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runkma.c
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/* Philip T.L.C. Clausen Jan 2017 [email protected] */
/*
* Copyright (c) 2017, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#define _XOPEN_SOURCE 600
#include <fcntl.h>
#include <limits.h>
#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "align.h"
#include "alnfrags.h"
#include "ankers.h"
#include "assembly.h"
#include "chain.h"
#include "compdna.h"
#include "conclave.h"
#include "ef.h"
#include "filebuff.h"
#include "frags.h"
#include "hashmapcci.h"
#include "kmapipe.h"
#include "nw.h"
#include "penalties.h"
#include "pherror.h"
#include "printconsensus.h"
#include "qseqs.h"
#include "runkma.h"
#include "sam.h"
#include "stdnuc.h"
#include "stdstat.h"
#include "tmp.h"
#include "tsv.h"
#include "updatescores.h"
#include "vcf.h"
#include "xml.h"
#ifndef _WIN32
#include <sys/ipc.h>
#include <sys/shm.h>
#include <sys/types.h>
#else
typedef int key_t;
#define ftok(charPtr, integer) (0)
#define shmget(key, size, permission) ((size != 0) ? (-1) : (-key))
#define shmat(shmid, NULL_Ptr, integer) (NULL)
#define shmdt(dest) fprintf(stderr, "sysV not available on Windows.\n")
#define shmctl(shmid, cmd, buf) fprintf(stderr, "sysV not available on Windows.\n")
#endif
#define nameSkip(infile, c) while((c = fgetc(infile)) != '\n' && c != EOF)
int load_DBs_KMA(char *templatefilename, long unsigned **alignment_scores, long unsigned **uniq_alignment_scores, int **template_lengths, unsigned shm) {
/* load DBs needed for KMA */
int file_len, shmid, DB_size;
FILE *DB_file;
key_t key;
/* allocate DBs */
file_len = strlen(templatefilename);
strcat(templatefilename, ".length.b");
DB_file = sfopen(templatefilename, "rb");
sfread(&DB_size, sizeof(int), 1, DB_file);
if(shm & 4) {
key = ftok(templatefilename, 'l');
shmid = shmget(key, DB_size * sizeof(int), 0666);
if(shmid < 0) {
fprintf(stderr, "No shared length\n");
exit(1);
} else {
*template_lengths = shmat(shmid, NULL, 0);
}
} else {
*template_lengths = smalloc(DB_size * sizeof(int));
/* load lengths */
sfread(*template_lengths, sizeof(int), DB_size, DB_file);
}
templatefilename[file_len] = 0;
fclose(DB_file);
/* allocate pointers */
*alignment_scores = calloc(DB_size, sizeof(long unsigned));
*uniq_alignment_scores = calloc(DB_size, sizeof(long unsigned));
if(!*alignment_scores || !*uniq_alignment_scores) {
ERROR();
}
return DB_size;
}
char * nameLoad(Qseqs *name, FILE *infile) {
int c, size;
unsigned char *ptr;
ptr = name->seq;
size = name->size - 1;
while((c = fgetc(infile)) != '\n' && c != EOF) {
*ptr++ = c;
if(--size == 0) {
size = name->size - 1;
name->seq = realloc(name->seq, (name->size <<= 1));
if(!name->seq) {
ERROR();
}
ptr = name->seq + size;
}
}
*ptr = 0;
return (char *) name->seq;
}
int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConClave, int kmersize, int minlen, Penalties *rewards, int extendedFeatures, double ID_t, double Depth_t, int mq, double scoreT, double mrc, double minFrac, double evalue, double support, int bcd, int ref_fsa, int print_matrix, int print_all, long unsigned tsv, int vcf, int xml, int sam, int nc, int nf, unsigned shm, int thread_num, int maxFrag, int verbose) {
int i, file_len, template, t_len, end, aln_len, status, sparse, fileCount;
int coverScore, seq_in_no, DB_size, counter;
int *bestTemplates, *bestTemplates_r, *best_start_pos, *best_end_pos;
int *matched_templates, *template_lengths, *Lengths;
unsigned *fragmentCounts, *readCounts;
long read_score, *seq_indexes;
long unsigned Nhits, template_tot_ulen, seqin_size;
long unsigned *w_scores, *uniq_alignment_scores, *alignment_scores;
double id, q_id, cover, q_cover, p_value;
long double depth, expected, q_value;
FILE *inputfile, *frag_in_raw, *res_out, *tsv_out, *name_file;
FILE *alignment_out, *consensus_out, *frag_out_raw, **template_fragments;
FILE *extendedFeatures_out, *xml_out;
time_t t0, t1;
FileBuff *frag_out, *frag_out_all, *matrix_out, *vcf_out;
Aln *aligned, *gap_align;
Assem *aligned_assem;
Frag **alignFrags;
CompDNA *qseq_comp, *qseq_r_comp;
Qseqs *qseq, *qseq_r, *header, *header_r, *template_name;
AssemInfo *matrix;
AlnPoints *points;
NWmat *NWmatrices;
Assemble_thread *threads, *thread, *next;
Aln_thread *alnThreads, *alnThread;
HashMapCCI **templates_index;
/* get lengths and names */
file_len = strlen(templatefilename);
DB_size = load_DBs_KMA(templatefilename, &alignment_scores, &uniq_alignment_scores, &template_lengths, shm);
if(!kmersize) {
kmersize = *template_lengths;
}
templatefilename[file_len] = 0;
template_name = setQseqs(256);
strcat(templatefilename, ".name");
name_file = sfopen(templatefilename, "rb");
templatefilename[file_len] = 0;
/* print sam-header */
if(sam) {
saminit(template_name, name_file, template_lengths, DB_size, exePrev);
}
/* open pipe */
status = 0;
inputfile = kmaPipe("-s2", "rb", 0, 0);
if(!inputfile) {
ERROR();
} else {
setvbuf(inputfile, NULL, _IOFBF, CHUNK);
}
/* load databases */
strcat(templatefilename, ".seq.b");
seq_in_no = open(templatefilename, O_RDONLY);
if(seq_in_no == -1) {
ERROR();
}
seqin_size = 4 * lseek(seq_in_no, 0, SEEK_END);
if(lseek(seq_in_no, 0, SEEK_SET) != 0) {
ERROR();
}
/*
seq_in = sfopen(templatefilename, "rb");
sfseek(seq_in, 0, SEEK_END);
seqin_size = 4 * ftell(seq_in);
sfseek(seq_in, 0, SEEK_SET);
seq_in_no = fileno(seq_in);
*/
templatefilename[file_len] = 0;
templates_index = calloc(DB_size, sizeof(HashMapCCI*));
if(!templates_index) {
ERROR();
}
alignLoadPtr = &alignLoad_fly;
if(kmersize < 4 || 31 < kmersize) {
kmersize = 16;
}
/* allocate stuff */
file_len = strlen(outputfilename);
seq_indexes = smalloc((DB_size + 1) * sizeof(long));
/* make file indexes of template indexing */
*seq_indexes = 0;
seq_indexes[1] = 0;
for(i = 2; i < DB_size; ++i) {
seq_indexes[i] = seq_indexes[i - 1] + ((template_lengths[i - 1] >> 5) + 1) * sizeof(long unsigned);
}
/* open outputfiles */
if(outputfilename) {
strcat(outputfilename, ".res");
res_out = sfopen(outputfilename, "w");
outputfilename[file_len] = 0;
if(tsv) {
strcat(outputfilename, ".tsv");
tsv_out = sfopen(outputfilename, "w");
outputfilename[file_len] = 0;
} else {
tsv_out = 0;
}
if(nf == 0) {
strcat(outputfilename, ".frag.gz");
frag_out = gzInitFileBuff(CHUNK);
openFileBuff(frag_out, outputfilename, "wb");
outputfilename[file_len] = 0;
} else {
frag_out = 0;
}
alignment_out = 0;
consensus_out = 0;
if((nc & 1) == 0) {
strcat(outputfilename, ".fsa");
consensus_out = sfopen(outputfilename, "w");
outputfilename[file_len] = 0;
}
if((nc & 2) == 0) {
strcat(outputfilename, ".aln");
alignment_out = sfopen(outputfilename, "w");
outputfilename[file_len] = 0;
strcat(outputfilename, ".fsa");
consensus_out = sfopen(outputfilename, "w");
outputfilename[file_len] = 0;
}
frag_out_raw = tmpF(0);
if(!frag_out_raw) {
ERROR();
}
if(print_matrix) {
matrix_out = gzInitFileBuff(CHUNK);
strcat(outputfilename, ".mat.gz");
openFileBuff(matrix_out, outputfilename, "wb");
outputfilename[file_len] = 0;
} else {
matrix_out = 0;
}
if(print_all) {
strcat(outputfilename, ".frag_raw.gz");
frag_out_all = gzInitFileBuff(CHUNK);
openFileBuff(frag_out_all, outputfilename, "wb");
outputfilename[file_len] = 0;
} else {
frag_out_all = 0;
}
if(vcf) {
vcf_out = gzInitFileBuff(CHUNK);
strcat(outputfilename, ".vcf.gz");
openFileBuff(vcf_out, outputfilename, "wb");
outputfilename[file_len] = 0;
} else {
vcf_out = 0;
}
} else {
fprintf(stderr, " No output file specified!\n");
exit(1);
}
fprintf(stderr, "# Running KMA.\n");
t0 = clock();
/* allocate stuff */
i = 1;
alnThreads = 0;
while(i < thread_num) {
/* allocate stuff */
matched_templates = smalloc(((DB_size + 1) << 1) * sizeof(int));
bestTemplates = smalloc(((DB_size + 1) << 1) * sizeof(int));
bestTemplates_r = smalloc(((DB_size + 1) << 1) * sizeof(int));
best_start_pos = smalloc((DB_size << 1) * sizeof(int));
best_end_pos = smalloc((DB_size << 1) * sizeof(int));
Lengths = smalloc((DB_size << 1) * sizeof(int));
qseq_comp = smalloc(sizeof(CompDNA));
qseq_r_comp = smalloc(sizeof(CompDNA));
allocComp(qseq_comp, 1024);
allocComp(qseq_r_comp, 1024);
/* allocate matrcies for NW */
NWmatrices = smalloc(sizeof(NWmat));
NWmatrices->NW_s = 1024 * 1024;
NWmatrices->NW_q = 1024;
NWmatrices->E = smalloc(NWmatrices->NW_s);
NWmatrices->D[0] = smalloc((NWmatrices->NW_q << 1) * sizeof(int));
NWmatrices->P[0] = smalloc((NWmatrices->NW_q << 1) * sizeof(int));
NWmatrices->D[1] = NWmatrices->D[0] + NWmatrices->NW_q;
NWmatrices->P[1] = NWmatrices->P[0] + NWmatrices->NW_q;
NWmatrices->rewards = rewards;
/* move it to the thread */
alnThread = smalloc(sizeof(Aln_thread));
alnThread->matched_templates = matched_templates;
alnThread->bestTemplates = bestTemplates;
alnThread->bestTemplates_r = bestTemplates_r;
alnThread->best_start_pos = best_start_pos;
alnThread->best_end_pos = best_end_pos;
alnThread->Lengths = Lengths;
alnThread->alignment_scores = alignment_scores;
alnThread->uniq_alignment_scores = uniq_alignment_scores;
alnThread->seq_indexes = seq_indexes;
alnThread->inputfile = inputfile;
alnThread->frag_out_raw = frag_out_raw;
alnThread->frag_out_all = frag_out_all;
alnThread->seq_in = seq_in_no;
alnThread->qseq_comp = qseq_comp;
alnThread->qseq_r_comp = qseq_r_comp;
alnThread->qseq = setQseqs(1024);
alnThread->qseq_r = setQseqs(1024);
alnThread->header = setQseqs(256);
alnThread->header_r = setQseqs(256);
alnThread->points = seedPoint_init(1024, rewards);
alnThread->NWmatrices = NWmatrices;
alnThread->kmersize = kmersize;
alnThread->minlen = minlen;
alnThread->template_lengths = template_lengths;
alnThread->templates_index = templates_index;
alnThread->mq = mq;
alnThread->sam = (sam == 1) ? 1 : 0;
alnThread->scoreT = scoreT;
alnThread->mrc = mrc;
alnThread->minFrac = minFrac;
alnThread->next = alnThreads;
alnThreads = alnThread;
/* start thread */
if((errno = pthread_create(&alnThread->id, NULL, &alnFrags_threaded, alnThread))) {
fprintf(stderr, "Error: %d (%s)\n", errno, strerror(errno));
fprintf(stderr, "Will continue with %d threads.\n", i);
alnThreads = alnThread->next;
free(alnThread);
i = thread_num;
} else {
++i;
}
}
/* allocate stuff */
matched_templates = smalloc(((DB_size + 1) << 1) * sizeof(int));
bestTemplates = smalloc(((DB_size + 1) << 1) * sizeof(int));
bestTemplates_r = smalloc(((DB_size + 1) << 1) * sizeof(int));
best_start_pos = smalloc((DB_size << 1) * sizeof(int));
best_end_pos = smalloc((DB_size << 1) * sizeof(int));
Lengths = smalloc((DB_size << 1) * sizeof(int));
qseq = setQseqs(1024);
qseq_r = setQseqs(1024);
header = setQseqs(256);
header_r = setQseqs(256);
qseq_comp = smalloc(sizeof(CompDNA));
qseq_r_comp = smalloc(sizeof(CompDNA));
allocComp(qseq_comp, 1024);
allocComp(qseq_r_comp, 1024);
points = seedPoint_init(1024, rewards);
/* allocate matrcies for NW */
NWmatrices = smalloc(sizeof(NWmat));
NWmatrices->NW_s = 1024 * 1024;
NWmatrices->NW_q = 1024;
NWmatrices->E = smalloc(NWmatrices->NW_s);
NWmatrices->D[0] = smalloc((NWmatrices->NW_q << 1) * sizeof(int));
NWmatrices->P[0] = smalloc((NWmatrices->NW_q << 1) * sizeof(int));
NWmatrices->D[1] = NWmatrices->D[0] + NWmatrices->NW_q;
NWmatrices->P[1] = NWmatrices->P[0] + NWmatrices->NW_q;
NWmatrices->rewards = rewards;
/* strat main thread */
alnThread = smalloc(sizeof(Aln_thread));
alnThread->matched_templates = matched_templates;
alnThread->bestTemplates = bestTemplates;
alnThread->bestTemplates_r = bestTemplates_r;
alnThread->best_start_pos = best_start_pos;
alnThread->best_end_pos = best_end_pos;
alnThread->Lengths = Lengths;
alnThread->alignment_scores = alignment_scores;
alnThread->uniq_alignment_scores = uniq_alignment_scores;
alnThread->seq_indexes = seq_indexes;
alnThread->inputfile = inputfile;
alnThread->frag_out_raw = frag_out_raw;
alnThread->frag_out_all = frag_out_all;
alnThread->seq_in = seq_in_no;
alnThread->qseq_comp = qseq_comp;
alnThread->qseq_r_comp = qseq_r_comp;
alnThread->qseq = qseq;
alnThread->qseq_r = qseq_r;
alnThread->header = header;
alnThread->header_r = header_r;
alnThread->points = points;
alnThread->NWmatrices = NWmatrices;
alnThread->kmersize = kmersize;
alnThread->minlen = minlen;
alnThread->mq = mq;
alnThread->sam = (sam == 1) ? 1 : 0;
alnThread->scoreT = scoreT;
alnThread->mrc = mrc;
alnThread->minFrac = minFrac;
alnThread->template_lengths = template_lengths;
alnThread->templates_index = templates_index;
alnThread->next = 0;
/* Get alignments */
alnFrags_threaded(alnThread);
free(alnThread);
/* join threads */
for(alnThread = alnThreads; alnThread != 0; alnThread = alnThread->next) {
/* join thread */
if((errno = pthread_join(alnThread->id, NULL))) {
ERROR();
}
}
kmaPipe(0, 0, inputfile, &i);
status |= i;
i = 0;
sfwrite(&i, sizeof(int), 1, frag_out_raw);
fflush(frag_out_raw);
freeComp(qseq_comp);
free(qseq_comp);
freeComp(qseq_r_comp);
free(qseq_r_comp);
if(header->size < header_r->size) {
free(header->seq);
header->size = header_r->size;
header->seq = smalloc(header->size);
}
if(qseq->size < qseq_r->size) {
free(qseq->seq);
qseq->size = qseq_r->size;
qseq->seq = smalloc(qseq->size);
}
/* Patricks features */
if(extendedFeatures) {
strcat(outputfilename, ".mapstat");
extendedFeatures_out = sfopen(outputfilename, "wb");
outputfilename[file_len] = 0;
initExtendedFeatures(extendedFeatures_out, templatefilename, *matched_templates, exePrev);
} else {
extendedFeatures_out = 0;
}
if(extendedFeatures || xml || tsv) {
fragmentCounts = calloc(DB_size, sizeof(unsigned));
readCounts = calloc(DB_size, sizeof(unsigned));
if(!fragmentCounts || !readCounts) {
ERROR();
}
} else {
fragmentCounts = 0;
readCounts = 0;
}
if(xml) {
if(xml == 2) {
xml_out = openInitXML("--", templatefilename, *matched_templates, 1, &exePrev);
} else {
strcat(outputfilename, ".xml");
xml_out = openInitXML(outputfilename, templatefilename, *matched_templates, 1, &exePrev);
outputfilename[file_len] = 0;
}
} else {
xml_out = 0;
}
/* clean threads */
i = 1;
threads = 0;
for(alnThread = alnThreads; alnThread != 0; alnThread = alnThreads) {
alnThreads = alnThread->next;
/* reuse what is possible */
thread = smalloc(sizeof(Assemble_thread));
thread->num = i;
thread->thread_num = thread_num;
thread->template = -2;
thread->mq = mq;
thread->minlen = minlen;
thread->scoreT = scoreT;
thread->mrc = mrc;
thread->evalue = evalue;
thread->bcd = bcd;
thread->sam = sam;
thread->ef = extendedFeatures;
thread->seq_in = 0;
thread->kmersize = kmersize;
thread->frag_out = frag_out;
thread->xml_out = xml_out;
thread->NWmatrices = alnThread->NWmatrices;
thread->qseq = alnThread->qseq;
thread->header = alnThread->header;
thread->points = alnThread->points;
thread->points->len = 0;
thread->next = threads;
threads = thread;
++i;
/* check header and qseq */
if(header->size < thread->header->size) {
header->size = thread->header->size;
free(header->seq);
header->seq = smalloc(header->size);
}
if(qseq->size < thread->qseq->size) {
qseq->size = thread->qseq->size;
free(qseq->seq);
qseq->seq = smalloc(qseq->size);
}
/* free the rest */
free(alnThread->matched_templates);
free(alnThread->bestTemplates);
free(alnThread->bestTemplates_r);
free(alnThread->best_start_pos);
free(alnThread->best_end_pos);
free(alnThread->Lengths);
freeComp(alnThread->qseq_comp);
free(alnThread->qseq_comp);
freeComp(alnThread->qseq_r_comp);
free(alnThread->qseq_r_comp);
destroyQseqs(alnThread->qseq_r);
destroyQseqs(alnThread->header_r);
free(alnThread);
}
if(kmaPipe == &kmaPipeFork) {
t1 = clock();
fprintf(stderr, "#\n# KMA mapping time\t%.2f s.\n", difftime(t1, t0) / 1000000);
} else {
fprintf(stderr, "# KMA mapping done\n");
}
fprintf(stderr, "#\n# Sort, output and select KMA alignments.\n");
t0 = clock();
/* Get best template for each mapped read
Best hit chosen as: highest mapping score then higest # unique maps */
alignFrags = calloc(DB_size, sizeof(Frag*));
w_scores = calloc(DB_size, sizeof(long unsigned));
if(!alignFrags || !w_scores) {
ERROR();
}
outputfilename[file_len] = 0;
frag_in_raw = frag_out_raw;
rewind(frag_in_raw);
outputfilename[file_len] = 0;
template_fragments = calloc(DB_size, sizeof(FILE*));
if(!template_fragments) {
ERROR();
}
/* Get expected values */
sparse = 0;
template_tot_ulen = 0;
i = DB_size;
while(--i) {
template_tot_ulen += template_lengths[i];
}
/* ConClave */
if(ConClave == 1) {
fileCount = ConClavePtr(frag_in_raw, &template_fragments, DB_size, maxFrag, w_scores, fragmentCounts, readCounts, alignment_scores, uniq_alignment_scores, template_lengths, header, qseq, bestTemplates, best_start_pos, best_end_pos, alignFrags);
} else if(ConClave == 2) {
fileCount = ConClave2Ptr(frag_in_raw, &template_fragments, DB_size, maxFrag, w_scores, fragmentCounts, readCounts, alignment_scores, uniq_alignment_scores, template_lengths, header, qseq, bestTemplates, best_start_pos, best_end_pos, alignFrags, template_tot_ulen, scoreT, evalue);
} else {
fileCount = 0;
}
free(alignFrags);
free(best_start_pos);
free(best_end_pos);
free(matched_templates);
free(bestTemplates);
destroyQseqs(qseq_r);
fclose(frag_out_raw);
if(frag_out_all) {
destroyGzFileBuff(frag_out_all);
}
/* Get expected values */
Nhits = 0;
i = DB_size;
while(--i) {
Nhits += w_scores[i];
}
Nhits = Nhits ? Nhits : 1;
t1 = clock();
fprintf(stderr, "# Total time for sorting and outputting KMA alignment\t%.2f s.\n", difftime(t1, t0) / 1000000);
fprintf(stderr, "#\n# Doing local assemblies of found templates, and output results\n");
t0 = clock();
/* print heading of resistance file: */
fprintf(res_out, "#Template\tScore\tExpected\tTemplate_length\tTemplate_Identity\tTemplate_Coverage\tQuery_Identity\tQuery_Coverage\tDepth\tq_value\tp_value\n");
if(tsv) {
initsv(tsv_out, tsv);
}
if(vcf) {
initialiseVcf(vcf_out, templatefilename);
}
/* Get expected values */
points->len = 0;
/* preallocate assembly matrices */
aligned_assem = smalloc(sizeof(Assem));
matrix = smalloc(sizeof(AssemInfo));
matrix->size = qseq->size;
for(i = 0; i < DB_size; ++i) {
if(matrix->size < template_lengths[i]) {
matrix->size = template_lengths[i];
}
}
if(alnToMatPtr == &alnToMat) {
matrix->size <<= 1;
} else {
matrix->size++;
}
matrix->assmb = smalloc(matrix->size * sizeof(Assembly));
aligned_assem->size = matrix->size;
aligned_assem->t = smalloc(aligned_assem->size);
aligned_assem->s = smalloc(aligned_assem->size);
aligned_assem->q = smalloc(aligned_assem->size);
/* allocate matrcies for NW */
i = 1;
thread = threads;
threads = 0;
while(thread) {
next = thread->next;
/* get remaining thread info */
aligned = smalloc(sizeof(Aln));
gap_align = smalloc(sizeof(Aln));
aligned->t = smalloc((qseq->size + 1) << 1);
aligned->s = smalloc((qseq->size + 1) << 1);
aligned->q = smalloc((qseq->size + 1) << 1);
gap_align->t = smalloc((qseq->size + 1) << 1);
gap_align->s = smalloc((qseq->size + 1) << 1);
gap_align->q = smalloc((qseq->size + 1) << 1);
thread->aligned = aligned;
thread->gap_align = gap_align;
thread->file_count = fileCount;
thread->files = template_fragments;
thread->aligned_assem = aligned_assem;
thread->matrix = matrix;
thread->spin = (sparse < 0) ? 10 : 100;
/* start thread */
if((errno = pthread_create(&thread->id, NULL, assembly_KMA_Ptr, thread))) {
fprintf(stderr, "Error: %d (%s)\n", errno, strerror(errno));
fprintf(stderr, "Will continue with %d threads.\n", i);
/* free tracebacks */
free(aligned->t);
free(aligned->s);
free(aligned->q);
free(aligned);
free(gap_align->t);
free(gap_align->s);
free(gap_align->q);
free(gap_align);
/* free remaining nodes */
while(thread) {
next = thread->next;
NWmatrices = thread->NWmatrices;
free(NWmatrices->E);
free(NWmatrices->D[0]);
free(NWmatrices->P[0]);
free(NWmatrices);
destroyQseqs(thread->qseq);
destroyQseqs(thread->header);
seedPoint_free(thread->points);
thread = next;
}
} else {
thread->next = threads;
threads = thread;
++i;
}
thread = next;
}
/* start main thread */
aligned = smalloc(sizeof(Aln));
gap_align = smalloc(sizeof(Aln));
aligned->t = smalloc((qseq->size + 1) << 1);
aligned->s = smalloc((qseq->size + 1) << 1);
aligned->q = smalloc((qseq->size + 1) << 1);
gap_align->t = smalloc((qseq->size + 1) << 1);
gap_align->s = smalloc((qseq->size + 1) << 1);
gap_align->q = smalloc((qseq->size + 1) << 1);
thread = smalloc(sizeof(Assemble_thread));
thread->num = 0;
thread->thread_num = thread_num;
thread->template = 0;
thread->mq = mq;
thread->minlen = minlen;
thread->scoreT = scoreT;
thread->mrc = mrc;
thread->evalue = evalue;
thread->bcd = bcd;
thread->sam = sam;
thread->ef = extendedFeatures;
thread->seq_in = 0;
thread->kmersize = kmersize;
thread->file_count = fileCount;
thread->files = template_fragments;
thread->frag_out = frag_out;
thread->xml_out = xml_out;
thread->aligned_assem = aligned_assem;
thread->aligned = aligned;
thread->gap_align = gap_align;
thread->NWmatrices = NWmatrices;
thread->matrix = matrix;
thread->qseq = qseq;
thread->header = header;
thread->points = points;
thread->points->len = 0;
thread->next = 0;
thread->spin = (sparse < 0) ? 10 : 100;
if(assembly_KMA_Ptr == &skip_assemble_KMA) {
alignLoadPtr = &alignLoad_skip;
}
if(verbose) {
fprintf(stderr, "# Template\tScore\tProgress\n");
}
/* Do local assemblies of fragments mapping to the same template */
depth = 0;
q_id = 0;
cover = 0;
q_cover = 0;
counter = 0;
for(template = 1; template < DB_size; ++template) {
if(w_scores[template] > 0) {
if(verbose) {
counter += w_scores[template];
fprintf(stderr, "# %d / %d\t%lu\t%3lu%%\n", template, DB_size, w_scores[template], 100 * counter / Nhits);
}
/* make p_value to see whether assembly is feasable */
read_score = w_scores[template];
t_len = template_lengths[template];
expected = t_len;
expected /= MAX(1, (template_tot_ulen - t_len));
expected *= (Nhits - read_score);
if(0 < expected) {
q_value = read_score - expected;
q_value /= (expected + read_score);
q_value *= (read_score - expected);
} else {
q_value = read_score;
}
p_value = p_chisqr(q_value);
if(cmp((p_value <= evalue && read_score > expected), (read_score >= scoreT * t_len))) {
thread->template_name = nameLoad(template_name, name_file);
thread->template_index = templates_index[template];
if(xml) {
newIterXML(xml_out, template, t_len, thread->template_name);
}
/* Do assembly */
//status |= assemblyPtr(aligned_assem, template, template_fragments, fileCount, frag_out, aligned, gap_align, qseq, header, matrix, points, NWmatrices);
thread->template = template;
thread->t_len = t_len;
assembly_KMA_Ptr(thread);
/* Depth, ID and coverage */
if(aligned_assem->cover > 0) {
coverScore = aligned_assem->cover;
depth = aligned_assem->depth;
depth /= t_len;
id = 100.0 * coverScore / t_len;
aln_len = aligned_assem->aln_len;
q_id = 100.0 * coverScore / aln_len;
cover = 100.0 * aln_len / t_len;
q_cover = 100.0 * t_len / aln_len;
} else {
aln_len = 0;
id = 0;
}
if(xml) {
capIterXML(xml_out, DB_size, seqin_size, t_len, readCounts[template], p_value, read_score, aligned_assem->q, aln_len);
}
if(ID_t <= id && 0 < id && Depth_t <= depth) {
/* Output result */
fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
if(consensus_out) {
printConsensus(aligned_assem, thread->template_name, alignment_out, consensus_out, ref_fsa);
}
/* print matrix */
if(matrix_out) {
updateMatrix(matrix_out, thread->template_name, templates_index[template]->seq, matrix, t_len);
}
if(extendedFeatures) {
printExtendedFeatures(thread->template_name, aligned_assem, fragmentCounts[template], readCounts[template], extendedFeatures_out);
}
if(vcf) {
updateVcf(thread->template_name, aligned_assem->t, evalue, support, bcd, t_len, matrix, vcf, vcf_out);
}
}
} else {
if((sam && !(sam & 2096)) || ID_t == 0.0) {
thread->template_index = templates_index[template];
thread->template_name = nameLoad(template_name, name_file);
thread->template = template;
skip_assemble_KMA(thread);
//skip_assemble_KMA(template, sam, t_len, thread->template_name, fileCount, template_fragments, aligned_assem, qseq, header);
if(ID_t == 0.0) {
depth = aligned_assem->depth;
depth /= t_len;
aln_len = aligned_assem->aln_len;
cover = 100.0 * aln_len / t_len;
q_cover = 100.0 * t_len / aln_len;
fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
if(extendedFeatures) {
printExtendedFeatures(thread->template_name, aligned_assem, fragmentCounts[template], readCounts[template], extendedFeatures_out);
}
}
} else {
nameSkip(name_file, end);
}
}
} else {
nameSkip(name_file, end);
}
hashMapCCI_destroy(templates_index[template]);
}
/* join threads */
thread->template = -1;
assembly_KMA_Ptr(thread);
for(thread = threads; thread != 0; thread = thread->next) {
/* join thread */
if((errno = pthread_join(thread->id, NULL))) {
ERROR();
}
}
/* Close files */
close(seq_in_no);
fclose(res_out);
if(tsv) {
fclose(tsv_out);
}
if(alignment_out) {
fclose(alignment_out);
}
if(consensus_out) {
fclose(consensus_out);
}
fclose(name_file);
if(frag_out) {
destroyGzFileBuff(frag_out);
}
if(matrix_out) {
destroyGzFileBuff(matrix_out);
}
if(extendedFeatures) {
fclose(extendedFeatures_out);
}
if(vcf) {
destroyGzFileBuff(vcf_out);
}
if(xml) {
closeCapXML(xml_out);
}
t1 = clock();
fprintf(stderr, "# Total time used for local assembly: %.2f s.\n#\n", difftime(t1, t0) / 1000000);
return status;
}
int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int ConClave, int kmersize, int minlen, Penalties *rewards, int extendedFeatures, double ID_t, double Depth_t, int mq, double scoreT, double mrc, double minFrac, double evalue, double support, int bcd, int ref_fsa, int print_matrix, int print_all, long unsigned tsv, int vcf, int xml, int sam, int nc, int nf, unsigned shm, int thread_num, int maxFrag, int verbose) {
/* runKMA_MEM is a memory saving version of runKMA,
at the cost it chooses best templates based on kmers
instead of alignment score. */
int i, file_len, rc_flag, template, bestHits, t_len, delta, aln_len, end;
int fileCount, coverScore, status, sparse, progress, seq_in_no, DB_size;
int flag, flag_r, *template_lengths;
int *matched_templates, *bestTemplates, *best_start_pos, *best_end_pos;
unsigned *fragmentCounts, *readCounts;
long best_read_score, read_score, seq_seeker;
long unsigned Nhits, template_tot_ulen, counter, seqin_size;
long unsigned *w_scores, *uniq_alignment_scores, *alignment_scores;
double id, cover, q_id, q_cover, p_value;
long double depth, q_value, expected;
FILE *inputfile, *frag_in_raw, *res_out, *tsv_out, *name_file;
FILE *alignment_out, *consensus_out, *frag_out_raw, **template_fragments;
FILE *extendedFeatures_out, *xml_out;
time_t t0, t1;
FileBuff *frag_out, *frag_out_all, *matrix_out, *vcf_out;
Aln *aligned, *gap_align;
Assem *aligned_assem;
Frag **alignFrags;
CompDNA *qseq_comp, *qseq_r_comp;
Qseqs *qseq, *qseq_r, *header, *header_r, *template_name;
AssemInfo *matrix;
AlnPoints *points;
NWmat *NWmatrices;
Assemble_thread *threads, *thread;
HashMapCCI *template_index;
/* get lengths and names */
file_len = strlen(templatefilename);
DB_size = load_DBs_KMA(templatefilename, &alignment_scores, &uniq_alignment_scores, &template_lengths, shm);
if(!kmersize) {
kmersize = *template_lengths;
}
templatefilename[file_len] = 0;
template_name = setQseqs(256);
strcat(templatefilename, ".name");
name_file = sfopen(templatefilename, "rb");
templatefilename[file_len] = 0;
if((verbose & 2)) {
progress = 1;
verbose = 0;
} else {
progress = 0;
}
/* print sam-header */
if(sam) {
saminit(template_name, name_file, template_lengths, DB_size, exePrev);
}
/* open pipe */
status = 0;
inputfile = kmaPipe("-s2", "rb", 0, 0);
if(!inputfile) {
ERROR();
} else {
setvbuf(inputfile, NULL, _IOFBF, CHUNK);
}
/* load databases */
alignLoadPtr = &alignLoad_fly_mem;
if(kmersize < 4 || 32 < kmersize) {
kmersize = 16;
}
strcat(templatefilename, ".seq.b");
seq_in_no = open(templatefilename, O_RDONLY);
if(seq_in_no == -1) {
ERROR();
}
seqin_size = 4 * lseek(seq_in_no, 0, SEEK_END);
if(lseek(seq_in_no, 0, SEEK_SET) != 0) {
ERROR();
}
templatefilename[file_len] = 0;
/* allocate stuff */
file_len = strlen(outputfilename);
qseq_comp = malloc(sizeof(CompDNA));
qseq_r_comp = malloc(sizeof(CompDNA));
if(!qseq_comp || !qseq_r_comp) {
ERROR();
}
delta = 1024;
allocComp(qseq_comp, delta);
allocComp(qseq_r_comp, delta);
qseq = setQseqs(delta);