/* The MIT License

Copyright (c) 2018- Dana-Farber Cancer Institute

2009-2018 Broad Institute, Inc.

2008-2009 Genome Research Ltd. (GRL)

Permission is hereby granted, free of charge, to any person obtaining

a copy of this software and associated documentation files (the

"Software"), to deal in the Software without restriction, including

without limitation the rights to use, copy, modify, merge, publish,

distribute, sublicense, and/or sell copies of the Software, and to

permit persons to whom the Software is furnished to do so, subject to

the following conditions:

The above copyright notice and this permission notice shall be

included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS

BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN

ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN

CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.

*/

#include <string.h>

#include <stdio.h>

#include <zlib.h>

#include <assert.h>

#include "bntseq.h"

#include "bwa.h"

#include "ksw.h"

#include "utils.h"

#include "kstring.h"

#include "kvec.h"

#ifdef USE_MALLOC_WRAPPERS

# include "malloc_wrap.h"

#endif

int bwa_verbose = 3;

int bwa_dbg = 0;

char bwa_rg_id[256];

char *bwa_pg;

/************************

* Batch FASTA/Q reader *

************************/

#include "kseq.h"

KSEQ_DECLARE(gzFile)

static inline void trim_readno(kstring_t *s)

{

if (s->l > 2 && s->s[s->l-2] == '/' && isdigit(s->s[s->l-1]))

s->l -= 2, s->s[s->l] = 0;

}

static inline char *dupkstring(const kstring_t *str, int dupempty)

{

char *s = (str->l > 0 || dupempty)? malloc(str->l + 1) : NULL;

if (!s) return NULL;

memcpy(s, str->s, str->l);

s[str->l] = '\0';

return s;

}

static inline void kseq2bseq1(const kseq_t *ks, bseq1_t *s)

{ // TODO: it would be better to allocate one chunk of memory, but probably it does not matter in practice

s->name = dupkstring(&ks->name, 1);

s->comment = dupkstring(&ks->comment, 0);

s->seq = dupkstring(&ks->seq, 1);

s->qual = dupkstring(&ks->qual, 0);

s->l_seq = ks->seq.l;

}

bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)

{

kseq_t *ks = (kseq_t*)ks1_, *ks2 = (kseq_t*)ks2_;

int size = 0, m, n;

bseq1_t *seqs;

m = n = 0; seqs = 0;

while (kseq_read(ks) >= 0) {

if (ks2 && kseq_read(ks2) < 0) { // the 2nd file has fewer reads

fprintf(stderr, "[W::%s] the 2nd file has fewer sequences.\n", __func__);

break;

}

if (n >= m) {

m = m? m<<1 : 256;

seqs = realloc(seqs, m * sizeof(bseq1_t));

}

trim_readno(&ks->name);

kseq2bseq1(ks, &seqs[n]);

seqs[n].id = n;

size += seqs[n++].l_seq;

if (ks2) {

trim_readno(&ks2->name);

kseq2bseq1(ks2, &seqs[n]);

seqs[n].id = n;

size += seqs[n++].l_seq;

}

if (size >= chunk_size && (n&1) == 0) break;

}

if (size == 0) { // test if the 2nd file is finished

if (ks2 && kseq_read(ks2) >= 0)

fprintf(stderr, "[W::%s] the 1st file has fewer sequences.\n", __func__);

}

*n_ = n;

return seqs;

}

void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2])

{

int i, has_last;

kvec_t(bseq1_t) a[2] = {{0,0,0}, {0,0,0}};

for (i = 1, has_last = 1; i < n; ++i) {

if (has_last) {

if (strcmp(seqs[i].name, seqs[i-1].name) == 0) {

kv_push(bseq1_t, a[1], seqs[i-1]);

kv_push(bseq1_t, a[1], seqs[i]);

has_last = 0;

} else kv_push(bseq1_t, a[0], seqs[i-1]);

} else has_last = 1;

}

if (has_last) kv_push(bseq1_t, a[0], seqs[i-1]);

sep[0] = a[0].a, m[0] = a[0].n;

sep[1] = a[1].a, m[1] = a[1].n;

}

/*****************

* CIGAR related *

*****************/

void bwa_fill_scmat(int a, int b, int8_t mat[25])

{

int i, j, k;

for (i = k = 0; i < 4; ++i) {

for (j = 0; j < 4; ++j)

mat[k++] = i == j? a : -b;

mat[k++] = -1; // ambiguous base

}

for (j = 0; j < 5; ++j) mat[k++] = -1;

}

// Generate CIGAR when the alignment end points are known

uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)

{

uint32_t *cigar = 0;

uint8_t tmp, *rseq;

int i;

int64_t rlen;

kstring_t str;

const char *int2base;

if (n_cigar) *n_cigar = 0;

if (NM) *NM = -1;

if (l_query <= 0 || rb >= re || (rb < l_pac && re > l_pac)) return 0; // reject if negative length or bridging the forward and reverse strand

rseq = bns_get_seq(l_pac, pac, rb, re, &rlen);

if (re - rb != rlen) goto ret_gen_cigar; // possible if out of range

if (rb >= l_pac) { // then reverse both query and rseq; this is to ensure indels to be placed at the leftmost position

for (i = 0; i < l_query>>1; ++i)

tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;

for (i = 0; i < rlen>>1; ++i)

tmp = rseq[i], rseq[i] = rseq[rlen - 1 - i], rseq[rlen - 1 - i] = tmp;

}

if (l_query == re - rb && w_ == 0) { // no gap; no need to do DP

// UPDATE: we come to this block now... FIXME: due to an issue in mem_reg2aln(), we never come to this block. This does not affect accuracy, but it hurts performance.

if (n_cigar) {

cigar = malloc(4);

cigar[0] = l_query<<4 | 0;

*n_cigar = 1;

}

for (i = 0, *score = 0; i < l_query; ++i)

*score += mat[rseq[i]*5 + query[i]];

} else {

int w, max_gap, max_ins, max_del, min_w;

// set the band-width

max_ins = (int)((double)(((l_query+1)>>1) * mat[0] - o_ins) / e_ins + 1.);

max_del = (int)((double)(((l_query+1)>>1) * mat[0] - o_del) / e_del + 1.);

max_gap = max_ins > max_del? max_ins : max_del;

max_gap = max_gap > 1? max_gap : 1;

w = (max_gap + abs((int)rlen - l_query) + 1) >> 1;

w = w < w_? w : w_;

min_w = abs((int)rlen - l_query) + 3;

w = w > min_w? w : min_w;

// NW alignment

if (bwa_verbose >= 4) {

printf("* Global bandwidth: %d\n", w);

printf("* Global ref: "); for (i = 0; i < rlen; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');

printf("* Global query: "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');

}

*score = ksw_global2(l_query, query, rlen, rseq, 5, mat, o_del, e_del, o_ins, e_ins, w, n_cigar, &cigar);

}

if (NM && n_cigar) {// compute NM and MD

int k, x, y, u, n_mm = 0, n_gap = 0;

str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR

int2base = rb < l_pac? "ACGTN" : "TGCAN";

for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {

int op, len;

cigar = (uint32_t*)str.s;

op = cigar[k]&0xf, len = cigar[k]>>4;

if (op == 0) { // match

for (i = 0; i < len; ++i) {

if (query[x + i] != rseq[y + i]) {

kputw(u, &str);

kputc(int2base[rseq[y+i]], &str);

++n_mm; u = 0;

} else ++u;

}

x += len; y += len;

} else if (op == 2) { // deletion

if (k > 0 && k < *n_cigar - 1) { // don't do the following if D is the first or the last CIGAR

kputw(u, &str); kputc('^', &str);

for (i = 0; i < len; ++i)

kputc(int2base[rseq[y+i]], &str);

u = 0; n_gap += len;

}

y += len;

} else if (op == 1) x += len, n_gap += len; // insertion

}

kputw(u, &str); kputc(0, &str);

*NM = n_mm + n_gap;

cigar = (uint32_t*)str.s;

}

if (rb >= l_pac) // reverse back query

for (i = 0; i < l_query>>1; ++i)

tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;

ret_gen_cigar:

free(rseq);

return cigar;

}

uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)

{

return bwa_gen_cigar2(mat, q, r, q, r, w_, l_pac, pac, l_query, query, rb, re, score, n_cigar, NM);

}

/*********************

* Full index reader *

*********************/

char *bwa_idx_infer_prefix(const char *hint)

{

char *prefix;

int l_hint;

FILE *fp;

l_hint = strlen(hint);

prefix = malloc(l_hint + 3 + 4 + 1);

strcpy(prefix, hint);

strcpy(prefix + l_hint, ".64.bwt");

if ((fp = fopen(prefix, "rb")) != 0) {

fclose(fp);

prefix[l_hint + 3] = 0;

return prefix;

} else {

strcpy(prefix + l_hint, ".bwt");

if ((fp = fopen(prefix, "rb")) == 0) {

free(prefix);

return 0;

} else {

fclose(fp);

prefix[l_hint] = 0;

return prefix;

}

}

}

bwt_t *bwa_idx_load_bwt(const char *hint)

{

char *tmp, *prefix;

bwt_t *bwt;

prefix = bwa_idx_infer_prefix(hint);

if (prefix == 0) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);

return 0;

}

tmp = calloc(strlen(prefix) + 5, 1);

strcat(strcpy(tmp, prefix), ".bwt"); // FM-index

bwt = bwt_restore_bwt(tmp);

strcat(strcpy(tmp, prefix), ".sa"); // partial suffix array (SA)

bwt_restore_sa(tmp, bwt);

free(tmp); free(prefix);

return bwt;

}

bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which)

{

bwaidx_t *idx;

char *prefix;

prefix = bwa_idx_infer_prefix(hint);

if (prefix == 0) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);

return 0;

}

idx = calloc(1, sizeof(bwaidx_t));

if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);

if (which & BWA_IDX_BNS) {

int i, c;

idx->bns = bns_restore(prefix);

for (i = c = 0; i < idx->bns->n_seqs; ++i)

if (idx->bns->anns[i].is_alt) ++c;

if (bwa_verbose >= 3)

fprintf(stderr, "[M::%s] read %d ALT contigs\n", __func__, c);

if (which & BWA_IDX_PAC) {

idx->pac = calloc(idx->bns->l_pac/4+1, 1);

err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence

err_fclose(idx->bns->fp_pac);

idx->bns->fp_pac = 0;

}

}

free(prefix);

return idx;

}

bwaidx_t *bwa_idx_load(const char *hint, int which)

{

return bwa_idx_load_from_disk(hint, which);

}

void bwa_idx_destroy(bwaidx_t *idx)

{

if (idx == 0) return;

if (idx->mem == 0) {

if (idx->bwt) bwt_destroy(idx->bwt);

if (idx->bns) bns_destroy(idx->bns);

if (idx->pac) free(idx->pac);

} else {

free(idx->bwt); free(idx->bns->anns); free(idx->bns);

if (!idx->is_shm) free(idx->mem);

}

free(idx);

}

int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)

{

int64_t k = 0, x;

int i;

// generate idx->bwt

x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;

x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;

x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;

// generate idx->bns and idx->pac

x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;

x = idx->bns->n_holes * sizeof(bntamb1_t); idx->bns->ambs = (bntamb1_t*)(mem + k); k += x;

x = idx->bns->n_seqs * sizeof(bntann1_t); idx->bns->anns = malloc(x); memcpy(idx->bns->anns, mem + k, x); k += x;

for (i = 0; i < idx->bns->n_seqs; ++i) {

idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;

idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;

}

idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;

assert(k == l_mem);

idx->l_mem = k; idx->mem = mem;

return 0;

}

int bwa_idx2mem(bwaidx_t *idx)

{

int i;

int64_t k, x, tmp;

uint8_t *mem;

// copy idx->bwt

x = idx->bwt->bwt_size * 4;

mem = realloc(idx->bwt->bwt, sizeof(bwt_t) + x); idx->bwt->bwt = 0;

memmove(mem + sizeof(bwt_t), mem, x);

memcpy(mem, idx->bwt, sizeof(bwt_t)); k = sizeof(bwt_t) + x;

x = idx->bwt->n_sa * sizeof(bwtint_t); mem = realloc(mem, k + x); memcpy(mem + k, idx->bwt->sa, x); k += x;

free(idx->bwt->sa);

free(idx->bwt); idx->bwt = 0;

// copy idx->bns

tmp = idx->bns->n_seqs * sizeof(bntann1_t) + idx->bns->n_holes * sizeof(bntamb1_t);

for (i = 0; i < idx->bns->n_seqs; ++i) // compute the size of heap-allocated memory

tmp += strlen(idx->bns->anns[i].name) + strlen(idx->bns->anns[i].anno) + 2;

mem = realloc(mem, k + sizeof(bntseq_t) + tmp);

x = sizeof(bntseq_t); memcpy(mem + k, idx->bns, x); k += x;

x = idx->bns->n_holes * sizeof(bntamb1_t); memcpy(mem + k, idx->bns->ambs, x); k += x;

free(idx->bns->ambs);

x = idx->bns->n_seqs * sizeof(bntann1_t); memcpy(mem + k, idx->bns->anns, x); k += x;

for (i = 0; i < idx->bns->n_seqs; ++i) {

x = strlen(idx->bns->anns[i].name) + 1; memcpy(mem + k, idx->bns->anns[i].name, x); k += x;

x = strlen(idx->bns->anns[i].anno) + 1; memcpy(mem + k, idx->bns->anns[i].anno, x); k += x;

free(idx->bns->anns[i].name); free(idx->bns->anns[i].anno);

}

free(idx->bns->anns);

// copy idx->pac

x = idx->bns->l_pac/4+1;

mem = realloc(mem, k + x);

memcpy(mem + k, idx->pac, x); k += x;

free(idx->bns); idx->bns = 0;

free(idx->pac); idx->pac = 0;

return bwa_mem2idx(k, mem, idx);

}

/***********************

* SAM header routines *

***********************/

void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)

{

int i, n_HD = 0, n_SQ = 0;

extern char *bwa_pg;

if (hdr_line) {

// check for HD line

const char *p = hdr_line;

if ((p = strstr(p, "@HD")) != 0) {

++n_HD;

}

// check for SQ lines

p = hdr_line;

while ((p = strstr(p, "@SQ\t")) != 0) {

if (p == hdr_line || *(p-1) == '\n') ++n_SQ;

p += 4;

}

}

if (n_SQ == 0) {

for (i = 0; i < bns->n_seqs; ++i) {

err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);

if (bns->anns[i].is_alt) err_printf("\tAH:*\n");

else err_fputc('\n', stdout);

}

} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)

fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);

if (n_HD == 0) {

err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");

}

if (hdr_line) err_printf("%s\n", hdr_line);

if (bwa_pg) err_printf("%s\n", bwa_pg);

}

static char *bwa_escape(char *s)

{

char *p, *q;

for (p = q = s; *p; ++p) {

if (*p == '\\') {

++p;

if (*p == 't') *q++ = '\t';

else if (*p == 'n') *q++ = '\n';

else if (*p == 'r') *q++ = '\r';

else if (*p == '\\') *q++ = '\\';

} else *q++ = *p;

}

*q = '\0';

return s;

}

char *bwa_set_rg(const char *s)

{

char *p, *q, *r, *rg_line = 0;

memset(bwa_rg_id, 0, 256);

if (strstr(s, "@RG") != s) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);

goto err_set_rg;

}

if (strstr(s, "\t") != NULL) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);

goto err_set_rg;

}

rg_line = strdup(s);

bwa_escape(rg_line);

if ((p = strstr(rg_line, "\tID:")) == 0) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);

goto err_set_rg;

}

p += 4;

for (q = p; *q && *q != '\t' && *q != '\n'; ++q);

if (q - p + 1 > 256) {

if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);

goto err_set_rg;

}

for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)

*r++ = *q;

return rg_line;

err_set_rg:

free(rg_line);

return 0;

}

char *bwa_insert_header(const char *s, char *hdr)

{

int len = 0;

if (s == 0 || s[0] != '@') return hdr;

if (hdr) {

len = strlen(hdr);

hdr = realloc(hdr, len + strlen(s) + 2);

hdr[len++] = '\n';

strcpy(hdr + len, s);

} else hdr = strdup(s);

bwa_escape(hdr + len);

return hdr;

}