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#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include <zlib.h>
#include <unistd.h>
#include "match.hh"
#include "stdhash.hh"
#include "main.h"
#include "bfa.h"
#define HIGHQ 30
#define WINSIZE 1000
template<class TYPE>
static long algo_extend(int size, const TYPE *array, int pos, int *begin, int *end)
{
if (array[pos] < 0) return -1;
long score, ret, max;
int max_pos;
max = score = 0; max_pos = -1;
for (int i = pos; i != size; ++i) {
score += array[i];
if (score > max) {
max = score;
max_pos = i;
}
if (score < 0) break;
}
*end = max_pos + 1; ret = max;
max = score = 0; max_pos = -1;
for (int i = pos; i >= 0; --i) {
score += array[i];
if (score > max) {
max = score;
max_pos = i;
}
if (score < 0) break;
}
*begin = max_pos; ret += max;
return ret - array[pos];
}
static void paircov_mask(short *counter, bit8_t *depth, int seqid, nst_bfa1_t *l, gzFile fp_map)
{
maqmap1_t *m1, mm1;
m1 = &mm1;
while (maqmap_read1(fp_map, m1)) {
if (int(m1->seqid) != seqid) continue;
if (m1->flag == (PAIRFLAG_PAIRED|PAIRFLAG_FR) && m1->dist > 0) { // pair depth
short *begin = counter + (m1->pos>>1);
short *end = begin + m1->dist;
for (short *p = begin; p != end; ++p)
if (*p < 0x7fff) ++(*p);
}
{ // read depth
bit8_t *begin = depth + (m1->pos>>1) - 1;
bit8_t *end = depth + m1->size + (m1->pos>>1);
for (bit8_t *p = begin; p != end; ++p)
if (*p < 0xff) ++(*p);
}
}
}
static int MIN_PAIRCOV = 1;
static int MIN_N_LEN = 250;
static void paircov_core(FILE *fp_bfa, gzFile fp_map)
{
nst_bfa1_t *l;
int seqid = 0, k, i;
hash_map_char<int> *hash_map = new hash_map_char<int>;
maqmap_t *mm = maqmap_read_header(fp_map); // skip the sequence names
for (k = 0; k != mm->n_ref; ++k) hash_map->insert(mm->ref_name[k], k);
k = mm->n_mapped_reads;
l = nst_load_bfa1(fp_bfa);
assert(l);
int ret = hash_map->find(l->name, &seqid);
assert(ret);
short *counter = (short*)calloc(l->ori_len, 2);
bit8_t *depth = (bit8_t*)calloc(l->ori_len, 1);
paircov_mask(counter, depth, seqid, l, fp_map);
// calculate mean
long double mean = 0.0, depth_mean = 0.0;
for (i = 0; i != l->ori_len; ++i) {
mean += counter[i];
depth_mean += depth[i];
}
mean /= l->ori_len; depth_mean /= l->ori_len;
fprintf(stderr, "mean=%Lf,depth_mean=%Lf\n", mean, depth_mean);
for (i = 0, k = -1; i < l->ori_len; ++i) {
int is_N = ((l->mask[i>>5]>>((31-(i&0x1f))<<1))&3)? 0 : 1;
if (is_N) {
int j;
for (j = i; j < l->ori_len; ++j)
if ((l->mask[j>>5]>>((31-(j&0x1f))<<1))&3) break;
if (j - i > MIN_N_LEN) {
if (k >= 0) printf("NN\t%s\t%d\t%d\t%d\n", l->name, k+1, i, i - k);
k = j;
}
i = j - 1;
}
}
// detect absolute break point
for (i = 0; i < l->ori_len; ++i) {
if (counter[i] > MIN_PAIRCOV) {
int j;
for (j = i; j < l->ori_len; ++j)
if (counter[j] <= MIN_PAIRCOV) break;
printf("AB\t%s\t%d\t%d\t%d\n", l->name, i+1, j, j - i);
i = j - 1;
}
}
free(counter); free(depth);
nst_delete_bfa1(l);
maq_delete_maqmap(mm);
delete hash_map;
}
int ma_paircov(int argc, char *argv[])
{
if (argc < 3) {
fprintf(stderr, "Usage: maq paircov [-d %d] [-n %d] <ref.bfa> <align.map>\n",
MIN_PAIRCOV, MIN_N_LEN);
return 1;
}
FILE *fp_bfa = fopen(argv[1], "r");
gzFile fp_map = gzopen(argv[2], "r");
assert(fp_bfa); assert(fp_map);
paircov_core(fp_bfa, fp_map);
fclose(fp_bfa);
gzclose(fp_map);
return 0;
}
static int abpair_usage()
{
fprintf(stderr, "maq abpair <input.map>\n");
return 0;
}
int ma_abpair(int argc, char *argv[])
{
if (argc == 1) return abpair_usage();
gzFile fpin = gzopen(argv[1], "r");
maqmap_t *mm = maqmap_read_header(fpin);
maqmap1_t *m1, mm1;
bit64_t n_diffchr, n_nomatch, n_good, n_badori, n_single, n_bad_dist;
bit64_t n_diffchr2, n_badori2, n_bad_dist2, n_good_alt, n_sw;
n_diffchr = n_nomatch = n_good = n_badori = n_single = n_bad_dist = n_sw = 0;
n_diffchr2 = n_badori2 = n_bad_dist2 = n_good_alt = 0;
fprintf(stdout, "CC\tDC readName chr coor altMapQ\n");
fprintf(stdout, "CC\tSC readName chr flag altMapQ coor1 coor2\n");
m1 = &mm1;
while (maqmap_read1(fpin, m1)) {
if (m1->flag && m1->alt_qual >= HIGHQ) ++n_good_alt;
if (m1->flag == 0) ++n_single;
else if (m1->flag == (PAIRFLAG_PAIRED|PAIRFLAG_FR)) ++n_good;
else if (m1->flag == (PAIRFLAG_FR|PAIRFLAG_SW)) ++n_sw;
else if (m1->flag == PAIRFLAG_NOMATCH) ++n_nomatch;
else if (m1->flag == PAIRFLAG_DIFFCHR) {
++n_diffchr; if (m1->alt_qual >= HIGHQ) ++n_diffchr2;
m1->name[MAX_NAMELEN-1] = 0;
if (m1->alt_qual > 0)
printf("DC\t%s\t%s\t%d\t%d\n", m1->name, mm->ref_name[m1->seqid],
(m1->pos>>1) + 1, m1->alt_qual);
} else {
if (m1->flag & PAIRFLAG_FR) { ++n_bad_dist; if (m1->alt_qual >= HIGHQ) ++n_bad_dist2; }
else { ++n_badori; if (m1->alt_qual >= HIGHQ) ++n_badori2; }
if (m1->dist > 0 && m1->alt_qual > 0) { // print out bad pairs
m1->name[MAX_NAMELEN-1] = 0;
printf("SC\t%s\t%s\t%d\t%d\t%d\t%d\n", m1->name, mm->ref_name[m1->seqid], m1->flag,
m1->alt_qual, (m1->pos>>1) + 1, (m1->pos>>1) + m1->size);
}
}
}
// print out stat in the stderr
bit64_t n_paired = mm->n_mapped_reads - n_single;
fprintf(stdout, "CC all the numbers mean 'number of reads', not 'number of pairs'.\n");
fprintf(stdout, "MM total mapped reads: %llu\n", mm->n_mapped_reads);
fprintf(stdout, "MM total mapped paired reads: %llu (/%llu = %.3f%%)\n",
n_paired, mm->n_mapped_reads, 100.0 * n_paired / mm->n_mapped_reads);
if (n_paired) {
fprintf(stdout, "MM correctly paired reads: %llu (/%llu = %.3f%%)\n",
n_good, n_paired , 100.0 * n_good / n_paired);
fprintf(stdout, "MM reads added by Smith-Waterman alignment: %llu\n", n_sw);
fprintf(stdout, "MM one end unmapped: %llu (/%llu = %.3f%%)\n",
n_nomatch, n_paired, 100.0 * n_nomatch / n_paired);
fprintf(stdout, "MM ends to difference chr: %llu (/%llu = %.3f%%)\n",
n_diffchr, n_paired, 100.0 * n_diffchr / n_paired);
fprintf(stdout, "MM bad orientation: %llu (/%llu = %.3f%%)\n",
n_badori, n_paired, 100.0 * n_badori / n_paired);
fprintf(stdout, "MM bad distance: %llu (/%llu = %.3f%%)\n",
n_bad_dist, n_paired, 100.0 * n_bad_dist / n_paired);
fprintf(stdout, "MM Q%d alt_qual: %llu\n", HIGHQ, n_good_alt);
fprintf(stdout, "MM Q%d ends to difference chr: %llu\n", HIGHQ, n_diffchr2);
fprintf(stdout, "MM Q%d bad orientation: %llu\n", HIGHQ, n_badori2);
fprintf(stdout, "MM Q%d bad distance: %llu\n", HIGHQ, n_bad_dist2);
}
maq_delete_maqmap(mm);
gzclose(fpin);
return 0;
}
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