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/*
Copyright (C) 2018-2019 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
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.
*/
/*
Test region description parser.
Usage: test-parse-reg [-c] file.bam region
test-parse-reg [-c] -m file.bam region,region...
test-parse-reg -t
-c is chr:pos is a single base coordinate, ie chr:pos-pos,
otherwise it is chr:pos-<end>
-m is multi-region list.
-t runs built-in tests
./test/test-parse-reg -c -m test/colons.bam "{chr1:100-200},{chr1}:100-200,{chr1:100-200}:100,{chr1,chr3},chr1:"
*/
#include <config.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <stdint.h>
#include <inttypes.h>
#include "../htslib/hts.h"
#include "../htslib/sam.h"
void reg_expected(sam_hdr_t *hdr, const char *reg, int flags,
char *reg_exp, int tid_exp, hts_pos_t beg_exp, hts_pos_t end_exp) {
const char *reg_out;
int tid_out = -1;
hts_pos_t beg_out = -1, end_out = -1;
reg_out = sam_parse_region(hdr, reg, &tid_out, &beg_out, &end_out, flags);
if ((reg_out != NULL) != (reg_exp != NULL) ||
(reg_out && reg_exp && strcmp(reg_out, reg_exp) != 0) ||
(reg_exp && tid_out != tid_exp) ||
(reg_exp && beg_out != beg_exp) ||
(reg_exp && end_out != end_exp)) {
fprintf(stderr, "Parsing \"%s\" expected return \"%s\", %d:%"PRIhts_pos"-%"PRIhts_pos", "
"but got \"%s\", %d:%"PRIhts_pos"-%"PRIhts_pos"\n",
reg,
reg_exp?reg_exp:"(null)", tid_exp, beg_exp, end_exp,
reg_out?reg_out:"(null)", tid_out, beg_out, end_out);
exit(1);
}
}
int reg_test(char *fn) {
samFile *fp;
sam_hdr_t *hdr;
if (!(fp = sam_open(fn, "r")))
return 1;
if (!(hdr = sam_hdr_read(fp)))
return 1;
// 0 chr1
// 1 chr1:100
// 2 chr1:100-200
// 3 chr2:100-200
// 4 chr3
// 5 chr1,chr3
// Check range extensions.
reg_expected(hdr, "chr1", 0, "", 0, 0, HTS_POS_MAX);
reg_expected(hdr, "chr1:50", 0, "", 0, 49, HTS_POS_MAX);
reg_expected(hdr, "chr1:50", HTS_PARSE_ONE_COORD, "", 0, 49, 50);
reg_expected(hdr, "chr1:50-100", 0, "", 0, 49, 100);
reg_expected(hdr, "chr1:50-", 0, "", 0, 49, HTS_POS_MAX);
reg_expected(hdr, "chr1:-50", 0, "", 0, 0, 50);
// Check quoting
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "chr1:100-200", 0, NULL, 0, 0, 0); // ambiguous
reg_expected(hdr, "{chr1}:100-200", 0, "", 0, 99, 200);
reg_expected(hdr, "{chr1:100-200}", 0, "", 2, 0, HTS_POS_MAX);
reg_expected(hdr, "{chr1:100-200}:100-200", 0, "", 2, 99, 200);
reg_expected(hdr, "{chr2:100-200}:100-200", 0, "", 3, 99, 200);
reg_expected(hdr, "chr2:100-200:100-200", 0, "", 3, 99, 200);
reg_expected(hdr, "chr2:100-200", 0, "", 3, 0, HTS_POS_MAX);
// Check numerics
reg_expected(hdr, "chr3", 0, "", 4, 0, HTS_POS_MAX);
reg_expected(hdr, "chr3:", 0, "", 4, 0, HTS_POS_MAX);
reg_expected(hdr, "chr3:1000-1500", 0, "", 4, 999, 1500);
reg_expected(hdr, "chr3:1,000-1,500", 0, "", 4, 999, 1500);
reg_expected(hdr, "chr3:1k-1.5K", 0, "", 4, 999, 1500);
reg_expected(hdr, "chr3:1e3-1.5e3", 0, "", 4, 999, 1500);
reg_expected(hdr, "chr3:1e3-15e2", 0, "", 4, 999, 1500);
// Check list mode
reg_expected(hdr, "chr1,chr3", HTS_PARSE_LIST, "chr3", 0, 0, HTS_POS_MAX);
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "chr1:100-200,chr3", HTS_PARSE_LIST, NULL, 0, 0, 0); // ambiguous
reg_expected(hdr, "{chr1,chr3}", HTS_PARSE_LIST, "", 5, 0, HTS_POS_MAX);
reg_expected(hdr, "{chr1,chr3},chr1", HTS_PARSE_LIST, "chr1", 5, 0, HTS_POS_MAX);
// incorrect usage; first reg is valid (but not what user expects).
reg_expected(hdr, "chr3:1,000-1,500", HTS_PARSE_LIST | HTS_PARSE_ONE_COORD, "000-1,500", 4, 0, 1);
// More expected failures
reg_expected(hdr, "chr2", 0, NULL, 0, 0, 0);
reg_expected(hdr, "chr1,", 0, NULL, 0, 0, 0);
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "{chr1", 0, NULL, 0, 0, 0);
reg_expected(hdr, "chr1:10-10", 0, "", 0, 9, 10); // OK
reg_expected(hdr, "chr1:10-9", 0, NULL, 0, 0, 0); // Issue#353
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "chr1:x", 0, NULL, 0, 0, 0);
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "chr1:1-y", 0, NULL, 0, 0, 0);
fprintf(stderr, "Expected error: ");
reg_expected(hdr, "chr1:1,chr3", 0, NULL, 0, 0, 0);
sam_hdr_destroy(hdr);
sam_close(fp);
exit(0);
}
int main(int argc, char **argv) {
sam_hdr_t *hdr;
samFile *fp;
int flags = 0;
while (argc > 1) {
if (strcmp(argv[1], "-m") == 0) {
flags |= HTS_PARSE_LIST;
argc--; argv++;
continue;
}
if (strcmp(argv[1], "-c") == 0) {
flags |= HTS_PARSE_ONE_COORD;
argc--; argv++;
continue;
}
// Automatic mode for test harness
if (strcmp(argv[1], "-t") == 0)
reg_test(argv[2]);
break;
}
// Interactive mode for debugging
if (argc != 3) {
fprintf(stderr, "Usage: test-parse-reg [-m] [-c] region[,region]...\n");
exit(1);
}
if (!(fp = sam_open(argv[1], "r"))) {
perror(argv[1]);
exit(1);
}
if (!(hdr = sam_hdr_read(fp))) {
fprintf(stderr, "Couldn't read header\n");
exit(1);
}
const char *reg = argv[2];
while (*reg) {
int tid;
hts_pos_t beg, end;
reg = sam_parse_region(hdr, reg, &tid, &beg, &end, flags);
if (!reg) {
fprintf(stderr, "Failed to parse region\n");
exit(1);
}
printf("%-20s %12"PRIhts_pos" %12"PRIhts_pos"\n",
tid == -1 ? "*" : hdr->target_name[tid],
beg, end);
}
sam_hdr_destroy(hdr);
sam_close(fp);
return 0;
}
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