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unpack.c
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unpack.c
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#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <stdio.h>
#include "cfile.h"
#include "vector.h"
#include "snames.h"
static int usage() {
fprintf(stderr, "\nUsage: yame unpack [options] <in.cx> [[sample 1], [sample 2], ...]\n\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -a Process all samples\n");
fprintf(stderr, " -C Output column names\n");
fprintf(stderr, " -R [PATH] Row coordinate .cr file name.\n");
fprintf(stderr, " -r 0: Row coordinate output in chrm-beg0-end1 (default, for cg).\n");
fprintf(stderr, " 1: Row coordinate output in chrm-beg0-end0 (for allc).\n");
fprintf(stderr, " 2 and other: Row coordinate output in chrm_beg1.\n");
fprintf(stderr, " -l [PATH] Path to the sample list. Ignored if sample names are provided on the command line.\n");
fprintf(stderr, " -H [N] Process N samples from the start of the list, where N is less than or equal to the\n");
fprintf(stderr, " total number of samples.\n");
fprintf(stderr, " -T [N] Process N samples from the end of the list, where N is less than or equal to the\n");
fprintf(stderr, " total number of samples. Requires index.\n");
fprintf(stderr, " -f [N] Display format for data format 3. Options are:\n");
fprintf(stderr, " N == 0: Compound MU\n");
fprintf(stderr, " N < 0: M<tab>U\n");
fprintf(stderr, " N > 0: Fraction (with number for the min coverage)\n");
fprintf(stderr, " -c Enable chunk process\n");
fprintf(stderr, " -s Chunk size (default is 1M)\n");
fprintf(stderr, " -u [int] number of bytes for each unit data while inflated. Lower number needs less memory\n");
fprintf(stderr, " efficient but could be lossier. Can only be 1-8.\n");
fprintf(stderr, " 0 means this will be inferred from data.\n");
fprintf(stderr, " -h Display this help message.\n\n");
return 1;
}
typedef struct cdata_pfmt_t {
int f3;
int f7;
} cdata_pfmt_t;
static void print_cdata1(cdata_t *c, uint64_t i, cdata_pfmt_t pfmt) {
switch (c->fmt) {
case '0': {
fputc(((c->s[i>>3]>>(i&0x7))&0x1)+'0', stdout);
break;
}
case '1': {
fputc(c->s[i], stdout);
break;
}
case '2': {
fprintf(stdout, "%s", f2_get_string(c, i));
break;
}
case '3': {
uint64_t mu = f3_get_mu(c, i);
if (pfmt.f3 == 0)
fprintf(stdout, "%"PRIu64"", mu);
else if (pfmt.f3 < 0)
fprintf(stdout, "%"PRIu64"\t%"PRIu64"",mu>>32, mu<<32>>32);
else {
uint64_t M = mu>>32;
uint64_t U = mu<<32>>32;
if ((M==0 && U==0) || (M+U) < (uint64_t) pfmt.f3) fputs("NA", stdout);
else fprintf(stdout, "%1.3f", (double) M/(M+U));
}
break;
}
case '4': {
if (((float_t*) (c->s))[i]<0) {
fputs("NA", stdout);
} else {
fprintf(stdout, "%1.3f", ((float_t*) (c->s))[i]);
}
break;
}
case '5': {
if (c->s[i] == 2) {
fputs("NA", stdout);
} else {
fputc(c->s[i]+'0', stdout);
}
break;
}
case '6': {
if ((c->s[i/4]>>(2*(i%4)+1))&1) {
fprintf(stdout, "%u\t1", ((c->s[i/4]>>(2*(i%4)))&1));
} else {
fputs("NA\t0", stdout);
}
break;
}
case '7': {
if (!fmt7_next_bed(c)) {
fprintf(stderr, "[%s:%d] next BED record unfound.\n", __func__, __LINE__);
fflush(stderr);
exit(1);
}
row_reader_t *rdr = (row_reader_t*) c->aux;
if (rdr->index != i+1) {
fprintf(stderr, "[%s:%d] row reader index mismatch (i=%"PRIu64", rdr.index=%"PRIu64").\n",
__func__, __LINE__, i, rdr->index);
fflush(stderr);
exit(1);
}
if (pfmt.f7 == 0) {
fprintf(stdout, "%s\t%"PRIu64"\t%"PRIu64"", rdr->chrm, rdr->value-1, rdr->value+1);
} else if (pfmt.f7 == 1) {
fprintf(stdout, "%s\t%"PRIu64"\t%"PRIu64"", rdr->chrm, rdr->value-1, rdr->value);
} else {
fprintf(stdout, "%s_%"PRIu64"", rdr->chrm, rdr->value);
}
break;
}
default: usage(); wzfatal("Unrecognized format: %c.\n", c->fmt);
}
}
static void print_cdata_chunk(cdata_v *cs, uint64_t s, cdata_pfmt_t pfmt) {
if (ref_cdata_v(cs, 0)->fmt == '7') {
fprintf(stderr, "[%s:%d] Unpack does not support format 7 chunking.\n", __func__, __LINE__);
fflush(stderr);
exit(1);
}
uint64_t i,m, k, kn = cs->size;
cdata_t expanded = {0};
decompress(ref_cdata_v(cs, 0), &expanded);
uint64_t n = expanded.n;
cdata_t *sliced = calloc(kn, sizeof(cdata_t));
for (m=0; m <= n/s; ++m) {
for (k=0; k<kn; ++k) {
decompress(ref_cdata_v(cs, k), &expanded);
slice(&expanded, m*s, (m+1)*s-1, &sliced[k]);
}
for (i=0; i<sliced[0].n; ++i) {
for (k=0; k<kn; ++k) {
if(k) fputc('\t', stdout);
print_cdata1(&sliced[k], i, pfmt);
}
fputc('\n', stdout);
}
}
for (k=0; k<kn; ++k) free(sliced[k].s);
free(expanded.s); free(sliced);
}
static void print_cdata(cdata_v *cs, cdata_pfmt_t pfmt, char *fname_row) {
uint64_t i, k, kn = cs->size;
cdata_t *inflated = calloc(kn, sizeof(cdata_t));
for (k=0; k<kn; ++k) {
cdata_t *c = ref_cdata_v(cs,k);
if (c->fmt == '7') {
memcpy(inflated+k, c, sizeof(cdata_t));
inflated[k].s = malloc(c->n);
memcpy(inflated[k].s, c->s, c->n);
} else {
decompress(c, inflated+k);
}
}
uint64_t n = 0;
if (inflated[0].fmt == '7') {
n = fmt7_data_length(&inflated[0]);
} else {
n = inflated[0].n;
}
cdata_t cr = {0};
if (fname_row) {
cfile_t cf_row = open_cfile(fname_row);
cr = read_cdata1(&cf_row);
}
for (i=0; i<n; ++i) {
if (cr.s) print_cdata1(&cr, i, pfmt);
for (k=0; k<kn; ++k) {
if(k || cr.s) fputc('\t', stdout);
print_cdata1(inflated+k, i, pfmt);
}
fputc('\n', stdout);
}
if (cr.s) free_cdata(&cr);
for (k=0; k<kn; ++k) free_cdata(&inflated[k]);
free(inflated);
}
int main_unpack(int argc, char *argv[]) {
int c, read_all = 0, chunk = 0;
cdata_pfmt_t pfmt = {0};
uint64_t chunk_size = 1000000; char *fname_snames = NULL;
int head = -1, tail = -1;
uint8_t unit = 0; // default: auto-inferred
int print_column_names = 0;
char *fname_row = NULL;
while ((c = getopt(argc, argv, "cs:l:H:T:f:u:CR:r:ah"))>=0) {
switch (c) {
case 'c': chunk = 1; break;
case 's': chunk_size = atoi(optarg); break;
case 'l': fname_snames = strdup(optarg); break;
case 'H': head = atoi(optarg); break;
case 'T': tail = atoi(optarg); break;
case 'u': unit = atoi(optarg); break;
case 'C': print_column_names = 1; break;
case 'R': fname_row = strdup(optarg); break;
case 'r': pfmt.f7 = atoi(optarg); break;
case 'a': read_all = 1; break;
case 'f': pfmt.f3 = atoi(optarg); break;
case 'h': return usage(); break;
default: usage(); wzfatal("Unrecognized option: %c.\n", c);
}
}
if (optind + 1 > argc) {
usage();
wzfatal("Please supply input file.\n");
}
char *fname_in = strdup(argv[optind]);
cfile_t cf = open_cfile(fname_in);
char *fname_index = get_fname_index(fname_in);
index_t *idx = loadIndex(fname_index);
if (fname_index) free(fname_index);
snames_t snames = {0};
if (optind + 1 < argc) { // The requested sample names from command line
for(int i = optind + 1; i < argc; ++i) {
snames.s = realloc(snames.s, (snames.n+1));
snames.s[snames.n++] = strdup(argv[i]);
}
} else { // from a file list
snames = loadSampleNames(fname_snames, 1);
}
// check if we have index
if ((tail > 0 && !idx) || (snames.n > 0 && strcmp(fname_in, "-") != 0 && !idx)) {
fprintf(stderr, "Error, the cx file needs indexing for random sample access.\n");
fflush(stderr);
exit(1);
}
// read in the cdata
cdata_v *cs = NULL;
if (idx && snames.n > 0) {
cs = read_cdata_with_snames(&cf, idx, &snames);
} else if (read_all) {
cs = read_cdata_all(&cf);
} else if (head > 0) {
cs = read_cdata_from_head(&cf, head);
} else if (tail > 0) {
cs = read_cdata_from_tail(&cf, idx, tail);
} else {
cs = read_cdata_from_head(&cf, 1);
}
// set unit size
if (unit > 8 || ((unit&0x1) && unit != 1 && unit)) {
fprintf(stderr, "[%s:%d] Unit size (%u) can only be 1,2,4,6,8.\n", __func__, __LINE__, unit);
fflush(stderr);
exit(1);
}
for (uint64_t i=0; i<cs->size; ++i) ref_cdata_v(cs, i)->unit = unit;
int col1_is_row_index=0;
if (ref_cdata_v(cs, 0)->fmt == '7') col1_is_row_index = 1;
// output headers
if (print_column_names) {
if (!snames.n) {
if (idx) {
int n0 = 0;
index_pair_t *idx_pairs = index_pairs(idx, &n0);
if (read_all) {
snames.n = n0;
snames.s = calloc(snames.n, sizeof(char*));
for (int i=0; i<snames.n; ++i) snames.s[i] = idx_pairs[i].key;
} else if (head > 0) {
snames.n = head;
snames.s = calloc(snames.n, sizeof(char*));
for (int i=0; i<snames.n; ++i) snames.s[i] = idx_pairs[i].key;
} else if (tail > 0) {
snames.n = tail;
snames.s = calloc(snames.n, sizeof(char*));
for (int i=0; i<tail; ++i) snames.s[i] = idx_pairs[n0-tail+i].key;
} else {
snames.n = 1; snames.s = calloc(1, sizeof(char*));
snames.s[0] = idx_pairs[0].key;
}
free(idx_pairs); // ownership of keys are transfered to snames.s
} else {
fprintf(stderr, "[%s:%d] Error, index file is missing for printing sample names.\n", __func__, __LINE__);
fflush(stderr);
exit(1);
}
}
if (fname_row || col1_is_row_index) {
if (pfmt.f7 == 0) fputs("chrm\tbeg0\tend1", stdout);
else if (pfmt.f7 == 1) fputs("chrm\tbeg0\tend0", stdout);
else fputs("chrm_beg1", stdout);
}
for (int i=0; i<snames.n; ++i) {
if (fname_row || col1_is_row_index || i) fputc('\t', stdout);
fputs(snames.s[i], stdout);
}
fputc('\n', stdout);
}
// output the cs
if (chunk) print_cdata_chunk(cs, chunk_size, pfmt); // TODO: chunking is a little redundant to rowsub
else print_cdata(cs, pfmt, fname_row);
// clean up
for (uint64_t i=0; i<cs->size; ++i) free_cdata(ref_cdata_v(cs,i));
free_cdata_v(cs);
bgzf_close(cf.fh);
free(fname_in);
if (idx) cleanIndex(idx);
cleanSampleNames(&snames);
return 0;
}