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juicer.c
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juicer.c
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/*********************************************************************************
* MIT License *
* *
* Copyright (c) 2021 Chenxi Zhou <[email protected]> *
* *
* 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. *
*********************************************************************************/
/********************************** Revision History *****************************
* *
* 22/06/21 - Chenxi Zhou: Created *
* *
*********************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include "khash.h"
#include "bamlite.h"
#include "ketopt.h"
#include "kvec.h"
#include "sdict.h"
#include "asset.h"
#include "version.h"
static double jc_realtime0;
enum fileTypes{NOSET, BED, BAM, BIN, PA5};
KHASH_SET_INIT_STR(str)
static int make_juicer_pre_file_from_bin(char *f, char *agp, char *fai, uint8_t mq, int scale, int count_gap, FILE *fo)
{
int ret;
FILE *fp;
uint32_t i, i0, i1, m;
uint64_t p0, p1, pair_n, pair_c, pair_u;
int64_t magic_number;
uint8_t buffer[BUFF_SIZE * 17];
CC_ERR_t err0, err1;
sdict_t *sdict = make_sdict_from_index(fai, 0);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
// check BIN file header consistency
if ((ret = file_sdict_match(f, sdict))) {
fprintf(stderr, "[E::%s] Not a valid BIN file or BIN file header does not match sequence dictionary: %d\n", __func__, ret);
fprintf(stderr, "[E::%s] Make sure no contig length threshold (YaHS option '-l') applied for the BIN file\n", __func__);
fprintf(stderr, "[E::%s] Consider using a BAM or BED file instead\n", __func__);
exit(EXIT_FAILURE);
}
fp = fopen(f, "r");
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, f);
exit(EXIT_FAILURE);
}
m = fread(&magic_number, sizeof(int64_t), 1, fp);
if (m != 1) bin_fread_error();
if (!is_valid_bin_header(magic_number)) {
fprintf(stderr, "[E::%s] not a valid BIN file\n", __func__);
exit(EXIT_FAILURE);
}
file_seek_skip_sdict(fp);
m = fread(&pair_n, sizeof(uint64_t), 1, fp);
if (m != 1) bin_fread_error();
pair_c = pair_u = 0;
while (pair_c < pair_n) {
m = fread(buffer, sizeof(uint8_t), BUFF_SIZE * 17, fp);
for (i = 0; i < m && pair_c < pair_n; i += 17, ++pair_c) {
if (*(uint8_t *) (buffer + i + 16) < mq)
continue;
err0 = sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i), *(uint32_t *) (buffer + i + 4), &i0, &p0, count_gap);
err1 = sd_coordinate_conversion(dict, *(uint32_t *) (buffer + i + 8), *(uint32_t *) (buffer + i + 12), &i1, &p1, count_gap);
if (err0 != CC_SUCCESS || err1 != CC_SUCCESS) {
// fprintf(stderr, "[W::%s] sequence not found \n", __func__);
++pair_u;
} else {
if (strcmp(dict->s[i0].name, dict->s[i1].name) <= 0)
fprintf(fo, "0\t%s\t%lu\t0\t1\t%s\t%lu\t1\n", dict->s[i0].name, p0 >> scale, dict->s[i1].name, p1 >> scale);
else
fprintf(fo, "0\t%s\t%lu\t1\t1\t%s\t%lu\t0\n", dict->s[i1].name, p1 >> scale, dict->s[i0].name, p0 >> scale);
}
}
}
fprintf(stderr, "[I::%s] %lu read pairs processed: %lu unmapped\n", __func__, pair_c, pair_u);
fclose(fp);
asm_destroy(dict);
sd_destroy(sdict);
return 0;
}
static int make_juicer_pre_file_from_bed(char *f, char *agp, char *fai, uint8_t mq, int scale, int count_gap, FILE *fo)
{
iostream_t *fp;
char *line;
char cname0[4096], cname1[4096], rname0[4096], rname1[4096];
uint32_t s0, s1, e0, e1, i0, i1;
uint64_t p0, p1, rec_c, pair_c;
uint8_t q0, q1;
int8_t buff;
CC_ERR_t err0, err1;
khash_t(str) *hmseq; // for absent sequences
khint_t k;
int absent;
hmseq = kh_init(str);
sdict_t *sdict = make_sdict_from_index(fai, 0);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
fp = iostream_open(f);
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, f);
exit(EXIT_FAILURE);
}
rec_c = pair_c = 0;
buff = 0;
while ((line = iostream_getline(fp)) != NULL) {
if (is_empty_line(line))
continue;
if (++rec_c % 1000000 == 0)
fprintf(stderr, "[I::%s] %lu million records processed, %lu read pairs \n", __func__, rec_c / 1000000, pair_c);
if (buff == 0) {
cname0[0] = rname0[0] = '\0';
s0 = e0 = UINT32_MAX;
q0 = 255;
sscanf(line, "%s %u %u %s %hhu", cname0, &s0, &e0, rname0, &q0);
++buff;
} else if (buff == 1) {
cname1[0] = rname1[0] = '\0';
s1 = e1 = UINT32_MAX;
q1 = 255;
sscanf(line, "%s %u %u %s %hhu", cname1, &s1, &e1, rname1, &q1);
if (is_read_pair(rname0, rname1)) {
buff = 0;
if (q0 < mq || q1 < mq)
continue;
err0 = sd_coordinate_conversion(dict, sd_get(sdict, cname0), s0 / 2 + e0 / 2 + (s0 & 1 && e0 & 1), &i0, &p0, count_gap);
err1 = sd_coordinate_conversion(dict, sd_get(sdict, cname1), s1 / 2 + e1 / 2 + (s1 & 1 && e1 & 1), &i1, &p1, count_gap);
if (err0 != CC_SUCCESS) {
if (err0 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname0, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname0);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname0);
}
} else if (err0 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__,
cname0, s0 / 2 + e0 / 2 + (s0 & 1 && e0 & 1));
}
} else if (err1 != CC_SUCCESS) {
if (err1 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname1, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname1);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname1);
}
} else if (err1 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__,
cname1, s1 / 2 + e1 / 2 + (s1 & 1 && e1 & 1));
}
} else {
if (strcmp(dict->s[i0].name, dict->s[i1].name) <= 0)
fprintf(fo, "0\t%s\t%lu\t0\t1\t%s\t%lu\t1\n", dict->s[i0].name, p0 >> scale, dict->s[i1].name, p1 >> scale);
else
fprintf(fo, "0\t%s\t%lu\t1\t1\t%s\t%lu\t0\n", dict->s[i1].name, p1 >> scale, dict->s[i0].name, p0 >> scale);
++pair_c;
}
} else {
buff = 1;
strcpy(cname0, cname1);
s0 = s1;
e0 = e1;
q0 = q1;
strcpy(rname0, rname1);
}
}
}
fprintf(stderr, "[I::%s] %ld read pairs processed\n", __func__, pair_c);
for (k = 0; k < kh_end(hmseq); ++k)
if (kh_exist(hmseq, k))
free((char *) kh_key(hmseq, k));
kh_destroy(str, hmseq);
iostream_close(fp);
asm_destroy(dict);
sd_destroy(sdict);
return 0;
}
static int make_juicer_pre_file_from_pa5(char *f, char *agp, char *fai, int8_t mq, int scale, int count_gap, FILE *fo)
{
iostream_t *fp;
char *line;
char cname0[4096], cname1[4096];
uint32_t x0, x1, i0, i1;
uint64_t p0, p1, rec_c, pair_c;
uint8_t q0, q1;
CC_ERR_t err0, err1;
khash_t(str) *hmseq; // for absent sequences
khint_t k;
int absent;
hmseq = kh_init(str);
sdict_t *sdict = make_sdict_from_index(fai, 0);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
fp = iostream_open(f);
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, f);
exit(EXIT_FAILURE);
}
rec_c = pair_c = 0;
while ((line = iostream_getline(fp)) != NULL) {
if (is_empty_line(line))
continue;
if (++rec_c % 1000000 == 0)
fprintf(stderr, "[I::%s] %lu million records processed, %lu read pairs \n", __func__, rec_c / 1000000, pair_c);
cname0[0] = cname1[0] = '\0';
x0 = x1 = UINT32_MAX;
q0 = q1 = 255;
sscanf(line, "%*s %s %u %s %u %hhu %hhu", cname0, &x0, cname1, &x1, &q0, &q1);
if (q0 < mq || q1 < mq)
continue;
err0 = sd_coordinate_conversion(dict, sd_get(sdict, cname0), x0, &i0, &p0, count_gap);
err1 = sd_coordinate_conversion(dict, sd_get(sdict, cname1), x1, &i1, &p1, count_gap);
if (err0 != CC_SUCCESS) {
if (err0 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname0, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname0);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname0);
}
} else if (err0 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__, cname0, x0);
}
} else if (err1 != CC_SUCCESS) {
if (err1 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname1, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname1);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname1);
}
} else if (err1 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__, cname1, x1);
}
} else {
if (strcmp(dict->s[i0].name, dict->s[i1].name) <= 0)
fprintf(fo, "0\t%s\t%lu\t0\t1\t%s\t%lu\t1\n", dict->s[i0].name, p0 >> scale, dict->s[i1].name, p1 >> scale);
else
fprintf(fo, "0\t%s\t%lu\t1\t1\t%s\t%lu\t0\n", dict->s[i1].name, p1 >> scale, dict->s[i0].name, p0 >> scale);
++pair_c;
}
}
fprintf(stderr, "[I::%s] %ld read pairs processed\n", __func__, pair_c);
for (k = 0; k < kh_end(hmseq); ++k)
if (kh_exist(hmseq, k))
free((char *) kh_key(hmseq, k));
kh_destroy(str, hmseq);
iostream_close(fp);
asm_destroy(dict);
sd_destroy(sdict);
return 0;
}
static char *parse_bam_rec(bam1_t *b, bam_header_t *h, uint8_t q, int32_t *s, int32_t *e, char **cname)
{
// 0x4 0x100 0x200 0x400 0x800
if ((b->core.flag & 0xF04) || (!b->core.flag) || b->core.qual < q)
return 0;
*cname = h->target_name[b->core.tid];
*s = b->core.pos;
*e = get_target_end(b);
return strdup(bam1_qname(b));
}
static int parse_bam_rec1(bam1_t *b, bam_header_t *h, char **cname0, int32_t *s0, char **cname1, int32_t *s1)
{
// 0x4 0x8 0x40 0x100 0x200 0x400 0x800
if ((b->core.flag & 0xF4C) || (!b->core.flag))
return 1;
*cname0 = h->target_name[b->core.tid];
*s0 = b->core.pos;
*cname1 = h->target_name[b->core.mtid];
*s1 = b->core.mpos;
return 0;
}
static int make_juicer_pre_file_from_bam(char *f, char *agp, char *fai, uint8_t mq, int scale, int count_gap, FILE *fo)
{
bamFile fp;
bam_header_t *h;
bam1_t *b;
char *cname0, *cname1, *rname0, *rname1;
int32_t s0, s1, e0, e1;
uint32_t i0, i1;
uint64_t p0, p1, rec_c, pair_c;
int8_t buff;
enum bam_sort_order so;
CC_ERR_t err0, err1;
khash_t(str) *hmseq; // for absent sequences
khint_t k;
int absent;
hmseq = kh_init(str);
sdict_t *sdict = make_sdict_from_index(fai, 0);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
fp = bam_open(f, "r");
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, f);
exit(EXIT_FAILURE);
}
h = bam_header_read(fp);
b = bam_init1();
so = bam_hrecs_sort_order(h);
cname0 = cname1 = rname0 = rname1 = 0;
s0 = s1 = e0 = e1 = 0;
i0 = i1 = 0;
p0 = p1 = 0;
rec_c = pair_c = 0;
buff = 0;
if (so == ORDER_NAME) {
// sorted by read names
while (bam_read1(fp, b) >= 0 ) {
if (++rec_c % 1000000 == 0)
fprintf(stderr, "[I::%s] %lu million records processed, %lu read pairs \n", __func__, rec_c / 1000000, pair_c);
if (buff == 0) {
rname0 = parse_bam_rec(b, h, mq, &s0, &e0, &cname0);
if (!rname0)
continue;
++buff;
} else if (buff == 1) {
rname1 = parse_bam_rec(b, h, mq, &s1, &e1, &cname1);
if (!rname1)
continue;
if (strcmp(rname0, rname1) == 0) {
buff = 0;
err0 = sd_coordinate_conversion(dict, sd_get(sdict, cname0), s0 / 2 + e0 / 2 + (s0 & 1 && e0 & 1), &i0, &p0, count_gap);
err1 = sd_coordinate_conversion(dict, sd_get(sdict, cname1), s1 / 2 + e1 / 2 + (s1 & 1 && e1 & 1), &i1, &p1, count_gap);
if (err0 != CC_SUCCESS) {
if (err0 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname0, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname0);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname0);
}
} else if (err0 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__,
cname0, s0 / 2 + e0 / 2 + (s0 & 1 && e0 & 1));
}
} else if (err1 != CC_SUCCESS) {
if (err1 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname1, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname1);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname1);
}
} else if (err1 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__,
cname1, s1 / 2 + e1 / 2 + (s1 & 1 && e1 & 1));
}
} else {
if (strcmp(dict->s[i0].name, dict->s[i1].name) <= 0)
fprintf(fo, "0\t%s\t%lu\t0\t1\t%s\t%lu\t1\n", dict->s[i0].name, p0 >> scale, dict->s[i1].name, p1 >> scale);
else
fprintf(fo, "0\t%s\t%lu\t1\t1\t%s\t%lu\t0\n", dict->s[i1].name, p1 >> scale, dict->s[i0].name, p0 >> scale);
++pair_c;
}
free(rname0);
free(rname1);
rname0 = 0;
rname1 = 0;
} else {
buff = 1;
cname0 = cname1;
s0 = s1;
e0 = e1;
free(rname0);
rname0 = rname1;
rname1 = 0;
}
}
}
} else {
// sorted by coordinates or others
if (mq > 0)
fprintf(stderr, "[W::%s] BAM file is not sorted by read name. Filtering by mapping quality %hhu suppressed \n", __func__, mq);
while (bam_read1(fp, b) >= 0 ) {
if (++rec_c % 1000000 == 0)
fprintf(stderr, "[I::%s] %lu million records processed, %lu read pairs \n", __func__, rec_c / 1000000, pair_c);
if(parse_bam_rec1(b, h, &cname0, &s0, &cname1, &s1))
continue;
err0 = sd_coordinate_conversion(dict, sd_get(sdict, cname0), s0, &i0, &p0, count_gap);
err1 = sd_coordinate_conversion(dict, sd_get(sdict, cname1), s1, &i1, &p1, count_gap);
if (err0 != CC_SUCCESS) {
if (err0 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname0, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname0);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname0);
}
} else if (err0 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__, cname0, s0);
}
} else if (err1 != CC_SUCCESS) {
if (err1 == SEQ_NOT_FOUND) {
k = kh_put(str, hmseq, cname1, &absent);
if (absent) {
kh_key(hmseq, k) = strdup(cname1);
fprintf(stderr, "[W::%s] sequence \"%s\" not found \n", __func__, cname1);
}
} else if (err1 == POS_NOT_IN_RANGE) {
fprintf(stderr, "[W::%s] sequence position \"%s:%u\" not in range \n", __func__, cname1, s1);
}
} else {
if (strcmp(dict->s[i0].name, dict->s[i1].name) <= 0)
fprintf(fo, "0\t%s\t%lu\t0\t1\t%s\t%lu\t1\n", dict->s[i0].name, p0 >> scale, dict->s[i1].name, p1 >> scale);
else
fprintf(fo, "0\t%s\t%lu\t1\t1\t%s\t%lu\t0\n", dict->s[i1].name, p1 >> scale, dict->s[i0].name, p0 >> scale);
++pair_c;
}
}
}
fprintf(stderr, "[I::%s] %lu read pairs processed\n", __func__, pair_c);
for (k = 0; k < kh_end(hmseq); ++k)
if (kh_exist(hmseq, k))
free((char *) kh_key(hmseq, k));
kh_destroy(str, hmseq);
if (rname0)
free(rname0);
if (rname1)
free(rname1);
bam_destroy1(b);
bam_header_destroy(h);
bam_close(fp);
asm_destroy(dict);
sd_destroy(sdict);
return 0;
}
static uint64_t assembly_annotation(const char *f, sdict_t *sdict, const char *out_agp, const char *out_annot,
const char *out_lift, int *scale, uint64_t max_s, uint64_t *g)
{
uint32_t i, j, c, n, m;
int *seqs;
FILE *fo_agp, *fo_annot, *fo_lift;
uint64_t genome_size, scaled_gs;
asm_dict_t *dict;
sd_seg_t seg;
fo_agp = fopen(out_agp, "w");
fo_annot = fopen(out_annot, "w");
fo_lift = fopen(out_lift, "w");
dict = make_asm_dict_from_agp(sdict, f, 1);
n = dict->u + dict->n;
seqs = (int *) calloc(n, sizeof(int));
genome_size = 0;
c = j = 0;
m = dict->s[j++].n;
for (i = 0; i < dict->u; ++i) {
seg = dict->seg[i];
fprintf(fo_agp, "assembly\t%lu\t%lu\t%u\t%s\t%s\t%u\t%u\t%s\n",
genome_size + 1, genome_size + seg.y, i + 1, agp_component_type_val(seg.t),
sdict->s[seg.c>>1].name, seg.x + 1, seg.x + seg.y, agp_orientation_val(seg.r));
fprintf(fo_annot, ">ctg%08u.1 %u %u\n", i + 1, i + 1, seg.y);
fprintf(fo_lift, "ctg%08u.1\t%u\t%u\t%u\t%s\t%s\t%u\t%u\t%s\n",
i + 1, 1, seg.y, 1, agp_component_type_val(seg.t), sdict->s[seg.c>>1].name,
seg.x + 1, seg.x + seg.y, agp_orientation_val(AGP_OT_PLUS));
if (i == m) {
m += dict->s[j++].n;
++c;
}
seqs[c++] = (int) (i + 1) * (seg.r == AGP_OT_MINUS? -1 : 1);
genome_size += seg.y;
}
for (i = 0; i < n; ++i) {
// seqs[n - 1] is always 0
if (seqs[i]) {
fprintf(fo_annot, "%d", seqs[i]);
fputc(seqs[i + 1]? ' ' : '\n', fo_annot);
}
}
fclose(fo_agp);
fclose(fo_annot);
fclose(fo_lift);
free(seqs);
asm_destroy(dict);
scaled_gs = linear_scale(genome_size, scale, max_s);
*g = genome_size;
return scaled_gs;
}
uint64_t assembly_scale_max_seq(asm_dict_t *dict, int *scale, uint64_t max_s, uint64_t *g)
{
uint32_t i;
uint64_t s;
sd_aseq_t seq;
s = 0;
for (i = 0; i < dict->n; ++i) {
seq = dict->s[i];
s = MAX(s, seq.len + seq.gap);
}
*g = s;
return linear_scale(s, scale, max_s);
}
static void print_help_pre(FILE *fp_help)
{
fprintf(fp_help, "Usage: juicer pre [options] <hic.bed>|<hic.bam>|<hic.pa5>|<hic.bin> <scaffolds.agp> <contigs.fa.fai>\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " -a preprocess for assembly mode\n");
fprintf(fp_help, " -q INT minimum mapping quality [10]\n");
fprintf(fp_help, " -o STR output file prefix (required for '-a' mode) [stdout]\n");
fprintf(fp_help, " --file-type STR input file type BED|BAM|PA5|BIN, file name extension is ignored if set\n");
fprintf(fp_help, " --version show version number\n");
}
static ko_longopt_t long_options[] = {
{ "file-type", ko_required_argument, 301 },
{ "seq-ctype", ko_required_argument, 302 },
{ "gap-ctype", ko_required_argument, 303 },
{ "gap-link", ko_required_argument, 304 },
{ "gap-size", ko_required_argument, 305 },
{ "help", ko_no_argument, 'h' },
{ "version", ko_no_argument, 'V' },
{ 0, 0, 0 }
};
static int main_pre(int argc, char *argv[])
{
FILE *fo;
char *fai, *agp, *agp1, *link_file, *out, *out1, *annot, *lift, *ext1, *ext2;
int mq, asm_mode;;
enum fileTypes f_type;
liftrlimit();
jc_realtime0 = realtime();
const char *opt_str = "q:ao:Vh";
ketopt_t opt = KETOPT_INIT;
int c, ret;
FILE *fp_help = stderr;
fai = agp = agp1 = link_file = out = out1 = annot = lift = 0;
mq = 10;
asm_mode = 0;
f_type = NOSET;
while ((c = ketopt(&opt, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'o') {
out = opt.arg;
} else if (c == 'q') {
mq = atoi(opt.arg);
} else if (c == 'a') {
asm_mode = 1;
} else if (c == 301) {
if (strcasecmp(opt.arg, "BED") == 0)
f_type = BED;
else if (strcasecmp(opt.arg, "BAM") == 0)
f_type = BAM;
else if (strcasecmp(opt.arg, "BIN") == 0)
f_type = BIN;
else if (strcasecmp(opt.arg, "PA5") == 0)
f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown file type: \"%s\"\n", __func__, opt.arg);
return 1;
}
} else if (c == 'h') {
fp_help = stdout;
} else if (c == 'V') {
puts(JUICER_VERSION);
return 0;
} else if (c == '?') {
fprintf(stderr, "[E::%s] unknown option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
} else if (c == ':') {
fprintf(stderr, "[E::%s] missing option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
}
if (fp_help == stdout) {
print_help_pre(stdout);
return 0;
}
if (asm_mode && !out) {
fprintf(stderr, "[E::%s] missing input: -o option is required for assembly mode (-a)\n", __func__);
return 1;
}
if (argc - opt.ind < 3) {
fprintf(stderr, "[E::%s] missing input: three positional options required\n", __func__);
print_help_pre(stderr);
return 1;
}
if (mq < 0 || mq > 255) {
fprintf(stderr, "[E::%s] invalid mapping quality threshold: %d\n", __func__, mq);
return 1;
}
uint8_t mq8;
mq8 = (uint8_t) mq;
link_file = argv[opt.ind];
agp = argv[opt.ind + 1];
fai = argv[opt.ind + 2];
if (f_type == NOSET) {
ext1 = strlen(link_file) >= 4? (link_file + strlen(link_file) - 4) : NULL;
ext2 = strlen(link_file) >= 7? (link_file + strlen(link_file) - 7) : NULL;
if (ext1 && !strcasecmp(ext1, ".bam")) f_type = BAM;
else if (ext1 && !strcasecmp(ext1, ".bin")) f_type = BIN;
else if ((ext1 && !strcasecmp(ext1, ".bed")) || (ext2 && !strcasecmp(ext2, ".bed.gz"))) f_type = BED;
else if ((ext1 && !strcasecmp(ext1, ".pa5")) || (ext2 && !strcasecmp(ext2, ".pa5.gz"))) f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown link file format. File extension .bam, .bed, .pa5 or .bin or --file-type is expected\n", __func__);
exit(EXIT_FAILURE);
}
}
if (f_type == BIN && (strcmp(link_file, "-") == 0 || *link_file == '<')) {
fprintf(stderr, "[E::%s] BIN file format from STDIN is not supported\n", __func__);
exit(EXIT_FAILURE);
}
if (out) {
out1 = (char *) malloc(strlen(out) + 35);
sprintf(out1, "%s.txt", out);
}
fo = out1 == 0? stdout : fopen(out1, "w");
if (fo == 0) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out);
exit(EXIT_FAILURE);
}
ret = 0;
sdict_t *sdict;
asm_dict_t *dict;
int scale;
uint64_t max_s, scaled_s;
sdict = make_sdict_from_index(fai, 0);
scale = 0;
max_s = scaled_s = 0;
agp1 = (char *) malloc(MAX(strlen(agp), out? strlen(out) : 0) + 35);
if (asm_mode) {
annot = (char *) malloc(strlen(out) + 35);
lift = (char *) malloc(strlen(out) + 35);
sprintf(agp1, "%s.assembly.agp", out);
sprintf(annot, "%s.assembly", out);
sprintf(lift, "%s.liftover.agp", out);
scaled_s = assembly_annotation(agp, sdict, agp1, annot, lift, &scale, (uint64_t) INT_MAX, &max_s);
dict = make_asm_dict_from_agp(sdict, agp1, 1);
} else {
sprintf(agp1, "%s", agp);
dict = make_asm_dict_from_agp(sdict, agp1, 1);
scaled_s = assembly_scale_max_seq(dict, &scale, (uint64_t) INT_MAX, &max_s);
}
if (f_type == BAM) {
fprintf(stderr, "[I::%s] make juicer pre input from BAM file %s\n", __func__, link_file);
ret = make_juicer_pre_file_from_bam(link_file, agp1, fai, mq8, scale, !asm_mode, fo);
} else if (f_type == BED) {
fprintf(stderr, "[I::%s] make juicer pre input from BED file %s\n", __func__, link_file);
ret = make_juicer_pre_file_from_bed(link_file, agp1, fai, mq8, scale, !asm_mode, fo);
} else if (f_type == PA5) {
fprintf(stderr, "[I::%s] make juicer pre input from PA5 file %s\n", __func__, link_file);
ret = make_juicer_pre_file_from_pa5(link_file, agp1, fai, mq8, scale, !asm_mode, fo);
} else if (f_type == BIN) {
fprintf(stderr, "[I::%s] make juicer pre input from BIN file %s\n", __func__, link_file);
ret = make_juicer_pre_file_from_bin(link_file, agp1, fai, mq8, scale, !asm_mode, fo);
}
if (asm_mode) {
fprintf(stderr, "[I::%s] genome size: %lu\n", __func__, max_s);
fprintf(stderr, "[I::%s] scale factor: %d\n", __func__, 1 << scale);
fprintf(stderr, "[I::%s] chromosome sizes for juicer_tools pre -\n", __func__);
fprintf(stderr, "PRE_C_SIZE: assembly %lu\n", scaled_s);
fprintf(stderr, "[I::%s] JUICER_PRE CMD: java -Xmx36G -jar ${juicer_tools} pre %s %s.hic <(echo \"assembly %lu\")\n",
__func__, out1, out, scaled_s);
} else {
if (scale) {
fprintf(stderr, "[W::%s] maximum scaffold length exceeds %d (=%lu)\n", __func__, INT_MAX, max_s);
fprintf(stderr, "[W::%s] using scale factor: %d\n", __func__, 1 << scale);
}
fprintf(stderr, "[I::%s] chromosome sizes for juicer_tools pre -\n", __func__);
uint32_t i;
sd_aseq_t seq;
for (i = 0; i < dict->n; ++i) {
seq = dict->s[i];
fprintf(stderr, "PRE_C_SIZE: %s %lu\n", seq.name, (seq.len + seq.gap) >> scale);
}
}
asm_destroy(dict);
sd_destroy(sdict);
if (out != 0)
fclose(fo);
if (out1)
free(out1);
if (agp1)
free(agp1);
if (annot)
free(annot);
if (lift)
free(lift);
fprintf(stderr, "[I::%s] Version: %s\n", __func__, JUICER_VERSION);
fprintf(stderr, "[I::%s] CMD: juicer", __func__);
int i;
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[I::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__,
realtime() - jc_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
return ret;
}
static int assembly_to_agp(char *assembly, char *lift, sdict_t *sdict, FILE *fo)
{
asm_dict_t *dict;
iostream_t *fp;
char *line;
char cname[1024], c0[1024], c1[1024], *cstr;
int32_t cid, sid, fid, sign;
uint32_t i, clen, mlen, s, p, *coords;
int64_t slen;
size_t m;
kvec_t(int) segs;
dict = make_asm_dict_from_agp(sdict, lift, 1);
m = 4;
coords = (uint32_t *) malloc(sizeof(uint32_t) * m * 3);
c0[0] = c1[0] = '\0';
mlen = 0;
sid = 0;
kv_init(segs);
fp = iostream_open(assembly);
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, assembly);
exit(EXIT_FAILURE);
}
while ((line = iostream_getline(fp)) != NULL) {
if (is_empty_line(line) || line[0] != '>')
continue;
sscanf(line, "%s %d %u", cname, &cid, &clen);
cstr = strstr(cname, ":::");
if (cstr != NULL) {
cname[cstr - cname] = '\0';
}
strcpy(c1, cname + 1);
if (!strcmp(c0, c1)) {
mlen += clen;
} else {
mlen = clen;
strcpy(c0, c1);
}
if (sd_coordinate_rev_conversion(dict, asm_sd_get(dict, c1), mlen - clen, &s, &p, 0) != CC_SUCCESS) {
fprintf(stderr, "[E::%s] coordinates conversion error %s %u\n", __func__, c1, mlen - clen);
exit(EXIT_FAILURE);
}
if (clen == 0)
fprintf(stderr, "[W::%s] segment of length zero in line: %s\n", __func__, line);
if (cid > m) {
m <<= 1;
coords = (uint32_t *) realloc(coords, sizeof(uint32_t) * m * 3);
}
cid -= 1;
coords[cid * 3] = s;
coords[cid * 3 + 1] = p + 1; // 0-based to 1-based coordinates
coords[cid * 3 + 2] = clen;
}
iostream_close(fp);
fp = iostream_open(assembly);
if (fp == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for reading\n", __func__, assembly);
exit(EXIT_FAILURE);
}
while ((line = iostream_getline(fp)) != NULL) {
if (is_empty_line(line) || line[0] == '>')
continue;
segs.n = 0;
char *eptr, *fptr;
cid = strtol(line, &eptr, 10);
if (coords[(abs(cid) - 1) * 3 + 2] > 0)
kv_push(int, segs, cid);
while (*eptr && *eptr != '\n') {
cid = strtol(eptr + 1, &fptr, 10);
if (coords[(abs(cid) - 1) * 3 + 2] > 0)
kv_push(int, segs, cid);
eptr = fptr;
}
if (segs.n == 0) continue;
++sid;
fid = 0;
slen = 0;
for (i = 0; i < segs.n; ++i) {
cid = segs.a[i];
sign = cid > 0;
cid = abs(cid) - 1;
fprintf(fo, "scaffold_%d\t%ld\t%ld\t%d\t%s\t%s\t%d\t%d\t%s\n", sid, slen + 1,
slen + coords[cid * 3 + 2], ++fid, agp_component_type_val(DEFAULT_AGP_SEQ_COMPONENT_TYPE),
sdict->s[coords[cid * 3]].name, coords[cid * 3 + 1], coords[cid * 3 + 1] + coords[cid * 3 + 2] - 1,
sign? agp_orientation_val(AGP_OT_PLUS) : agp_orientation_val(AGP_OT_MINUS));
slen += coords[cid * 3 + 2];
if (i != segs.n - 1) {
fprintf(fo, "scaffold_%d\t%ld\t%ld\t%d\t%s\t%d\t%s\t%s\t%s\n", sid, slen + 1,
slen + DEFAULT_AGP_GAP_SIZE, ++fid, agp_component_type_val(DEFAULT_AGP_GAP_COMPONENT_TYPE),
DEFAULT_AGP_GAP_SIZE, agp_gap_type_val(DEFAULT_AGP_GAP_TYPE), agp_linkage_val(AGP_LG_YES),
agp_linkage_evidence_val(DEFAULT_AGP_LINKAGE_EVIDENCE));
slen += DEFAULT_AGP_GAP_SIZE;
}
}
}
iostream_close(fp);
free(coords);
kv_destroy(segs);
asm_destroy(dict);
return 0;
}
static void print_help_post(FILE *fp_help)
{
fprintf(fp_help, "Usage: juicer post [options] <review.assembly> <liftover.agp> <contigs.fa[.fai]>\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " -o STR output file prefix (required for scaffolds FASTA output) [stdout]\n");
fprintf(fp_help, " --seq-ctype STR AGP output sequence component type [%s]\n", agp_component_type_val(DEFAULT_AGP_SEQ_COMPONENT_TYPE));
fprintf(fp_help, " --gap-ctype STR AGP output gap component type [%s]\n", agp_component_type_val(DEFAULT_AGP_GAP_COMPONENT_TYPE));
fprintf(fp_help, " --gap-link STR AGP output gap linkage evidence [%s]\n", agp_linkage_evidence_val(DEFAULT_AGP_LINKAGE_EVIDENCE));
fprintf(fp_help, " --gap-size INT AGP output gap size between sequence component [%d]\n", DEFAULT_AGP_GAP_SIZE);
fprintf(fp_help, " --version show version number\n");
}
static int main_post(int argc, char *argv[])
{
FILE *fo;
char *fa, *fa1, *out, *out1;
liftrlimit();
jc_realtime0 = realtime();
const char *opt_str = "o:Vh";
ketopt_t opt = KETOPT_INIT;
int c, ret, is_fai;
FILE *fp_help = stderr;
sdict_t *sdict;
fa = fa1 = out = out1 = 0;
while ((c = ketopt(&opt, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 302) {
DEFAULT_AGP_SEQ_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_N ||
DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_U)
fprintf(stderr, "[W::%s] a GAP component identifier will be used for sequences: %s\n",
__func__, opt.arg);
} else if (c == 303) {
DEFAULT_AGP_GAP_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_N &&
DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_U)
fprintf(stderr, "[W::%s] a SEQ component identifier will be used for gaps: %s\n",
__func__, opt.arg);
} else if (c == 304) {
DEFAULT_AGP_LINKAGE_EVIDENCE = agp_linkage_evidence_key(opt.arg);
} else if (c == 305) {
DEFAULT_AGP_GAP_SIZE = atoi(opt.arg);
} else if (c == 'o') {
out = opt.arg;
} else if (c == 'h') {
fp_help = stdout;
} else if (c == 'V') {
puts(JUICER_VERSION);
return 0;
} else if (c == '?') {
fprintf(stderr, "[E::%s] unknown option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
} else if (c == ':') {
fprintf(stderr, "[E::%s] missing option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
}
if (fp_help == stdout) {
print_help_post(stdout);
return 0;
}
if (argc - opt.ind < 3) {
fprintf(stderr, "[E::%s] missing input: three positional options required\n", __func__);
print_help_post(stderr);
return 1;
}
if (out) {
out1 = (char *) malloc(strlen(out) + 35);
sprintf(out1, "%s.FINAL.agp", out);
}
fo = out1 == 0? stdout : fopen(out1, "w");
if (fo == 0) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out);