++)
for (unsigned int j = 0; j < lm.exons_spos->seg_list.size(); j++)
if (sm.exons_spos->seg_list[i].same_exon(lm.exons_spos->seg_list[j])) {
// => assume genomic locations
tlen = lm.spos + lm.matched_len - sm.spos;
if (tlen <= maxTlen)
mr.update(sm, lm, chr, shift, tlen, 0, on_cdna, ((pair_type == 0) ? CONCRD : CONGEN), r1_sm);
else
mr.update(sm, lm, chr, shift, tlen, 0, on_cdna, DISCRD, r1_sm);
}
}
if (sm.exons_epos == NULL or lm.exons_spos == NULL) {
tlen = lm.spos - sm.epos - 1 + sm.matched_len + lm.matched_len;
if (tlen <= maxTlen)
mr.update(sm, lm, chr, shift, tlen, 0, false, CONGNM, r1_sm);
else if (tlen <= MAXDISCRDTLEN)
mr.update(sm, lm, chr, shift, tlen, 0, false, CONGNM, r1_sm);
} else {
int intron_num;
tlen = calc_tlen(sm, lm, intron_num);
//fprintf(stdout, "tlen: %d\n", tlen);
if (tlen >= 0 and tlen <= maxTlen) {
mr.update(sm, lm, chr, shift, tlen, intron_num, on_cdna, ((pair_type == 0) ? CONCRD : CONGEN), r1_sm);
} else {
if (tlen < 0) {
tlen = lm.spos - sm.epos - 1 + sm.matched_len + lm.matched_len;
intron_num = 0;
}
mr.update(sm, lm, chr, shift, tlen, intron_num, on_cdna, DISCRD, r1_sm);
}
}
if (mr.type == CONCRD)
return true;
else
return false;
}
bool check_chimeric(const MatchedMate &sm, const MatchedMate &lm, MatchedRead &mr, const string &chr, uint32_t shift,
bool r1_sm) {
if (mr.type == CONCRD)
return false;
if (sm.exons_spos == NULL or lm.exons_spos == NULL)
return false;
//fprintf(stderr, "Left Mate [%u-%u] dir=%d, type=%d, Right Mate[%u-%u] dir=%d, type=%d\n", sm.spos, sm.epos, sm.dir, sm.type, lm.spos, lm.epos, lm.dir, lm.type);
for (unsigned int i = 0; i < sm.exons_spos->seg_list.size(); i++)
for (unsigned int j = 0; j < lm.exons_spos->seg_list.size(); j++)
if (sm.exons_spos->seg_list[i].same_gene(lm.exons_spos->seg_list[j]) and sm.spos < lm.spos) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHIORF, r1_sm);
return true;
}
return false;
}
// check for one valid split mate
// -> one fully mapped mate and one partially mapped
bool check_bsj(MatchedMate &sm, MatchedMate &lm, MatchedRead &mr, const string &chr, uint32_t shift, bool r1_sm) {
if (mr.type == CONCRD or mr.type == DISCRD)
return false;
if ((!sm.right_ok) or (!lm.left_ok))
return false;
if (sm.exons_spos == NULL or lm.exons_spos == NULL) {
if ((sm.exons_spos != NULL and same_gene(sm, lm)) or (lm.exons_spos != NULL and same_gene(lm, sm))) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHIBSJ, r1_sm);
return true;
}
// checking for ciRNA
//fprintf(stderr, "R1 start ind: %d\tR2 end ind: %d\n To beg of intron: %d\n", sm.exon_ind_spos, lm.exon_ind_epos, sm.spos - gtf_parser.get_interval_epos(sm.exon_ind_spos));
if ((intronic_bs[contigNum][sm.spos]) and ((intronic_bs[contigNum][lm.spos])) and
(sm.exon_ind_spos >= 0) and (lm.exon_ind_epos >= 0) and (sm.exon_ind_spos == lm.exon_ind_epos) and
(sm.spos - gtf_parser.get_interval_epos(sm.exon_ind_spos) <= LARIAT2BEGTH)) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHIBSJ, r1_sm);
return true;
}
return false;
}
for (unsigned int i = 0; i < sm.exons_spos->seg_list.size(); i++)
for (unsigned int j = 0; j < lm.exons_spos->seg_list.size(); j++)
if (sm.exons_spos->seg_list[i].same_gene(lm.exons_spos->seg_list[j])) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHIBSJ, r1_sm);
return true;
}
return false;
}
// check for two valid split mates
// -> two partially mapped mates
bool check_2bsj(MatchedMate &sm, MatchedMate &lm, MatchedRead &mr, const string &chr, uint32_t shift, bool r1_sm) {
if (mr.type < CHI2BSJ)
return false;
if (sm.spos > lm.spos)
return false;
// ...<----
// ...-->
if (sm.right_ok and lm.right_ok and (sm.spos != lm.spos))
return false;
// <--...
// --->...
if (sm.left_ok and lm.left_ok and (sm.epos != lm.epos))
return false;
// ...<--- --->...
// OR
// ...--> <--...
//if sm.right_ok and lm.left_ok -> continue
// o.w.
if (sm.left_ok and lm.right_ok)
return false;
if (sm.exons_spos == NULL or lm.exons_spos == NULL) {
if ((sm.exons_spos != NULL and same_gene(sm, lm)) or (lm.exons_spos != NULL and same_gene(lm, sm))) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHI2BSJ, r1_sm);
return true;
}
// checking for ciRNA
//fprintf(stderr, "R1 start ind: %d\tR2 end ind: %d\n To beg of intron: %d\n", sm.exon_ind_spos, lm.exon_ind_epos, sm.spos - gtf_parser.get_interval_epos(sm.exon_ind_spos));
if ((intronic_bs[contigNum][sm.spos]) and ((intronic_bs[contigNum][lm.spos])) and
(sm.exon_ind_spos >= 0) and (lm.exon_ind_epos >= 0) and (sm.exon_ind_spos == lm.exon_ind_epos) and
(sm.spos - gtf_parser.get_interval_epos(sm.exon_ind_spos) <= LARIAT2BEGTH)) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHI2BSJ, r1_sm);
return true;
}
return false;
}
for (unsigned int i = 0; i < sm.exons_spos->seg_list.size(); i++)
for (unsigned int j = 0; j < lm.exons_spos->seg_list.size(); j++)
if (sm.exons_spos->seg_list[i].same_gene(lm.exons_spos->seg_list[j])) {
mr.update(sm, lm, chr, shift, lm.epos - sm.spos + 1, 0, false, CHI2BSJ, r1_sm);
return true;
}
return false;
}
void intersect_trans(const vector <uint32_t> &tid_l1, const vector <uint32_t> &tid_l2, vector <uint32_t> &common_tid) {
for (unsigned int i = 0; i < tid_l1.size(); i++) {
for (unsigned int j = 0; j < tid_l2.size(); j++) {
uint32_t tid1 = tid_l1[i];
uint32_t tid2 = tid_l2[j];
if (tid1 == tid2) {
common_tid.push_back(tid1);
break;
}
}
}
}
bool same_transcript(const IntervalInfo<UniqSeg> *s, const IntervalInfo<UniqSeg> *r, vector <uint32_t> &common_tid) {
common_tid.clear();
if (s == NULL or r == NULL)
return false;
vector <uint32_t> seg1_tid;
vector <uint32_t> seg2_tid;
for (unsigned int i = 0; i < s->seg_list.size(); i++)
for (unsigned int k = 0; k < s->seg_list[i].trans_id.size(); k++)
seg1_tid.push_back(s->seg_list[i].trans_id[k]);
for (unsigned int j = 0; j < r->seg_list.size(); j++)
for (unsigned int l = 0; l < r->seg_list[j].trans_id.size(); l++)
seg2_tid.push_back(r->seg_list[j].trans_id[l]);
intersect_trans(seg1_tid, seg2_tid, common_tid);
return common_tid.size() != 0;
}
bool same_transcript(const IntervalInfo<UniqSeg> *s, const IntervalInfo<UniqSeg> *r, const IntervalInfo<UniqSeg> *q,
vector <uint32_t> &common_tid) {
common_tid.clear();
if (s == NULL or r == NULL or q == NULL)
return false;
vector <uint32_t> sr_common_tid;
bool sr_intersect = same_transcript(s, r, sr_common_tid);
if (!sr_intersect)
return false;
vector <uint32_t> seg_tid;
for (unsigned int i = 0; i < s->seg_list.size(); i++)
for (unsigned int k = 0; k < s->seg_list[i].trans_id.size(); k++)
seg_tid.push_back(s->seg_list[i].trans_id[k]);
intersect_trans(sr_common_tid, seg_tid, common_tid);
return common_tid.size() != 0;
}
bool same_transcript(const IntervalInfo<UniqSeg> *s, const IntervalInfo<UniqSeg> *r,
const IntervalInfo<UniqSeg> *q, const IntervalInfo<UniqSeg> *p, vector <uint32_t> &common_tid) {
common_tid.clear();
if (s == NULL or r == NULL or q == NULL or p == NULL)
return false;
vector <uint32_t> sr_common_tid;
bool sr_intersect = same_transcript(s, r, sr_common_tid);
if (!sr_intersect)
return false;
vector <uint32_t> qp_common_tid;
bool qp_intersect = same_transcript(q, p, qp_common_tid);
if (!qp_intersect)
return false;
intersect_trans(sr_common_tid, qp_common_tid, common_tid);
return common_tid.size() != 0;
}
bool same_transcript(vector <MatchedMate> &segments, vector <uint32_t> &common_tid) {
common_tid.clear();
vector<const IntervalInfo<UniqSeg> *> mpos_ol; // mid_pos_overlap
for (unsigned int i = 0; i < segments.size(); ++i) {
const IntervalInfo<UniqSeg> *s = overlap_to_mpos(segments[i]);
mpos_ol.push_back(s);
}
if (segments.size() == 4)
return same_transcript(mpos_ol[0], mpos_ol[1], mpos_ol[2], mpos_ol[3], common_tid);
else if (segments.size() == 3)
return same_transcript(mpos_ol[0], mpos_ol[1], mpos_ol[2], common_tid);
else if (segments.size() == 2)
return same_transcript(mpos_ol[0], mpos_ol[1], common_tid);
return false;
}
bool same_transcript(vector <MatchedMate> &segments, int size, vector <uint32_t> &common_tid) {
bool success;
if (size == 2) {
overlap_to_spos(segments[0]);
overlap_to_spos(segments[1]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[1]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, common_tid);
if (success)
return success;
overlap_to_epos(segments[0]);
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, common_tid);
if (success)
return success;
}
if (size == 3) {
overlap_to_spos(segments[0]);
overlap_to_spos(segments[1]);
overlap_to_spos(segments[2]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[2]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_epos, common_tid);
if (success)
return success;
overlap_to_epos(segments[1]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_epos, common_tid);
if (success)
return success;
overlap_to_epos(segments[0]);
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_epos, common_tid);
if (success)
return success;
}
if (size == 4) {
overlap_to_spos(segments[0]);
overlap_to_spos(segments[1]);
overlap_to_spos(segments[2]);
overlap_to_spos(segments[3]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_spos,
segments[3].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[2]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_epos,
segments[3].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[1]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_spos,
segments[3].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_epos,
segments[3].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[0]);
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_spos,
segments[3].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_epos,
segments[3].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_spos,
segments[3].exons_spos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_epos,
segments[3].exons_spos, common_tid);
if (success)
return success;
overlap_to_epos(segments[3]);
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_spos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_spos, segments[2].exons_epos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_spos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_spos, segments[1].exons_epos, segments[2].exons_epos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_spos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_spos, segments[2].exons_epos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_spos,
segments[3].exons_epos, common_tid);
if (success)
return success;
common_tid.clear();
success = same_transcript(segments[0].exons_epos, segments[1].exons_epos, segments[2].exons_epos,
segments[3].exons_epos, common_tid);
if (success)
return success;
}
return false;
}
bool same_gene(const IntervalInfo<UniqSeg> *s, const IntervalInfo<UniqSeg> *r) {
if (s == NULL or r == NULL)
return false;
for (unsigned int i = 0; i < s->seg_list.size(); i++)
for (unsigned int j = 0; j < r->seg_list.size(); j++)
if (s->seg_list[i].gene_id == r->seg_list[j].gene_id)
return true;
return false;
}
bool same_gene(const IntervalInfo<UniqSeg> *mate, uint32_t s, uint32_t e) {
GeneInfo *ginfo;
for (unsigned int i = 0; i < mate->seg_list.size(); i++) {
ginfo = gtf_parser.get_gene_info(mate->seg_list[i].gene_id);
if (ginfo->start <= s and e <= ginfo->end)
return true;
}
return false;
}
bool same_gene(const MatchedMate &mm, const MatchedMate &other) {
GeneInfo *ginfo;
for (unsigned int i = 0; i < mm.exons_spos->seg_list.size(); i++) {
ginfo = gtf_parser.get_gene_info(mm.exons_spos->seg_list[i].gene_id);
//fprintf(stderr, "Gene[%d][%s]: [%d - %d], [%d - %d]\n", i, mm.exons_spos->seg_list[i].gene_id.c_str(), ginfo->start, ginfo->end, other.spos, other.epos);
if (ginfo->start <= other.spos and other.epos <= ginfo->end)
return true;
}
return false;
}
bool same_gene(uint32_t sme, const IntervalInfo<GeneInfo> *smg, uint32_t lms, const IntervalInfo<GeneInfo> *lmg) {
if (smg == NULL or lmg == NULL)
return false;
if (smg->seg_list.size() == 0 or lmg->seg_list.size() == 0)
return false;
bool same_intron;
int step = 10;
for (unsigned int i = 0; i < smg->seg_list.size(); i++)
for (unsigned int j = 0; j < lmg->seg_list.size(); j++)
if (smg->seg_list[i].start == lmg->seg_list[j].start and smg->seg_list[i].end == lmg->seg_list[j].end) {
same_intron = true;
for (uint32_t k = sme; k <= lms; k += step)
if (!(intronic_bs[contigNum][k])) {
same_intron = false;
break;
}
if (same_intron)
return true;
}
return false;
}
void overlap_to_epos(MatchedMate &mr) {
if (mr.looked_up_epos or mr.exons_epos != NULL)
return;
mr.exons_epos = gtf_parser.get_location_overlap_ind(mr.epos, false, mr.exon_ind_epos);
mr.looked_up_epos = true;
//fprintf(stdout, "End Seg list size: %d\n", mr.exons_epos->seg_list.size());
}
void overlap_to_spos(MatchedMate &mr) {
if (mr.looked_up_spos or mr.exons_spos != NULL)
return;
mr.exons_spos = gtf_parser.get_location_overlap_ind(mr.spos, false, mr.exon_ind_spos);
mr.looked_up_spos = true;
//fprintf(stdout, "Start Seg list size: %d\n", mr.exons_spos->seg_list.size());
}
const IntervalInfo<UniqSeg> *overlap_to_mpos(MatchedMate &mr) {
int ind;
return gtf_parser.get_location_overlap_ind((mr.spos + mr.epos) / 2, false, ind);
}
void gene_overlap(MatchedMate &mr) {
if (mr.looked_up_gene or mr.gene_info != NULL)
return;
mr.gene_info = gtf_parser.get_gene_overlap(mr.spos, false);
mr.looked_up_gene = true;
}
void get_junctions(MatchedMate &mm) {
overlap_to_spos(mm);
overlap_to_epos(mm);
mm.junc_info.clear();
if (mm.exons_spos == NULL or mm.exons_epos == NULL)
return;
for (unsigned int i = 0; i < mm.exons_spos->seg_list.size(); ++i) {
for (unsigned int j = 0; j < mm.exons_spos->seg_list[i].trans_id.size(); ++j) {
uint32_t covered = 0;
uint32_t tid = mm.exons_spos->seg_list[i].trans_id[j];
int start_ind = gtf_parser.get_trans_start_ind(contigNum, tid);
uint32_t start_table_ind = mm.exon_ind_spos - start_ind;
if (start_table_ind < 0) // assert
continue;
uint32_t end_table_ind = mm.exon_ind_epos - start_ind;
// transcript does not contain lm exon
if (mm.exon_ind_epos < start_ind or
end_table_ind >= gtf_parser.trans2seg[contigNum][tid].size() or
gtf_parser.trans2seg[contigNum][tid][end_table_ind] == 0)
continue;
// no junction
if (start_table_ind == end_table_ind) {
return;
}
uint32_t junc_start = mm.exons_spos->epos;
const IntervalInfo<UniqSeg> *this_region;
covered = mm.exons_spos->epos - mm.spos + 1;
int this_it_ind = mm.exon_ind_spos;
for (uint32_t k = start_table_ind + 1; k < end_table_ind; k++) {
this_it_ind++;
if (gtf_parser.trans2seg[contigNum][tid][k] != 0) {
this_region = gtf_parser.get_interval(this_it_ind);
//fprintf(stderr, "[%u-%u]\n", junc_start, this_region->spos);
mm.junc_info.push_back(junc_start, this_region->spos, covered);
covered += this_region->epos - this_region->spos + 1;
junc_start = this_region->epos;
}
}
mm.junc_info.push_back(junc_start, mm.exons_epos->spos, covered);
covered += mm.epos - mm.exons_epos->spos + 1;
//fprintf(stderr, "While building: Covered = %d\n", covered);
//fprintf(stderr, "on read: [%d-%d] matched_len: %d\n", mm.qspos, mm.qepos, mm.matched_len);
//mm.junc_info.print();
if (abs(static_cast<int32_t> (covered - mm.matched_len)) <= INDELTH)
return;
else
mm.junc_info.clear();
}
}
}
string get_consensus(const string &s1, const string &s2) {
string res = "";
if (s1.length() != s2.length())
return res;
for (unsigned int i = 0; i < s1.length(); ++i) {
res += (s1[i] == s2[i]) ? s1[i] : 'N';
}
return res;
}
string get_consensus(const vector <string> &vseq) {
string res = "";
if (vseq.size() == 0)
return res;
for (unsigned int i = 1; i < vseq.size(); ++i) {
if (vseq[i].length() != vseq[i - 1].length())
return res;
}
unsigned int counts[ASCISIZE];
char nuc[4] = {'A', 'C', 'G', 'T'};
for (unsigned int i = 0; i < vseq[0].length(); ++i) {
memset(counts, 0, sizeof(int) * ASCISIZE);
for (unsigned int j = 0; j < vseq.size(); ++j)
++counts[static_cast<uint8_t> (vseq[j][i])];
counts[static_cast<uint8_t> ('A')] += counts[static_cast<uint8_t> ('a')];
counts[static_cast<uint8_t> ('C')] += counts[static_cast<uint8_t> ('c')];
counts[static_cast<uint8_t> ('G')] += counts[static_cast<uint8_t> ('g')];
counts[static_cast<uint8_t> ('T')] += counts[static_cast<uint8_t> ('t')];
counts[static_cast<uint8_t> ('N')] += counts[static_cast<uint8_t> ('n')];
counts[static_cast<uint8_t> ('a')] = 0;
counts[static_cast<uint8_t> ('c')] = 0;
counts[static_cast<uint8_t> ('g')] = 0;
counts[static_cast<uint8_t> ('t')] = 0;
counts[static_cast<uint8_t> ('n')] = 0;
unsigned int max_cnt = 0;
char ch = 'N';
for (int k = 0; k < 4; ++k) {
if (counts[static_cast<uint8_t> (nuc[k])] > max_cnt) {
max_cnt = counts[static_cast<uint8_t> (nuc[k])];
ch = nuc[k];
}
}
if (max_cnt >= (vseq.size() / 2))
res += ch;
else
res += 'N';
}
return res;
}
void reverse_str(char *s, int n, char *revs) {
for (int i = 0; i < n; ++i)
revs[i] = s[n - i - 1];
revs[n] = '\0';
}
// is a on the left side?
bool is_left_chain(chain_t a, chain_t b, int read_length) {
uint32_t a_beg = a.frags[0].rpos;
uint32_t b_beg = b.frags[0].rpos;
uint32_t a_end = a.frags[a.chain_len - 1].rpos + a.frags[a.chain_len - 1].len - 1;
uint32_t b_end = b.frags[b.chain_len - 1].rpos + b.frags[b.chain_len - 1].len - 1;
// check whether they are overlapping
bool non_overlaping = (b_beg > a_end) or (a_beg > b_end);
if (non_overlaping) {
// fprintf(stderr, "NOV\n");
return a_beg < b_beg;
} else {
uint32_t i = 0, j = 0;
int best_distance = INF;
int best_i = -1;
int best_j = -1;
while (i < a.chain_len and j < b.chain_len) {
uint32_t bj_beg = b.frags[j].rpos;
uint32_t ai_end = a.frags[i].rpos + a.frags[i].len - 1;
if (ai_end < bj_beg) {
int distance = bj_beg - ai_end;
if (distance < best_distance) {
best_distance = distance;
best_i = i;
best_j = j;
}
++i;
continue;
}
uint32_t ai_beg = a.frags[i].rpos;
uint32_t bj_end = b.frags[j].rpos + b.frags[j].len - 1;
if (bj_end < ai_beg) {
int distance = ai_beg - bj_end;
if (distance < best_distance) {
best_distance = distance;
best_i = i;
best_j = j;
}
++j;
continue;
}
best_i = i;
best_j = j;
break;
}
uint32_t common_bp = maxM(a.frags[best_i].rpos, b.frags[best_j].rpos);
int32_t a_ov_qpos = a.frags[best_i].qpos + (common_bp - a.frags[best_i].rpos);
int32_t b_ov_qpos = b.frags[best_j].qpos + (common_bp - b.frags[best_j].rpos);
// fprintf(stderr, "OV -> Decision made\n");
if (a_ov_qpos < read_length and b_ov_qpos < read_length)
return a_ov_qpos >= b_ov_qpos;
// fprintf(stderr, "OV -> Ambiguous\n");
return a_beg < b_beg;
}
}
void remove_side_introns(MatchedMate &mm, int rlen) {
overlap_to_spos(mm);
if (mm.exons_spos == NULL) {
const IntervalInfo<UniqSeg> *it_seg = gtf_parser.get_interval(mm.exon_ind_spos + 1);
if (it_seg == NULL) {
// fprintf(stderr, "Failed to remove intron left\n");
return;
}
int diff = it_seg->spos - mm.spos;
// fprintf(stderr, "left intron retention: %d bp\n", diff);
if (diff > 0 and (static_cast<uint32_t> (diff)) < mm.matched_len) {
// update mm
mm.spos = it_seg->spos;
mm.qspos += diff;
mm.matched_len -= diff;
if ((mm.qspos - 1) < (rlen - mm.qepos)) // left-side matched
mm.sclen_left += diff;
mm.looked_up_spos = false;
mm.exons_spos = NULL;
// fprintf(stderr, "Removed left intron retention: %d bp\n", diff);
}
}
overlap_to_epos(mm);
if (mm.exons_epos == NULL) {
const IntervalInfo<UniqSeg> *it_seg = gtf_parser.get_interval(mm.exon_ind_epos);
if (it_seg == NULL) {
// fprintf(stderr, "Failed to remove intron right\n");
return;
}
int diff = mm.epos - it_seg->epos;
// fprintf(stderr, "right intron retention: %d bp\n", diff);
if (diff > 0 and (static_cast<uint32_t> (diff)) < mm.matched_len) {
// update mm
mm.epos = it_seg->epos;
mm.qepos -= diff;
mm.matched_len -= diff;
if ((mm.qspos - 1) > (rlen - mm.qepos)) // right-side matched
mm.sclen_right += diff;
mm.looked_up_epos = false;
mm.exons_epos = NULL;
// fprintf(stderr, "Removed right intron retention: %d bp\n", diff);
}
}
}