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/* Philip T.L.C. Clausen Jan 2017 plan@dtu.dk */
/*
* 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 <math.h>
#include <stdio.h>
#include <time.h>
#include "assembly.h"
#include "ef.h"
#include "stdnuc.h"
#include "threader.h"
#include "vcf.h"
#include "version.h"
void initExtendedFeatures(FILE *out, char *templatefilename, unsigned totFrags, char *cmd) {
char Date[11];
time_t t1;
struct tm *tm;
fprintf(out, "## method\tKMA\n");
fprintf(out, "## version\t%s\n", KMA_VERSION);
fprintf(out, "## database\t%s\n", noFolder(templatefilename));
fprintf(out, "## fragmentCount\t%u\n", totFrags);
time(&t1);
tm = localtime(&t1);
strftime(Date, sizeof(Date), "%Y-%m-%d", tm);
fprintf(out, "## date\t%s\n", Date);
fprintf(out, "## command\t%s\n", cmd);
fprintf(out, "# refSequence\treadCount\tfragmentCount\tmapScoreSum\trefCoveredPositions\trefConsensusSum\tbpTotal\tdepthVariance\tnucHighDepthVariance\tdepthMax\tsnpSum\tinsertSum\tdeletionSum\treadCountAln\tfragmentCountAln\n");
}
void getExtendedFeatures(Assem *aligned_assem, AssemInfo *matrix, long unsigned *seq, int t_len, int thread_num) {
static volatile int Lock = 0, next, thread_wait = 0;
volatile int *excludeMatrix = &Lock;
unsigned pos, end, asm_len, chunk, nucHighVar, maxDepth, depthUpdate;
long unsigned snpSum, insertSum, deletionSum;
double highVar;
Assembly *assembly;
/* init */
asm_len = matrix->len;
assembly = matrix->assmb;
maxDepth = 0;
nucHighVar = 0;
snpSum = 0;
insertSum = 0;
deletionSum = 0;
highVar = (long double)(aligned_assem->depth) / t_len + 3 * sqrt(aligned_assem->var);
chunk = 8112;
lock(excludeMatrix);
if(!thread_wait) {
next = 0;
thread_wait = thread_num;
aligned_assem->fragmentCountAln = (((aligned_assem->readCountAln >> 1) + (aligned_assem->readCountAln & 1)) <= aligned_assem->fragmentCountAln) ? (aligned_assem->fragmentCountAln) : ((aligned_assem->readCountAln >> 1) + (aligned_assem->readCountAln & 1));
}
unlock(excludeMatrix);
/* get nucHighVar */
while(chunk) {
lock(excludeMatrix);
pos = next;
if((next += chunk) < 0) {
next = asm_len;
}
unlock(excludeMatrix);
/* call chunk */
if(pos < asm_len) {
end = pos + chunk;
if(asm_len < end) {
end = asm_len;
chunk = 0;
}
while(pos < end) {
depthUpdate = assembly[pos].counts[0] + assembly[pos].counts[1] + assembly[pos].counts[2] + assembly[pos].counts[3] + assembly[pos].counts[4];
if(pos < t_len) {
deletionSum += assembly[pos].counts[5];
snpSum += (depthUpdate - assembly[pos].counts[getNuc(seq, pos)]);
} else {
insertSum += depthUpdate;
}
depthUpdate += assembly[pos].counts[5];
if(maxDepth < depthUpdate) {
maxDepth = depthUpdate;
}
if(highVar < depthUpdate) {
++nucHighVar;
}
++pos;
}
} else {
chunk = 0;
}
}
lock(excludeMatrix);
aligned_assem->nucHighVar += nucHighVar;
if(aligned_assem->maxDepth < maxDepth) {
aligned_assem->maxDepth = maxDepth;
}
aligned_assem->snpSum += snpSum;
aligned_assem->insertSum += insertSum;
aligned_assem->deletionSum += deletionSum;
--thread_wait;
unlock(excludeMatrix);
wait_atomic(thread_wait);
}
void printExtendedFeatures(char *template_name, Assem *aligned_assem, unsigned fragmentCount, unsigned readCount, FILE *outfile) {
if(aligned_assem) {
fprintf(outfile, "%s\t%u\t%u\t%lu\t%u\t%u\t%lu\t%f\t%u\t%u\t%lu\t%lu\t%lu\t%u\t%u\n", template_name, readCount, fragmentCount, aligned_assem->score, aligned_assem->aln_len, aligned_assem->cover, aligned_assem->depth, aligned_assem->var, aligned_assem->nucHighVar, aligned_assem->maxDepth, aligned_assem->snpSum, aligned_assem->insertSum, aligned_assem->deletionSum, aligned_assem->readCountAln, aligned_assem->fragmentCountAln);
} else {
fprintf(outfile, "%s\t%u\t%u\t%u\t%u\t%u\t%u\t%f\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", template_name, 0, 0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0, 0, 0);
}
}
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