/
main.c
459 lines (437 loc) · 17 KB
/
main.c
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/* main.c
* Created by Mengyao Zhao on 06/23/11.
* Version 0.1.5
* Last revision by Mengyao Zhao on 06/27/14.
*/
#include <stdlib.h>
#include <stdint.h>
#include <emmintrin.h>
#include <zlib.h>
#include <stdio.h>
#include <time.h>
#include <string.h>
#include <math.h>
#include <unistd.h>
#include "ssw.h"
#include "kseq.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1)
#define UNLIKELY(x) __builtin_expect((x),0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif
/*! @function
@abstract Round an integer to the next closest power-2 integer.
@param x integer to be rounded (in place)
@discussion x will be modified.
*/
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
KSEQ_INIT(gzFile, gzread)
static void reverse_comple(const char* seq, char* rc) {
int32_t end = strlen(seq), start = 0;
static const int8_t rc_table[128] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 84, 4, 71, 4, 4, 4, 67, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 65, 65, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 84, 4, 71, 4, 4, 4, 67, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 65, 65, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
rc[end] = '\0';
-- end;
while (LIKELY(start < end)) {
rc[start] = (char)rc_table[(int8_t)seq[end]];
rc[end] = (char)rc_table[(int8_t)seq[start]];
++ start;
-- end;
}
if (start == end) rc[start] = (char)rc_table[(int8_t)seq[start]];
}
static void ssw_write (const s_align* a,
const kseq_t* ref_seq,
const kseq_t* read,
const char* read_seq, // strand == 0: original read; strand == 1: reverse complement read
const int8_t* table,
int8_t strand, // 0: forward aligned ; 1: reverse complement aligned
int8_t sam) { // 0: Blast like output; 1: Sam format output
if (sam == 0) { // Blast like output
fprintf(stdout, "target_name: %s\nquery_name: %s\noptimal_alignment_score: %d\t", ref_seq->name.s, read->name.s, a->score1);
if (a->score2 > 0) fprintf(stdout, "suboptimal_alignment_score: %d\t", a->score2);
if (strand == 0) fprintf(stdout, "strand: +\t");
else fprintf(stdout, "strand: -\t");
if (a->ref_begin1 + 1) fprintf(stdout, "target_begin: %d\t", a->ref_begin1 + 1);
fprintf(stdout, "target_end: %d\t", a->ref_end1 + 1);
if (a->read_begin1 + 1) fprintf(stdout, "query_begin: %d\t", a->read_begin1 + 1);
fprintf(stdout, "query_end: %d\n\n", a->read_end1 + 1);
if (a->cigar) {
int32_t c = 0, left = 0, e = 0, qb = a->ref_begin1, pb = a->read_begin1;
uint32_t i;
while (e < a->cigarLen || left > 0) {
int32_t count = 0;
int32_t q = qb;
int32_t p = pb;
fprintf(stdout, "Target: %8d ", q + 1);
for (c = e; c < a->cigarLen; ++c) {
char letter = cigar_int_to_op(a->cigar[c]);
uint32_t length = cigar_int_to_len(a->cigar[c]);
uint32_t l = (count == 0 && left > 0) ? left: length;
for (i = 0; i < l; ++i) {
if (letter == 'I') fprintf(stdout, "-");
else {
fprintf(stdout, "%c", *(ref_seq->seq.s + q));
++ q;
}
++ count;
if (count == 60) goto step2;
}
}
step2:
fprintf(stdout, " %d\n ", q);
q = qb;
count = 0;
for (c = e; c < a->cigarLen; ++c) {
char letter = cigar_int_to_op(a->cigar[c]);
uint32_t length = cigar_int_to_len(a->cigar[c]);
uint32_t l = (count == 0 && left > 0) ? left: length;
for (i = 0; i < l; ++i){
if (letter == 'M') {
if (table[(int)*(ref_seq->seq.s + q)] == table[(int)*(read_seq + p)])fprintf(stdout, "|");
else fprintf(stdout, "*");
++q;
++p;
} else {
fprintf(stdout, " ");
if (letter == 'I') ++p;
else ++q;
}
++ count;
if (count == 60) {
qb = q;
goto step3;
}
}
}
step3:
p = pb;
fprintf(stdout, "\nQuery: %8d ", p + 1);
count = 0;
for (c = e; c < a->cigarLen; ++c) {
char letter = cigar_int_to_op(a->cigar[c]);
uint32_t length = cigar_int_to_len(a->cigar[c]);
uint32_t l = (count == 0 && left > 0) ? left: length;
for (i = 0; i < l; ++i) {
if (letter == 'D') fprintf(stdout, "-");
else {
fprintf(stdout, "%c", *(read_seq + p));
++p;
}
++ count;
if (count == 60) {
pb = p;
left = l - i - 1;
e = (left == 0) ? (c + 1) : c;
goto end;
}
}
}
e = c;
left = 0;
end:
fprintf(stdout, " %d\n\n", p);
}
}
}else { // Sam format output
fprintf(stdout, "%s\t", read->name.s);
if (a->score1 == 0) fprintf(stdout, "4\t*\t0\t255\t*\t*\t0\t0\t*\t*\n");
else {
int32_t c, l = a->read_end1 - a->read_begin1 + 1, qb = a->ref_begin1, pb = a->read_begin1, p;
uint32_t mapq = -4.343 * log(1 - (double)abs(a->score1 - a->score2)/(double)a->score1);
mapq = (uint32_t) (mapq + 4.99);
mapq = mapq < 254 ? mapq : 254;
if (strand) fprintf(stdout, "16\t");
else fprintf(stdout, "0\t");
fprintf(stdout, "%s\t%d\t%d\t", ref_seq->name.s, a->ref_begin1 + 1, mapq);
for (c = 0; c < a->cigarLen; ++c) {
char letter = cigar_int_to_op(a->cigar[c]);
uint32_t length = cigar_int_to_len(a->cigar[c]);
fprintf(stdout, "%lu%c", (unsigned long)length, letter);
}
fprintf(stdout, "\t*\t0\t0\t");
for (c = a->read_begin1; c <= a->read_end1; ++c) fprintf(stdout, "%c", read_seq[c]);
fprintf(stdout, "\t");
if (read->qual.s && strand) {
p = a->read_end1;
for (c = 0; c < l; ++c) {
fprintf(stdout, "%c", read->qual.s[p]);
--p;
}
}else if (read->qual.s){
p = a->read_begin1;
for (c = 0; c < l; ++c) {
fprintf(stdout, "%c", read->qual.s[p]);
++p;
}
} else fprintf(stdout, "*");
fprintf(stdout, "\tAS:i:%d", a->score1);
mapq = 0; // counter of difference
for (c = 0; c < a->cigarLen; ++c) {
char letter = cigar_int_to_op(a->cigar[c]);
uint32_t length = cigar_int_to_len(a->cigar[c]);
if (letter == 'M') {
for (p = 0; p < length; ++p){
if (table[(int)*(ref_seq->seq.s + qb)] != table[(int)*(read_seq + pb)]) ++mapq;
++qb;
++pb;
}
} else if (letter == 'I') {
pb += length;
mapq += length;
} else {
qb += length;
mapq += length;
}
}
fprintf(stdout,"\tNM:i:%d\t", mapq);
if (a->score2 > 0) fprintf(stdout, "ZS:i:%d\n", a->score2);
else fprintf(stdout, "\n");
}
}
}
int main (int argc, char * const argv[]) {
clock_t start, end;
float cpu_time;
gzFile read_fp, ref_fp;
kseq_t *read_seq, *ref_seq;
int32_t l, m, k, match = 2, mismatch = 2, gap_open = 3, gap_extension = 1, path = 0, reverse = 0, n = 5, sam = 0, protein = 0, header = 0, s1 = 67108864, s2 = 128, filter = 0;
int8_t* mata = (int8_t*)calloc(25, sizeof(int8_t));
const int8_t* mat = mata;
char mat_name[16];
mat_name[0] = '\0';
int8_t* ref_num = (int8_t*)malloc(s1);
int8_t* num = (int8_t*)malloc(s2), *num_rc = 0;
char* read_rc = 0;
static const int8_t mat50[] = {
// A R N D C Q E G H I L K M F P S T W Y V B Z X *
5, -2, -1, -2, -1, -1, -1, 0, -2, -1, -2, -1, -1, -3, -1, 1, 0, -3, -2, 0, -2, -1, -1, -5, // A
-2, 7, -1, -2, -4, 1, 0, -3, 0, -4, -3, 3, -2, -3, -3, -1, -1, -3, -1, -3, -1, 0, -1, -5, // R
-1, -1, 7, 2, -2, 0, 0, 0, 1, -3, -4, 0, -2, -4, -2, 1, 0, -4, -2, -3, 5, 0, -1, -5, // N
-2, -2, 2, 8, -4, 0, 2, -1, -1, -4, -4, -1, -4, -5, -1, 0, -1, -5, -3, -4, 6, 1, -1, -5, // D
-1, -4, -2, -4, 13, -3, -3, -3, -3, -2, -2, -3, -2, -2, -4, -1, -1, -5, -3, -1, -3, -3, -1, -5, // C
-1, 1, 0, 0, -3, 7, 2, -2, 1, -3, -2, 2, 0, -4, -1, 0, -1, -1, -1, -3, 0, 4, -1, -5, // Q
-1, 0, 0, 2, -3, 2, 6, -3, 0, -4, -3, 1, -2, -3, -1, -1, -1, -3, -2, -3, 1, 5, -1, -5, // E
0, -3, 0, -1, -3, -2, -3, 8, -2, -4, -4, -2, -3, -4, -2, 0, -2, -3, -3, -4, -1, -2, -1, -5, // G
-2, 0, 1, -1, -3, 1, 0, -2, 10, -4, -3, 0, -1, -1, -2, -1, -2, -3, 2, -4, 0, 0, -1, -5, // H
-1, -4, -3, -4, -2, -3, -4, -4, -4, 5, 2, -3, 2, 0, -3, -3, -1, -3, -1, 4, -4, -3, -1, -5, // I
-2, -3, -4, -4, -2, -2, -3, -4, -3, 2, 5, -3, 3, 1, -4, -3, -1, -2, -1, 1, -4, -3, -1, -5, // L
-1, 3, 0, -1, -3, 2, 1, -2, 0, -3, -3, 6, -2, -4, -1, 0, -1, -3, -2, -3, 0, 1, -1, -5, // K
-1, -2, -2, -4, -2, 0, -2, -3, -1, 2, 3, -2, 7, 0, -3, -2, -1, -1, 0, 1, -3, -1, -1, -5, // M
-3, -3, -4, -5, -2, -4, -3, -4, -1, 0, 1, -4, 0, 8, -4, -3, -2, 1, 4, -1, -4, -4, -1, -5, // F
-1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -4, -1, -3, -4, 10, -1, -1, -4, -3, -3, -2, -1, -1, -5, // P
1, -1, 1, 0, -1, 0, -1, 0, -1, -3, -3, 0, -2, -3, -1, 5, 2, -4, -2, -2, 0, 0, -1, -5, // S
0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 2, 5, -3, -2, 0, 0, -1, -1, -5, // T
-3, -3, -4, -5, -5, -1, -3, -3, -3, -3, -2, -3, -1, 1, -4, -4, -3, 15, 2, -3, -5, -2, -1, -5, // W
-2, -1, -2, -3, -3, -1, -2, -3, 2, -1, -1, -2, 0, 4, -3, -2, -2, 2, 8, -1, -3, -2, -1, -5, // Y
0, -3, -3, -4, -1, -3, -3, -4, -4, 4, 1, -3, 1, -1, -3, -2, 0, -3, -1, 5, -3, -3, -1, -5, // V
-2, -1, 5, 6, -3, 0, 1, -1, 0, -4, -4, 0, -3, -4, -2, 0, 0, -5, -3, -3, 6, 1, -1, -5, // B
-1, 0, 0, 1, -3, 4, 5, -2, 0, -3, -3, 1, -1, -4, -1, 0, -1, -2, -2, -3, 1, 5, -1, -5, // Z
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -5, // X
-5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, 1 // *
};
/* This table is used to transform amino acid letters into numbers. */
int8_t aa_table[128] = {
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
23, 0, 20, 4, 3, 6, 13, 7, 8, 9, 23, 11, 10, 12, 2, 23,
14, 5, 1, 15, 16, 23, 19, 17, 22, 18, 21, 23, 23, 23, 23, 23,
23, 0, 20, 4, 3, 6, 13, 7, 8, 9, 23, 11, 10, 12, 2, 23,
14, 5, 1, 15, 16, 23, 19, 17, 22, 18, 21, 23, 23, 23, 23, 23
};
/* This table is used to transform nucleotide letters into numbers. */
int8_t nt_table[128] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
int8_t* table = nt_table;
// Parse command line.
while ((l = getopt(argc, argv, "m:x:o:e:a:f:pcrsh")) >= 0) {
switch (l) {
case 'm': match = atoi(optarg); break;
case 'x': mismatch = atoi(optarg); break;
case 'o': gap_open = atoi(optarg); break;
case 'e': gap_extension = atoi(optarg); break;
case 'a': strcpy(mat_name, optarg); break;
case 'f': filter = atoi(optarg); break;
case 'p': protein = 1; break;
case 'c': path = 1; break;
case 'r': reverse = 1; break;
case 's': sam = 1; break;
case 'h': header = 1; break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: ssw_test [options] ... <target.fasta> <query.fasta>(or <query.fastq>)\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, "\t-m N\tN is a positive integer for weight match in genome sequence alignment. [default: 2]\n");
fprintf(stderr, "\t-x N\tN is a positive integer. -N will be used as weight mismatch in genome sequence alignment. [default: 2]\n");
fprintf(stderr, "\t-o N\tN is a positive integer. -N will be used as the weight for the gap opening. [default: 3]\n");
fprintf(stderr, "\t-e N\tN is a positive integer. -N will be used as the weight for the gap extension. [default: 1]\n");
fprintf(stderr, "\t-p\tDo protein sequence alignment. Without this option, the ssw_test will do genome sequence alignment.\n");
fprintf(stderr, "\t-a FILE\tFILE is either the Blosum or Pam weight matrix. [default: Blosum50]\n");
fprintf(stderr, "\t-c\tReturn the alignment path.\n");
fprintf(stderr, "\t-f N\tN is a positive integer. Only output the alignments with the Smith-Waterman score >= N.\n");
fprintf(stderr, "\t-r\tThe best alignment will be picked between the original read alignment and the reverse complement read alignment.\n");
fprintf(stderr, "\t-s\tOutput in SAM format. [default: no header]\n");
fprintf(stderr, "\t-h\tIf -s is used, include header in SAM output.\n\n");
return 1;
}
// initialize scoring matrix for genome sequences
for (l = k = 0; LIKELY(l < 4); ++l) {
for (m = 0; LIKELY(m < 4); ++m) mata[k++] = l == m ? match : -mismatch; /* weight_match : -weight_mismatch */
mata[k++] = 0; // ambiguous base
}
for (m = 0; LIKELY(m < 5); ++m) mata[k++] = 0;
if (protein == 1 && (! strcmp(mat_name, "\0"))) {
n = 24;
table = aa_table;
mat = mat50;
} else if (strcmp(mat_name, "\0")) {
// Parse score matrix.
FILE *f_mat = fopen(mat_name, "r");
char line[128];
mata = (int8_t*)realloc(mata, 1024 * sizeof(int8_t));
k = 0;
m = 0;
while (fgets(line, 128, f_mat)) {
if (line[0] == '*' || (line[0] >= 'A' && line[0] <= 'Z')) {
if (line[0] >= 'A' && line[0] <= 'Z') aa_table[(int)line[0]] = aa_table[(int)line[0] + 32] = m;
char str[4], *s = str;
str[0] = '\0';
l = 1;
while (line[l]) {
if ((line[l] >= '0' && line[l] <= '9') || line[l] == '-') *s++ = line[l];
else if (str[0] != '\0') {
*s = '\0';
mata[k++] = (int8_t)atoi(str);
s = str;
str[0] = '\0';
}
++l;
}
if (str[0] != '\0') {
*s = '\0';
mata[k++] = (int8_t)atoi(str);
s = str;
str[0] = '\0';
}
++m;
}
}
if (k == 0) {
fprintf(stderr, "Problem of reading the weight matrix file.\n");
return 1;
}
fclose(f_mat);
n = m;
table = aa_table;
mat = mata;
}
read_fp = gzopen(argv[optind + 1], "r");
read_seq = kseq_init(read_fp);
if (sam && header && path) {
fprintf(stdout, "@HD\tVN:1.4\tSO:queryname\n");
ref_fp = gzopen(argv[optind], "r");
ref_seq = kseq_init(ref_fp);
while ((l = kseq_read(ref_seq)) >= 0) fprintf(stdout, "@SQ\tSN:%s\tLN:%d\n", ref_seq->name.s, (int32_t)ref_seq->seq.l);
kseq_destroy(ref_seq);
gzclose(ref_fp);
} else if (sam && !path) {
fprintf(stderr, "SAM format output is only available together with option -c.\n");
sam = 0;
}
// alignment
if (reverse == 1 && n == 5) {
read_rc = (char*)malloc(s2);
num_rc = (int8_t*)malloc(s2);
}
start = clock();
while (kseq_read(read_seq) >= 0) {
s_profile* p, *p_rc = 0;
int32_t readLen = read_seq->seq.l;
int32_t maskLen = readLen / 2;
// int32_t maskLen = 2*readLen;
while (readLen >= s2) {
++s2;
kroundup32(s2);
num = (int8_t*)realloc(num, s2);
if (reverse == 1 && n == 5) {
read_rc = (char*)realloc(read_rc, s2);
num_rc = (int8_t*)realloc(num_rc, s2);
}
}
for (m = 0; m < readLen; ++m) num[m] = table[(int)read_seq->seq.s[m]];
p = ssw_init(num, readLen, mat, n, 2);
if (reverse == 1 && n == 5) {
reverse_comple(read_seq->seq.s, read_rc);
for (m = 0; m < readLen; ++m) num_rc[m] = table[(int)read_rc[m]];
p_rc = ssw_init(num_rc, readLen, mat, n, 2);
}else if (reverse == 1 && n == 24) {
fprintf (stderr, "Reverse complement alignment is not available for protein sequences. \n");
return 1;
}
ref_fp = gzopen(argv[optind], "r");
ref_seq = kseq_init(ref_fp);
while (kseq_read(ref_seq) >= 0) {
s_align* result, *result_rc = 0;
int32_t refLen = ref_seq->seq.l;
int8_t flag = 0;
while (refLen > s1) {
++s1;
kroundup32(s1);
ref_num = (int8_t*)realloc(ref_num, s1);
}
for (m = 0; m < refLen; ++m) ref_num[m] = table[(int)ref_seq->seq.s[m]];
if (path == 1) flag = 2;
result = ssw_align (p, ref_num, refLen, gap_open, gap_extension, flag, filter, 0, maskLen);
if (reverse == 1 && protein == 0)
result_rc = ssw_align(p_rc, ref_num, refLen, gap_open, gap_extension, flag, filter, 0, maskLen);
if (result_rc && result_rc->score1 > result->score1 && result_rc->score1 >= filter) {
if (sam) ssw_write (result_rc, ref_seq, read_seq, read_rc, table, 1, 1);
else ssw_write (result_rc, ref_seq, read_seq, read_rc, table, 1, 0);
}else if (result && result->score1 >= filter){
if (sam) ssw_write(result, ref_seq, read_seq, read_seq->seq.s, table, 0, 1);
else ssw_write(result, ref_seq, read_seq, read_seq->seq.s, table, 0, 0);
} else if (! result) return 1;
if (result_rc) align_destroy(result_rc);
align_destroy(result);
}
if(p_rc) init_destroy(p_rc);
init_destroy(p);
kseq_destroy(ref_seq);
gzclose(ref_fp);
}
end = clock();
cpu_time = ((float) (end - start)) / CLOCKS_PER_SEC;
fprintf(stderr, "CPU time: %f seconds\n", cpu_time);
if (num_rc) {
free(num_rc);
free(read_rc);
}
kseq_destroy(read_seq);
gzclose(read_fp);
free(num);
free(ref_num);
free(mata);
return 0;
}