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lamsa_aln.c
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#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <getopt.h>
#include <zlib.h>
#include <unistd.h>
#include <ctype.h>
#include <time.h>
#include <pthread.h>
#include "lamsa_aln.h"
#include "lamsa_dp_con.h"
#include "bwt.h"
#include "bntseq.h"
#include "frag_check.h"
#include "split_mapping.h"
#include "bwt_aln.h"
#include "kseq.h"
#include "kstring.h"
#include "gem_parse.h"
#define LINE_SIZE 65536
extern char lamsa_pg[1024];
int lamsa_aln_usage(void)
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: lamsa aln [options] <ref.fa> <read.fa/fq>\n\n");
fprintf(stderr, "Algorithm options:\n\n");
fprintf(stderr, " -t --thread [INT] Number of threads. [1]\n");
//fprintf(stderr, " -s [INT] The seeding program, <gem(0)>, <bwa(1)> or <soap2-dp(2)>. [0]\n");
fprintf(stderr, " -l --seed-len [INT] Length of seeding fragments. [%d]\n", SEED_LEN);
fprintf(stderr, " -i --seed-inv [INT] Distance between neighboring seeding fragments. [%d]\n", SEED_STEP);
fprintf(stderr, " -p --max-loci [INT] Maximum allowed number of seeding fragments' hits. [%d]\n", SEED_PER_LOCI);
fprintf(stderr, " -V --SV-len [INT] Expected maximum length of SV. [%d]\n", SV_MAX_LEN);
fprintf(stderr, " -v --ovlp-rat [FLOAT] Minimum overlapping ratio to cluster two skeletons or alignment records.\n");
fprintf(stderr, " [%.2f]\n", OVLP_RAT);
fprintf(stderr, " -s --max-skel [INT] Maximum number of skeletons that are reserved in a cluster. [%d]\n", MAX_SKEL);
fprintf(stderr, " -R --max-reg [INT] Maximum allowed length of unaligned read part to trigger a bwt-based query.\n");
fprintf(stderr, " [%d]\n", MAX_BWT_REG);
fprintf(stderr, " -k --bwt-kmer [INT] Length of BWT-seed. [%d]\n", BWT_KMER);
fprintf(stderr, " -f --fastest Use GEM-mapper's fastest mode(--fast-mapping=0). [false]\n\n");
fprintf(stderr, "Scoring options:\n\n");
fprintf(stderr, " -m --match-sc [INT] Match score for SW-alignment. [%d]\n", MAT_SCORE);
fprintf(stderr, " -M --mis-pen [INT] Mismatch penalty for SW-alignment. [%d]\n", MIS_PEN);
fprintf(stderr, " -O --open-pen [INT(,INT,INT,INT)]\n");
fprintf(stderr, " Gap open penalty for SW-alignment(end2end-global: insertion, deletion,\n");
fprintf(stderr, " one-end-extend: insertion, deletion). [%d(,%d,%d,%d)]\n", OPEN_PEN, OPEN_PEN, OPEN_PEN, OPEN_PEN);
fprintf(stderr, " -E --ext-pen [INT(,INT,INT,INT)]\n");
fprintf(stderr, " Gap extension penalty for SW-alignment(end2end-global: insertion, deletion,\n");
fprintf(stderr, " one-end-extend: insertion, deletion). [%d(,%d,%d,%d)]\n", EXT_PEN, EXT_PEN, EXT_PEN, EXT_PEN);
fprintf(stderr, " -w --band-width[INT] Band width for banded-SW. [%d]\n", BAND_W);
fprintf(stderr, " -b --end-bonus [INT] Penalty for end-clipping. [%d]\n\n", END_BONUS);
fprintf(stderr, "Read options:\n\n");
fprintf(stderr, " -e --err-rate [FLOAT] Maximum error rate of read. [%.2f]\n", ED_RATE);
fprintf(stderr, " -d --diff-rate [FLOAT] Maximum length difference ratio between read and reference. [%.2f]\n", ID_RATE);
fprintf(stderr, " -x --mis-rate [FLOAT] Maximum error rate of mismatch within reads. [%.2f]\n\n", MIS_RATE);
fprintf(stderr, " -T --read-type [STR] Specifiy the type of reads and set multiple parameters unless overriden.\n");
fprintf(stderr, " [null] (Illumina Moleculo)\n");
fprintf(stderr, " pacbio (PacBio SMRT): -i%d -l%d -m%d -M%d -O%d,%d,%d,%d -E%d,%d,%d,%d -w%d -b%d -e%.2f -d%.2f\n", PB_SEED_STEP, PB_SEED_LEN, PB_MAT_SCORE, PB_MIS_PEN, PB_INS_OPEN_PEN, PB_DEL_OPEN_PEN, PB_INS_EXT_OPEN_PEN, PB_DEL_EXT_OPEN_PEN, PB_INS_EXT_PEN, PB_DEL_EXT_PEN, PB_INS_EXT_EXT_PEN, PB_DEL_EXT_EXT_PEN, PB_BAND_W, PB_END_BONUS, PB_ED_RATE, PB_ID_RATE);
fprintf(stderr, " ont2d (Oxford Nanopore): -i%d -l%d -m%d -M%d -O%d,%d,%d,%d -E%d,%d,%d,%d -w%d -b%d -e%.2f -d%.2f\n\n", ON_SEED_STEP, ON_SEED_LEN, ON_MAT_SCORE, ON_MIS_PEN, ON_INS_OPEN_PEN, ON_DEL_OPEN_PEN, ON_INS_EXT_OPEN_PEN, ON_DEL_EXT_OPEN_PEN, ON_INS_EXT_PEN, ON_DEL_EXT_PEN, ON_INS_EXT_EXT_PEN, ON_DEL_EXT_EXT_PEN, ON_BAND_W, ON_END_BONUS, ON_ED_RATE, ON_ID_RATE);
fprintf(stderr, "Output options:\n\n");
fprintf(stderr, " -r --max-out [INT] Maximum number of output records for a specific split read region. [%d]\n", RES_MAX_N);
fprintf(stderr, " -g --gap-split [INT] Minimum length of gap that causes a split-alignment. [%d]\n", SPLIT_ALN_LEN);
fprintf(stderr, " -S --soft-clip Use soft clipping for supplementary alignment. [false]\n");
fprintf(stderr, " -C --comment Append FASTQ comment to SAM output. [false]\n");
fprintf(stderr, " -o --output [STR] Output file (SAM format). [stdout]\n\n");
//fprintf(stderr, " -N Do NOT excute seeding program, when seeds' alignment result existed already.\n");
//fprintf(stderr, " -I Seed information file has already existed.\n");
//fprintf(stderr, " -A [STR] The seeds' alignment result. When '-N' is used. [\"seed_prefix.out.0\"]\n");
fprintf(stderr, " -h --help Print this short usage.\n");
fprintf(stderr, " -H --HELP Print a detailed usage.\n\n");
return 1;
}
int lamsa_aln_de_usage(void)
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: lamsa aln [options] <ref.fa> <read.fa/fq>\n\n");
fprintf(stderr, "Algorithm options:\n\n");
fprintf(stderr, " -t --thread [INT] Number of threads. [1]\n");
//fprintf(stderr, " -s [INT] The seeding program, <gem(0)>, <bwa(1)> or <soap2-dp(2)>. [0]\n");
fprintf(stderr, " -l --seed-len [INT] Length of seeding fragments. Moreover, LAMSA splits the read into a\n");
fprintf(stderr, " series of -l bp long fragments, and employs NGS aligner to generate the\n");
fprintf(stderr, " approximate matches of the fragments. [50]\n");
fprintf(stderr, " -i --seed-inv [INT] Distance between neighboring seeding fragments. LAMSA extracts seeding\n");
fprintf(stderr, " fragments starting at every -i bp of the read. [%d]\n", SEED_STEP);
fprintf(stderr, " -p --max-loci [INT] Maximum allowed number of hits. If a seeding fragment has more than -p\n");
fprintf(stderr, " approximate matches, LAMSA would consider the seed is too repetitive, and\n");
fprintf(stderr, " discard all the matches. [%d]\n", SEED_PER_LOCI);
fprintf(stderr, " -V --SV-len [INT] Expected maximum length of SV. If the genomic distance of two seeding\n");
fprintf(stderr, " fragments is longer than -V bp, they cannot be connected to build a legal\n");
fprintf(stderr, " edge in the sparse dynamic programming process. [%d]\n", SV_MAX_LEN);
fprintf(stderr, " -v --ovlp-rat [FLOAT] Minimum overlapping ratio to cluster two skeletons or alignment records.\n");
fprintf(stderr, " (0~1) [%.1f]\n", OVLP_RAT);
fprintf(stderr, " -s --max-skel [INT] Maximum number of skeletons that are reserved in a cluster for a specific\n");
fprintf(stderr, " read region. For a specific region of read, LAMSA reserves the top -s\n");
fprintf(stderr, " skeletons. These skeletons are used to generate best and alternative\n");
fprintf(stderr, " alignment records. [%d]\n", MAX_SKEL);
fprintf(stderr, " -R --max-reg [INT] Maximum allowed length of unaligned read part to trigger a bwt-based query.\n");
fprintf(stderr, " For a read part being unaligned after all the sparse dynamic programming\n");
fprintf(stderr, " process-based split alignment, if it is longer than -R bp, LAMSA will not\n");
fprintf(stderr, " further process it; otherwise, LAMSA will query the exact matches of the\n");
fprintf(stderr, " k-mers of the unaligned part as hits to further align the read part. [%d]\n", MAX_BWT_REG);
fprintf(stderr, " -k --bwt-kmer [INT] Length of BWT-seed. For the unaligned read part shorter than -R bp, LAMSA\n");
fprintf(stderr, " will extract all its -k bp tokens and query their exact matches as hits. [%d]\n", BWT_KMER);
fprintf(stderr, " -f --fastest Use GEM-mapper's fastest mode(--fast-mapping=0). LAMSA uses GEM-mapper's\n");
fprintf(stderr, " fast mode(--fast-mapping) in default. Fastest mode will significantly\n");
fprintf(stderr, " improve the speed of LAMSA while the sensitivity and accuracy of alignments\n");
fprintf(stderr, " will drop a little. [false]\n\n");
fprintf(stderr, "Scoring options:\n\n");
fprintf(stderr, " -m --match-sc [INT] Match score for SW-alignment. [%d]\n", MAT_SCORE);
fprintf(stderr, " -M --mis-pen [INT] Mismatch penalty for SW-alignment. [%d]\n", MIS_PEN);
fprintf(stderr, " -O --open-pen [INT(,INT,INT,INT)]\n");
fprintf(stderr, " Gap open penalty for SW-alignment(end2end-global: insertion, deletion,\n");
fprintf(stderr, " one-end-extend:insertion, deletion). [%d(,%d,%d,%d)]\n", OPEN_PEN, OPEN_PEN, OPEN_PEN, OPEN_PEN);
fprintf(stderr, " -E --ext-pen [INT(,INT,INT,INT)]\n");
fprintf(stderr, " Gap extension penalty for SW-alignment(end2end-global: insertion, deletion,\n");
fprintf(stderr, " one-end-extend:insertion, deletion). A gap of length k costs O + k*E.\n");
fprintf(stderr, " (i.e. -O is for opening a zero-length gap) [%d(,%d,%d,%d)]\n", EXT_PEN, EXT_PEN, EXT_PEN, EXT_PEN);
fprintf(stderr, " -w --band-wid [INT] Band width for banded-SW. [%d]\n", BAND_W);
fprintf(stderr, " -b --end-bonus [INT] Penalty for end-clipping. [%d]\n\n", END_BONUS);
fprintf(stderr, "Read options:\n\n");
fprintf(stderr, " -e --err-rate [FLOAT] Maximum error rate of read. [%.2f]\n", ED_RATE);
fprintf(stderr, " -d --diff-rate [FLOAT] Maximum length difference ratio between read and reference. [%.2f]\n", ID_RATE);
fprintf(stderr, " -x --mis-rate [FLOAT] Maximum error rate of mismatch within reads. [%.2f]\n\n", MIS_RATE);
fprintf(stderr, " -T --read-type [STR] Specifiy the type of reads and set multiple parameters unless overriden.\n");
fprintf(stderr, " [null] (Illumina Moleculo):\n");
fprintf(stderr, " pacbio (PacBio SMRT): -i%d -l%d -m%d -M%d -O%d,%d,%d,%d -E%d,%d,%d,%d -b%d -e%.2f -d%.2f\n", PB_SEED_STEP, PB_SEED_LEN, PB_MAT_SCORE, PB_MIS_PEN, PB_INS_OPEN_PEN, PB_DEL_OPEN_PEN, PB_INS_EXT_OPEN_PEN, PB_DEL_EXT_OPEN_PEN, PB_INS_EXT_PEN, PB_DEL_EXT_PEN, PB_INS_EXT_EXT_PEN, PB_DEL_EXT_EXT_PEN, PB_END_BONUS, PB_ED_RATE, PB_ID_RATE);
fprintf(stderr, " ont2d (Oxford Nanopore): -i%d -l%d -m%d -M%d -O%d,%d,%d,%d -E%d,%d,%d,%d -b%d -e%.2f -d%.2f\n\n", ON_SEED_STEP, ON_SEED_LEN, ON_MAT_SCORE, ON_MIS_PEN, ON_INS_OPEN_PEN, ON_DEL_OPEN_PEN, ON_INS_EXT_OPEN_PEN, ON_DEL_EXT_OPEN_PEN, ON_INS_EXT_PEN, ON_DEL_EXT_PEN, ON_INS_EXT_EXT_PEN, ON_DEL_EXT_EXT_PEN, ON_END_BONUS, ON_ED_RATE, ON_ID_RATE);
fprintf(stderr, "Output options:\n\n");
fprintf(stderr, " -r --max-out [INT] Maximum number of output records for a specific split read region. For a\n");
fprintf(stderr, " specific region, LAMSA reserves the top -r alignment records. The record\n");
fprintf(stderr, " with highest alignment score is considered as best alignment, others are\n");
fprintf(stderr, " considered as alternative alignments. Moreover, if the score of an alternative\n");
fprintf(stderr, " alignment is less than half of the best alignment, it will not be output.\n");
fprintf(stderr, " [%d]\n", RES_MAX_N);
fprintf(stderr, " -g --gap-split [INT] Minimum length of gap that causes a split-alignment. To avoid generating\n");
fprintf(stderr, " insertion(I) or deletion(D) longer than -g bp in the SAM cigar. [%d]\n", SPLIT_ALN_LEN);
fprintf(stderr, " -S --soft-clip Use soft clipping for supplementary alignment. It is strongly recommended\n");
fprintf(stderr, " to turn off this option to reduce the redundancy of output when mapping\n");
fprintf(stderr, " relatively long reads. [false]\n");
fprintf(stderr, " -C --comment Append FASTQ comment to SAM output. [false]\n");
fprintf(stderr, " -o --output [STR] Output file (SAM format). [stdout]\n\n");
//fprintf(stderr, " -N Do NOT excute seeding program, when seeds' alignment result existed already.\n");
//fprintf(stderr, " -I Seed information file has already existed.\n");
//fprintf(stderr, " -A [STR] The seeds' alignment result. When '-N' is used. [\"seed_prefix.out.0\"]\n");
fprintf(stderr, " -h --help Print a short usage.\n");
fprintf(stderr, " -H --HELP Print this detailed usage.\n\n");
return 1;
}
int f_BCC_score_table[10] = {
1, //F_MATCH
1, //F_SPLIT_MATCH
1, //F_MISMATCH
1, //F_LONG_MISMATCH
-3, //F_INSERT
-3, //F_DELETE
-3, //F_CHR_DIF
-3, //F_REVERSE
-6, //F_UNCONNECT
-6, //F_UNMATCH
};
// for debug
char READ_NAME[1024];
seed_msg *seed_init_msg(void)
{
seed_msg *msg = (seed_msg*)malloc(sizeof(seed_msg));
msg->read_all = 0;
msg->read_m = READ_MAX_NUM;
msg->seed_all = (int *)calloc(READ_MAX_NUM, sizeof(int));
msg->read_len = (int *)malloc(READ_MAX_NUM * sizeof(int));
/*
msg->read_name = (char **)malloc(READ_MAX_NUM * sizeof(char*));
int i;
for (i = 0; i < READ_MAX_NUM; ++i)
msg->read_name[i] = (char*)malloc(1024 * sizeof(char));
*/
msg->last_len = (int *)malloc(READ_MAX_NUM * sizeof(int));
msg->seed_max = 0;
msg->read_max_len = 0;
return msg;
}
void seed_free_msg(seed_msg *msg)
{
free(msg->seed_all);
free(msg->read_len);
free(msg->last_len);
free(msg);
}
int split_seed(const char *prefix, lamsa_aln_para AP, seed_msg *s_msg)
{
gzFile infp;
kseq_t *seq;
char out_f[1024], seed_head[1024], seed_seq[1024], seed_info[1024];
FILE *outfp, *infofp;
int m_read, seed_all, i;
void *new_p;
if ((infp = gzopen(prefix, "r")) == NULL) {
fprintf(stderr, "[lamsa_aln] Can't open read file %s\n", prefix); exit(1);
}
seq = kseq_init(infp);
strcpy(out_f, prefix); strcat(out_f, ".seed");
if ((outfp = fopen(out_f, "w")) == NULL) {
fprintf(stderr, "[lamsa_aln] Can't open seed file %s\n", out_f); exit(1);
}
strcpy(seed_info, prefix); strcat(seed_info, ".seed.info");
if ((infofp = fopen(seed_info, "w")) == NULL) {
fprintf(stderr, "[lamsa_aln] Can't open seed info file %s\n", seed_info); exit(1);
}
fprintf(stderr, "[lamsa_aln] Generating seed ... ");
int seed_len=AP.seed_len, seed_step=AP.seed_step;
m_read = s_msg->read_m;
while (kseq_read(seq) >= 0)
{
if (seq->seq.l < seed_len) seed_all = 0;
else seed_all = (1+ (seq->seq.l - seed_len) / seed_step);
seed_seq[seed_len] = '\n';
if (seed_all > s_msg->seed_max) s_msg->seed_max = seed_all;
if ((int)seq->seq.l > s_msg->read_max_len) s_msg->read_max_len = seq->seq.l;
if (s_msg->read_all == m_read-1)
{
m_read <<= 1;
if ((new_p = (int*)realloc(s_msg->seed_all, m_read * sizeof(int))) == NULL)
{
free(s_msg->seed_all);
fprintf(stderr, "\n[lamsa_aln] Can't allocate more memory for seed_all[].\n"); exit(1);
}
s_msg->seed_all = (int*)new_p;
if ((new_p = (int*)realloc(s_msg->last_len, m_read * sizeof(int))) == NULL)
{
free(s_msg->last_len);
fprintf(stderr, "\n[lamsa_aln] Can't allocate more memory for last_len[].\n"); exit(1);
}
s_msg->last_len = (int*)new_p;
if ((new_p = (int*)realloc(s_msg->read_len, m_read * sizeof(int))) == NULL)
{
free(s_msg->read_len);
fprintf(stderr, "\n[lamsa_aln] Can't allocate more memory for read_len[].\n"); exit(1);
}
s_msg->read_len = (int*)new_p;
}
++s_msg->read_all;
s_msg->seed_all[s_msg->read_all] = s_msg->seed_all[s_msg->read_all-1] + seed_all;
s_msg->last_len[s_msg->read_all] = seq->seq.l - seed_len - (seed_all-1) * seed_step;
s_msg->read_len[s_msg->read_all] = seq->seq.l;
s_msg->read_m = m_read;
for (i = 0; i < seed_all; ++i)
{
sprintf(seed_head, ">%s_%d:%d\n", seq->name.s, i, i*seed_step);
strncpy(seed_seq, seq->seq.s+i*seed_step, seed_len);
seed_seq[seed_len+1] = '\0';
fputs(seed_head, outfp);
fputs(seed_seq, outfp);
}
fprintf(infofp, "%s %d %d %d\n", seq->name.s, seed_all, s_msg->last_len[s_msg->read_all], (int)seq->seq.l);
}
fprintf(stderr, "done!\n");
gzclose(infp);
fclose(outfp);
fclose(infofp);
kseq_destroy(seq);
return 0;
}
int split_seed_info(const char *prefix, lamsa_aln_para AP, seed_msg *s_msg)
{
char seed_info[1024];
char read_name[1024];
FILE *infofp;
int m_read, seed_all, last_len, len, n;
int seed_len=AP.seed_len, seed_step=AP.seed_step;
void *new_p;
strcpy(seed_info, prefix); strcat(seed_info, ".seed.info");
if ((infofp = fopen(seed_info, "r")) == NULL)
{
fprintf(stderr, "[split seed] Can't open %s.\n", seed_info); exit(1);
}
m_read = s_msg->read_m;
fprintf(stderr, "[lamsa_aln] Parsing seeds' information ... ");
while ((n = fscanf(infofp, "%s %d %d %d", read_name, &seed_all, &last_len, &len)) != EOF)
{
if (n != 4)
{
fprintf(stderr, "\n[split seed] INFO file error.[2]\n"); exit(1);
}
if (seed_all > s_msg->seed_max) s_msg->seed_max = seed_all;
if (len > s_msg->read_max_len) s_msg->read_max_len = len;
if (s_msg->read_all == m_read-1)
{
m_read <<= 1;
if ((new_p = (int*)realloc(s_msg->seed_all, m_read * sizeof(int))) == NULL)
{
free(s_msg->seed_all);
fprintf(stderr, "\n[lamsa aln] Can't allocate more memory for seed_all[].\n"); exit(1);
}
s_msg->seed_all = (int*)new_p;
if ((new_p = (int*)realloc(s_msg->last_len, m_read * sizeof(int))) == NULL)
{
free(s_msg->last_len);
fprintf(stderr, "\n[lamsa aln] Can't allocate more memory for last_len[].\n"); exit(1);
}
s_msg->last_len = (int*)new_p;
if ((new_p = (int*)realloc(s_msg->read_len, m_read * sizeof(int))) == NULL)
{
free(s_msg->read_len);
fprintf(stderr, "\n[lamsa aln] Can't allocate more memory for read_len[].\n"); exit(1);
}
s_msg->read_len = (int*)new_p;
}
++s_msg->read_all;
s_msg->seed_all[s_msg->read_all] = s_msg->seed_all[s_msg->read_all-1] + seed_all;
s_msg->last_len[s_msg->read_all] = last_len;
s_msg->read_len[s_msg->read_all] = len;
s_msg->read_m = m_read;
if (last_len != len - seed_len - (seed_all-1)*seed_step)
{
fprintf(stderr, "\n%s %d %d %d %d %d", read_name, seed_all, last_len, len, seed_all, seed_step);
fprintf(stderr, "\n[split seed] INFO file error.[3]\n"); exit(1);
}
}
fprintf(stderr, "done!\n");
fclose(infofp);
return 0;
}
aln_res *aln_init_res(int l_m, int n, int XA_max)
{
int i, j, k;
aln_res *a_res = (aln_res*)calloc(n, sizeof(aln_res));
for (k = 0; k < n; ++k) {
aln_res *p = a_res+k;
p->l_m = l_m, p->l_n = 0;
p->la = (line_aln_res*)malloc(l_m * sizeof(line_aln_res));
//p->read_len = read_len;
for (i = 0; i < l_m; ++i) {
p->la[i].res_m = 10, p->la[i].cur_res_n = 0;
p->la[i].res = (res_t*)malloc(10 * sizeof(res_t));
for (j = 0; j < 10; ++j) {
p->la[i].res[j].c_m = CIGAR_LEN_M;
p->la[i].res[j].cigar = (cigar32_t*)malloc(CIGAR_LEN_M * sizeof(cigar32_t));
p->la[i].res[j].cigar_len = 0;
}
p->la[i].tol_score = p->la[i].tol_NM = 0;
// XA_res
p->la[i].XA_m = XA_max;
p->la[i].XA_n = 0;
p->la[i].XA = (res_t**)malloc(XA_max * sizeof(res_t*));
}
}
return a_res;
}
void aln_reset_res(aln_res *a_res, int n, int read_len)
{
int i, j, k;
for (k = 0; k < n; ++k) {
aln_res *p = a_res+k;
p->l_n = 0;
p->read_len = read_len;
for (i = 0; i < p->l_m; ++i) {
p->la[i].cur_res_n = 0;
for (j = 0; j < p->la[i].res_m; ++j) {
p->la[i].res[j].cigar_len = 0;
}
p->la[i].tol_score = p->la[i].tol_NM = 0;
// XA_res
p->la[i].XA_n = 0;
}
}
}
void aln_reloc_res(aln_res *a_res, int line_n, int XA_m)
{
int i, j;
if ((a_res->la = (line_aln_res*)realloc(a_res->la, line_n * sizeof(line_aln_res))) == NULL) {
fprintf(stderr, "[aln_reloc_res] Not enough memory.\n"); exit(0);
}
for (i = a_res->l_m; i < line_n; ++i) {
a_res->la[i].res_m = 10, a_res->la[i].cur_res_n = 0;
a_res->la[i].res = (res_t*)malloc(10 * sizeof(res_t));
for (j = 0; j < 10; ++j) {
a_res->la[i].res[j].c_m = CIGAR_LEN_M;
a_res->la[i].res[j].cigar = (cigar32_t*)malloc(CIGAR_LEN_M * sizeof(cigar32_t));
a_res->la[i].res[j].cigar_len = 0;
}
a_res->la[i].tol_score = a_res->la[i].tol_NM = 0;
//XA
a_res->la[i].XA_m = XA_m;
a_res->la[i].XA_n = 0;
a_res->la[i].XA = (res_t**)malloc(XA_m * sizeof(res_t*));
}
a_res->l_m = line_n;
}
void aln_res_free(aln_res *res, int n)
{
int i,j,k;
for (k = 0; k < n; ++k) {
aln_res *p = res+k;
for (i = 0; i < p->l_m; ++i) {
for (j = 0; j < p->la[i].res_m; ++j) {
free(p->la[i].res[j].cigar);
}
free(p->la[i].res); free(p->la[i].XA);
}
free(p->la);
}
free(res);
}
aln_reg *aln_init_reg(int read_len)
{
aln_reg *reg = (aln_reg*)malloc(sizeof(aln_reg));
reg->reg_n = 0; reg->reg_m = 1;
reg->read_len = read_len;
reg->reg = (reg_t*)malloc(sizeof(reg_t));
reg->reg->beg_n = reg->reg->end_n = 0;
reg->reg->beg_m = reg->reg->end_m = 10;
reg->reg->ref_beg = (reg_b*)malloc(10 * sizeof(reg_b));
reg->reg->ref_end = (reg_b*)malloc(10 * sizeof(reg_b));
return reg;
}
void aln_free_reg(aln_reg *reg) {
int i;
for (i = 0; i < reg->reg_m; ++i) {
free(reg->reg[i].ref_beg); free(reg->reg[i].ref_end);
}
free(reg->reg); free(reg);
}
int reg_comp(const void *a, const void *b) { return (*(reg_t*)a).beg - (*(reg_t*)b).beg; }
void aln_sort_reg(aln_reg *a_reg) { qsort(a_reg->reg, a_reg->reg_n, sizeof(reg_t), reg_comp); }
void push_reg_b(reg_t *reg1, int beg_n, reg_b beg[], int end_n, reg_b end[]) {
int i;
for (i = 0; i < beg_n; ++i) {
if (reg1->beg_n == reg1->beg_m) {
reg1->beg_m <<= 1;
reg1->ref_beg = (reg_b*)realloc(reg1->ref_beg, reg1->beg_m * sizeof(reg_b));
}
reg1->ref_beg[reg1->beg_n] = beg[i];
reg1->beg_n++;
}
for (i = 0; i < end_n; ++i) {
if (reg1->end_n == reg1->end_m) {
reg1->end_m <<= 1;
reg1->ref_end = (reg_b*)realloc(reg1->ref_end, reg1->end_m * sizeof(reg_b));
}
reg1->ref_end[reg1->end_n] = end[i];
reg1->end_n++;
}
}
void aln_merg_reg(aln_reg *a_reg, int thd) {
//if (a_reg->reg_n == 0)return;
int cur_i = 0, i;
for (i = 1; i < a_reg->reg_n; ++i) {
// merge when the distance between two regs is smaller than the 'thd'
if(a_reg->reg[i].beg - a_reg->reg[cur_i].end - 1 < thd) {
if(a_reg->reg[i].end > a_reg->reg[cur_i].end) a_reg->reg[cur_i].end = a_reg->reg[i].end;
push_reg_b(a_reg->reg+cur_i, a_reg->reg[i].beg_n, a_reg->reg[i].ref_beg,a_reg->reg[i].end_n, a_reg->reg[i].ref_end);
} else {
cur_i++;
if (cur_i != i) {
a_reg->reg[cur_i].beg = a_reg->reg[i].beg;
a_reg->reg[cur_i].end = a_reg->reg[i].end;
a_reg->reg[cur_i].beg_n = a_reg->reg[cur_i].end_n = 0;
push_reg_b(a_reg->reg+cur_i, a_reg->reg[i].beg_n, a_reg->reg[i].ref_beg,a_reg->reg[i].end_n, a_reg->reg[i].ref_end);
}
}
}
a_reg->reg_n = cur_i+1;
}
void reg_reloc(reg_t **r, int r_n, int r_m) {
*r = (reg_t*)realloc(*r, r_m * sizeof(reg_t));
int i;
for (i = r_n; i < r_m; ++i) {
(*r)[i].end_n = (*r)[i].beg_n = 0;
(*r)[i].end_m = (*r)[i].beg_m = 10;
(*r)[i].ref_beg = (reg_b*)malloc(10 * sizeof(reg_b));
(*r)[i].ref_end = (reg_b*)malloc(10 * sizeof(reg_b));
}
}
void push_reg(aln_reg *reg, int beg, int end, int beg_n, reg_b ref_beg[], int end_n, reg_b ref_end[])
{
int r_n = reg->reg_n;
if (r_n == reg->reg_m) {
reg->reg_m <<= 1;
reg_reloc(&(reg->reg), r_n, reg->reg_m);
}
reg->reg[r_n].beg = beg;
reg->reg[r_n].end = end;
reg->reg[r_n].beg_n = reg->reg[r_n].end_n = 0;
push_reg_b(reg->reg+r_n, beg_n, ref_beg, end_n, ref_end);
reg->reg_n++;
}
/*typedef struct {
int refid, is_rev;
uint64_t ref_beg, ref_end;
int beg, end;
} reg_t;*/
// dump remain-regions that are longger than 'thd'
int get_remain_reg(aln_reg *a_reg, aln_reg *remain_reg, lamsa_aln_para *AP, int reg_min_thd, int reg_max_thd)
{
if (a_reg->reg_n == 0) {
if (reg_min_thd < a_reg->read_len && a_reg->read_len <= reg_max_thd) {
push_reg(remain_reg, 1, a_reg->read_len, 0, 0, 0, 0);
return 1;
} else return 0;
}
aln_sort_reg(a_reg); aln_merg_reg(a_reg, AP->bwt_seed_len);
int i;
if (a_reg->reg[0].beg > reg_min_thd && a_reg->reg[0].beg-1 <= reg_max_thd)
push_reg(remain_reg, 1, a_reg->reg[0].beg-1, 0, 0, a_reg->reg[0].beg_n, a_reg->reg[0].ref_beg);
for (i = 1; i < a_reg->reg_n; ++i) {
if (a_reg->reg[i].beg - a_reg->reg[i-1].end > reg_min_thd && a_reg->reg[i].beg-1-a_reg->reg[i-1].end <= reg_max_thd)
push_reg(remain_reg, a_reg->reg[i-1].end+1, a_reg->reg[i].beg-1, a_reg->reg[i-1].end_n, a_reg->reg[i-1].ref_end, a_reg->reg[i].beg_n, a_reg->reg[i].ref_beg);
}
if (a_reg->read_len - a_reg->reg[i-1].end > reg_min_thd && a_reg->read_len-a_reg->reg[i-1].end <= reg_max_thd)
push_reg(remain_reg, a_reg->reg[i-1].end+1, a_reg->read_len, a_reg->reg[i-1].end_n, a_reg->reg[i-1].ref_end, 0, 0);
return remain_reg->reg_n;
}
void push_reg_res(aln_reg *reg, res_t *res)
{
int r_n = reg->reg_n;
if (r_n == reg->reg_m) {
reg->reg_m <<= 1;
reg_reloc(&(reg->reg), r_n, reg->reg_m);
}
reg->reg[r_n].ref_beg[0].chr = reg->reg[r_n].ref_end[0].chr = res->chr;
reg->reg[r_n].ref_beg[0].is_rev = reg->reg[r_n].ref_end[0].is_rev = 1-res->nstrand;
if (res->nstrand == 1) { // '+'
reg->reg[r_n].beg = (res->cigar[0] & 0xf) == CSOFT_CLIP ? ((res->cigar[0]>>4)+1):1;
reg->reg[r_n].end = (res->cigar[res->cigar_len-1] & 0xf) == CSOFT_CLIP ? (reg->read_len - (res->cigar[res->cigar_len-1]>>4)):reg->read_len;
reg->reg[r_n].ref_beg[0].ref_pos = res->offset;
reg->reg[r_n].ref_end[0].ref_pos = res->offset+refInCigar(res->cigar, res->cigar_len)-1;
} else { // '-'
reg->reg[r_n].beg = (res->cigar[res->cigar_len-1] & 0xf) == CSOFT_CLIP ? ((res->cigar[res->cigar_len-1]>>4) + 1):1;
reg->reg[r_n].end = (res->cigar[0] & 0xf) == CSOFT_CLIP ? (reg->read_len - (res->cigar[0]>>4)):reg->read_len;
reg->reg[r_n].ref_end[0].ref_pos = res->offset;
reg->reg[r_n].ref_beg[0].ref_pos = res->offset+refInCigar(res->cigar, res->cigar_len)-1;
}
res->reg_beg = reg->reg[r_n].beg;
res->reg_end = reg->reg[r_n].end;
reg->reg[r_n].beg_n = reg->reg[r_n].end_n = 1;
reg->reg_n++;
}
void get_reg(aln_res *res, aln_reg *reg)
{
int i, j;
for (i = 0; i < res->l_n; ++i) {
if (res->la[i].tol_score < 0) continue;
for (j = 0; j <= res->la[i].cur_res_n; ++j)
push_reg_res(reg, res->la[i].res+j);
}
}
int get_cover_res(aln_reg *reg, aln_res *res, int qua_i, int *cov_qua_i, qua_node *qua, int head[], int head_n, float ovlp_r)
{
extern float cover_rate(int s1, int e1, int s2, int e2);
int reg_i, i, j, res_i, l_i;
int _res_i = qua[qua_i].x, _l_i = qua[qua_i].y, _r_i; // new res
for (_r_i = 0; _r_i <= (res+_res_i)->la[_l_i].cur_res_n; ++_r_i) {
res_t *_r = (res+_res_i)->la[_l_i].res+_r_i;
reg_i = 0;
for (i = 0; i < head_n; ++i) { // existing ress and regs
res_i = qua[head[i]].x;
l_i = qua[head[i]].y;
for (j = 0; j <= (res+res_i)->la[l_i].cur_res_n; ++j) {
if (cover_rate(reg->reg[reg_i].beg, reg->reg[reg_i].end, _r->reg_beg, _r->reg_end) >= ovlp_r) {
*cov_qua_i = head[i];
return 1; // cover
}
reg_i++;
}
}
}
return 0;// Not cover
}
int res_comp(const void*a,const void*b)
{
if ((*(qua_node*)b).a-(*(qua_node*)a).a)
return (*(qua_node*)b).a-(*(qua_node*)a).a;
else return (*(qua_node*)b).b-(*(qua_node*)a).b;
}
float get_cov_f(aln_res *res, aln_reg *reg)
{
float cov_f; int i, cov=0;
reg->reg_n = 0;
for (i = 0; i < 3; ++i) get_reg(res+i, reg);
aln_sort_reg(reg); aln_merg_reg(reg, 0);
for (i = 0; i < reg->reg_n; ++i)
cov += (reg->reg[i].end-reg->reg[i].beg+1);
cov_f = (cov+0.0)/reg->read_len;
return cov_f;
}
// rearrange the aln_res (merge and filter by the score and cover-region)
void rearr_aln_res(aln_res *res, int n, float ovlp_r)
{
extern void copy_res(res_t *f, res_t *t);
int a_i, i, j; aln_res *p;
// sort by score;
qua_node *qua = (qua_node*)malloc(10 * sizeof(qua_node));
int qua_n = 0, qua_m = 10;
int head[1024], head_n=0;
for (a_i = 0; a_i < n; ++a_i) {
p = res+a_i;
for (i = 0; i < p->l_n; ++i) {
if (p->la[i].tol_score < 0) { p->la[i].merg_msg = (line_node){0, -1}; continue; }
if (qua_n == qua_m) {
qua = (qua_node*)realloc(qua, qua_m * 2 * sizeof(qua_node));
qua_m <<= 1;
}
qua[qua_n++] = (qua_node){a_i, i, p->la[i].tol_score, p->la[i].line_score};
}
}
if (qua_n == 0) {free(qua); return;}
qsort(qua, qua_n, sizeof(qua_node), res_comp);
aln_reg *reg = aln_init_reg(res->read_len);
// set the res with the biggest score: qua[0]
for (i = 0; i <= (res+qua[0].x)->la[qua[0].y].cur_res_n; ++i) push_reg_res(reg, (res+qua[0].x)->la[qua[0].y].res+i);
head[head_n++] = 0;
// NOT merg
(res+qua[0].x)->la[qua[0].y].merg_msg = (line_node){1, 0}; // NOT merge and ONLY best
for (i = 0; i < qua_n; ++i) (res+qua[i].x)->la[qua[i].y].mapQ = 255;
int mapq_max = MAPQ_MAX * res->cov_f;
int cov_qua_i;
for (i = 1; i < qua_n; ++i) {
if (!get_cover_res(reg, res, i, &cov_qua_i, qua, head, head_n, ovlp_r)) { // NOT cover
// NOT merg
for (j = 0; j <= (res+qua[i].x)->la[qua[i].y].cur_res_n; ++j) push_reg_res(reg, (res+qua[i].x)->la[qua[i].y].res+j);
head[head_n++] = i;
(res+qua[i].x)->la[qua[i].y].merg_msg = (line_node){1, 0}; // NOT merge and ONLY best
} else if (qua[i].a > qua[cov_qua_i].a/2
&& (res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].XA_n + (res+qua[i].x)->la[qua[i].y].cur_res_n
< (res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].XA_m) {
// head_i.merg_flag = MERG_HEAD
for (j = 0; j <= (res+qua[i].x)->la[qua[i].y].cur_res_n; ++j) {
(res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].XA[(res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].XA_n] = (res+qua[i].x)->la[qua[i].y].res+j;
(res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].XA_n++;
}
(res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].merg_msg.y = 1; // {1,1}, Merge, has alternative
// set mapQ for primary
uint8_t tmpQ = mapq_max * (qua[cov_qua_i].a - qua[i].a)/qua[cov_qua_i].a;
if (tmpQ < ((res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].mapQ))
(res+qua[cov_qua_i].x)->la[qua[cov_qua_i].y].mapQ = tmpQ;
(res+qua[i].x)->la[qua[i].y].merg_msg = (line_node){2, 0}; // Merge, body
} else {
// DUMP
(res+qua[i].x)->la[qua[i].y].merg_msg = (line_node){0, -1}; // DUMP
}
}
// re-set mapQ, based on head_n
for (i = 0; i < qua_n; ++i) {
if ((res+qua[i].x)->la[qua[i].y].merg_msg.x != 1) continue;
if ((res+qua[i].x)->la[qua[i].y].mapQ == 255) {
(res+qua[i].x)->la[qua[i].y].mapQ = mapq_max / head_n;
} else (res+qua[i].x)->la[qua[i].y].mapQ /= head_n;
}
free(qua); aln_free_reg(reg);
}
frag_dp_node ***fnode_alloc(int seed_m, int per_aln_m)
{
int i, j;
frag_dp_node ***f_node;
f_node = (frag_dp_node***)malloc(sizeof(frag_dp_node**));
(*f_node) = (frag_dp_node**)malloc(seed_m * sizeof(frag_dp_node*));
for (i = 0; i < seed_m; ++i) {
(*f_node)[i] = (frag_dp_node*)malloc(per_aln_m * sizeof(frag_dp_node));
for (j = 0; j < per_aln_m; ++j) {
(*f_node)[i][j].seed_i = i, (*f_node)[i][j].aln_i = j;
(*f_node)[i][j].son_max = 4; // son_max
(*f_node)[i][j].son = (line_node*)calloc(4, sizeof(line_node));
}
}
return f_node;
}
void fnode_init(frag_dp_node **f_node, int seed_m, int per_aln_m)
{
int i, j;
for (i = 0; i < seed_m; ++i) {
for (j = 0; j < per_aln_m; ++j) {
f_node[i][j].in_de = 0;
f_node[i][j].son_n = 0;
f_node[i][j].max_score = 0;
}
}
}
void fnode_free(frag_dp_node ***f_node, int seed_m, int per_aln_m)
{
int i, j;
for (i = 0; i < seed_m; ++i) {
for (j = 0; j < per_aln_m; ++j)
free((*f_node)[i][j].son);
free((*f_node)[i]);
}
free(*f_node);
free(f_node);
}
void map_cal_msg(map_msg *m_msg, bntseq_t *bns)
{
int i;
for (i = 0; i < m_msg->map_n; ++i) {
m_msg->map[i].nchr = bns_get_rid(bns, m_msg->map[i].chr);
m_msg->map[i].nstrand = (m_msg->map[i].strand=='+'?1:-1);
}
}
void init_aln_per_para(lamsa_aln_per_para *APP, seed_msg *s_msg, int read_n)
{
APP->last_len = s_msg->last_len[read_n];
APP->seed_all = s_msg->seed_all[read_n] - s_msg->seed_all[read_n-1];
}
typedef struct {
//char *name; // read name
//uint8_t *seq; // 0/1/2/3/4:A/C/G/T/N
//uint8_t *rseq;
//char *qual;
//int len; // read length
lamsa_aln_per_para *APP; // parameter for this read
map_msg *m_msg; // seeds' mapping infomation
// size: seed_all * sizeof(map_msg)
aln_res *a_res; // [3] alignment results
} lamsa_seq_t; // whole_seqs_size = n_seqs * sizeof(lamsa_seq_t)
typedef struct {
int tid; // local id of thread
lamsa_aln_para *AP; // common parameter for all reads
bwt_t *bwt; // bwt index
uint8_t *pac; // pac of reference
bntseq_t *bns; // reference
int n_seqs;
lamsa_seq_t *lamsa_seqs; // auxiliary: rseq, APP, m_msg, a_res
kseq_t *w_seqs; // whole seqs to be processed
frag_dp_node ***f_node; // DP nodes
line_node *line, *_line; // line:[start ... end][start ... end] ... []
int *line_start_len, *line_rank, *line_select_rank;// [start, len][start, len] ... []
int *_line_start_len, *_line_rank;
int line_n_max;
//frag_msg **f_msg; // alignment information of fragments of read
uint32_t *hash_num; // hash index
uint64_t **hash_node;
} thread_aux_t; // whole_aux_size = n_thread * sizeof(thread_aux_t)
int COUNT=0;
int THREAD_READ_I;
pthread_rwlock_t RWLOCK;
int lamsa_main_aln(thread_aux_t *aux)
{
lamsa_aln_para *AP = aux->AP; bwt_t *bwt = aux->bwt; uint8_t *pac = aux->pac; bntseq_t *bns = aux->bns;
frag_dp_node ***f_node = aux->f_node;
line_node *line = aux->line, *_line = aux->_line;
int *line_start_len = aux->line_start_len; int *_line_start_len = aux->_line_start_len;
int *line_rank = aux->line_rank; int *_line_rank = aux->_line_rank; int *line_select_rank = aux->line_select_rank;
frag_msg **f_msg = (frag_msg**)malloc(sizeof(frag_msg*));;
uint32_t *hash_num = aux->hash_num; uint64_t **hash_node = aux->hash_node;
int line_n_max = aux->line_n_max;
int i = 0, j;
while (1) {
pthread_rwlock_wrlock(&RWLOCK);
i = THREAD_READ_I++;
pthread_rwlock_unlock(&RWLOCK);
if (i >= aux->n_seqs) break;
lamsa_seq_t *la_seqs = aux->lamsa_seqs + i; lamsa_aln_per_para *APP = la_seqs->APP;
kseq_t *seqs = aux->w_seqs+i;
strcpy(READ_NAME, seqs->name.s);
// set map_msg
int seed_out_i;
for (seed_out_i = 0; seed_out_i < APP->seed_out; ++seed_out_i) {
gem_map_msg(la_seqs->m_msg+seed_out_i, AP->per_aln_m);
//if ((la_seqs->m_msg+seed_out_i)->map_n > 0) {
map_cal_msg(la_seqs->m_msg+seed_out_i, bns);
}
// aln_res
aln_reset_res(la_seqs->a_res, 3, seqs->seq.l);
// aln_reg
aln_reg *a_reg = aln_init_reg(seqs->seq.l);
int line_n = frag_line_BCC(la_seqs->m_msg, f_msg, APP, AP, seqs, line, line_start_len, line_rank, line_select_rank, f_node, _line, line_n_max);
uint8_t *bseq = (uint8_t*)malloc(seqs->seq.l * sizeof(uint8_t));
for (j = 0; j < (int)seqs->seq.l; ++j) bseq[j] = nst_nt4_table[(int)(seqs->seq.s[j])];
uint8_t *rbseq=NULL;
if (line_n > 0) {
frag_check(la_seqs->m_msg, f_msg, la_seqs->a_res, bns, pac, bseq, &rbseq, APP, AP, seqs, line_n, &hash_num, &hash_node);
get_reg(la_seqs->a_res, a_reg);
}
// remain region
line_n = frag_line_remain(a_reg, la_seqs->m_msg, f_msg, APP, AP, seqs, line, line_start_len, line_rank, line_select_rank, f_node, _line, _line_start_len, _line_rank, line_n_max);
if (line_n > 0) {
frag_check(la_seqs->m_msg, f_msg, la_seqs->a_res+1, bns, pac, bseq, &rbseq, APP, AP, seqs, line_n, &hash_num, &hash_node);
get_reg(la_seqs->a_res+1, a_reg);
}
// bwt aln
bwt_aln_remain(a_reg, la_seqs->a_res+2, bwt, bns, pac, bseq, &rbseq, AP, seqs);
get_reg(la_seqs->a_res+2, a_reg);
la_seqs->a_res->cov_f = get_cov_f(la_seqs->a_res, a_reg);
// rearrange a_res(0,1,2)
rearr_aln_res(la_seqs->a_res, 3, AP->ovlp_rat);
aln_free_reg(a_reg); if (rbseq) free(rbseq); free(bseq);
COUNT++;
#ifdef __DEBUG__
fprintf(stderr, "%16d reads have been aligned.\n", COUNT);
#else
if (COUNT % 100000 == 0) fprintf(stderr, "%16d reads have been aligned.\n", COUNT);
#endif
}
free(f_msg);
return 0;
}
static void *lamsa_thread_aln(void *aux)
{
thread_aux_t *a = (thread_aux_t*)aux;
lamsa_main_aln(a);
return 0;
}
void bseq_reco(char *seq, int len)
{
int i;
for (i = 0; i < len>>1; ++i) {
char tmp = seq[len-1-i];
if (tmp < 4) tmp = 3 - tmp;
seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3-seq[i];
seq[i] = tmp;
}
if (len & 1) seq[i] = (seq[i] >= 4)? seq[i] : 3-seq[i];
}
lamsa_seq_t *lamsa_seq_init(int chunk_read_n, int seed_m, int x)
{
int i;
lamsa_seq_t *seqs = (lamsa_seq_t*)calloc(chunk_read_n, sizeof(lamsa_seq_t));
if (seqs == NULL) { fprintf(stderr, "[lamsa_seq_init] Not enough memory.\n"); exit(1); }
for (i = 0; i < chunk_read_n; ++i) {
seqs[i].a_res = aln_init_res(1, 3, x); // aln_res, remain_res, bwt_remain_res
seqs[i].APP = (lamsa_aln_per_para*)malloc(sizeof(lamsa_aln_per_para));
//seqs[i].m_msg = map_init_msg(seed_m);
}
return seqs;
}
// => seqs(name, seq, (map_msg,APP) * seed_num), n_seqs
// => seqs(aln_res) in thread
int lamsa_read_seq(lamsa_seq_t *la_seqs, kseq_t *read_seq_t, FILE *seed_mapfp,
char *gem_line, int line_size, seed_msg *s_msg, int chunk_read_n)
{
kseq_t *s = read_seq_t;
int i;
lamsa_seq_t *p=NULL; int n = 0;
while (kseq_read(s+n) >= 0)
{
p = &la_seqs[n++];
// APP, seed_mapfp
++(s_msg->read_count);
init_aln_per_para(p->APP, s_msg, s_msg->read_count);
p->m_msg = map_init_msg(p->APP->seed_all);
int seed_all = p->APP->seed_all;
int seed_n = 0, seed_out = 0;
while (seed_n < seed_all) {
if (gem_map_read(seed_mapfp, p->m_msg+seed_out, gem_line, line_size)) {
p->m_msg[seed_out].seed_id = seed_n+1;
++seed_out;
}
++seed_n;
}
p->APP->seed_out = seed_out;
if (n >= chunk_read_n) break;
}
return n;
}
void lamsa_free_read_seq(lamsa_seq_t *seqs, int n_seqs)
{
int i;
for (i = 0; i < n_seqs; ++i) {
lamsa_seq_t *p = seqs+i;
free(p->APP);
aln_res_free(p->a_res, 3);
}
free(seqs);
}
void aux_dp_init(thread_aux_t *aux, seed_msg *s_msg, lamsa_aln_para AP)
{
aux->f_node = fnode_alloc(s_msg->seed_max+2, AP.per_aln_m);
int line_m = s_msg->seed_max * AP.per_aln_m;
int line_node_m = line_m * (1+L_EXTRA);
aux->line = (line_node*)malloc(line_node_m * sizeof(line_node)); aux->_line = (line_node*)malloc(line_node_m * sizeof(line_node));
aux->line_start_len = (int*)malloc(line_m * 2 * sizeof(int)); aux->_line_start_len = (int*)malloc(line_m * 2 * sizeof(int));
aux->line_rank = (int*)malloc(line_m * sizeof(int)); aux->_line_rank = (int*)malloc(line_m * sizeof(int));
aux->line_select_rank = (int*)malloc(line_m * sizeof(int));
aux->line_n_max = line_m;
aux->hash_num = (uint32_t*)calloc(pow(NT_N, AP.hash_key_len), sizeof(uint32_t));
aux->hash_node = (uint64_t**)calloc(pow(NT_N, AP.hash_key_len), sizeof(uint64_t*));
}
void aux_dp_free(thread_aux_t *aux, seed_msg *s_msg, lamsa_aln_para *AP)
{
fnode_free(aux->f_node, s_msg->seed_max+2, AP->per_aln_m);
free(aux->line); free(aux->_line);
free(aux->line_start_len); free(aux->_line_start_len); free(aux->line_rank); free(aux->_line_rank); free(aux->line_select_rank);
int i;
for (i = 0; i < pow(NT_N, AP->hash_key_len); ++i) free(aux->hash_node[i]);
free(aux->hash_node); free(aux->hash_num);
//frag_free_msg(*(aux->f_msg), aux->line_m); free(aux->f_msg);
}
//merg_msg: {1, 0} -> NOT merged or ONLY best
// {1, n} -> merged, best, has n alternative res
// {2, i} -> merged, alternative and best is `i`
// {0,-1} -> dumped