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sift_bam_max_cov.cpp
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sift_bam_max_cov.cpp
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#include <stdio.h>
// #include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <cstring>
#include <string>
#include <getopt.h>
#include <stdint.h>
#include <limits.h>
#include <map>
#include <set>
#include <utility>
#include <vector>
#include <string>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
enum test_op {
READ_COMPRESSED = 1,
WRITE_COMPRESSED = 2,
READ_CRAM = 4,
WRITE_CRAM = 8,
WRITE_UNCOMPRESSED = 16,
};
void insert_or_increment(std::map<int32_t, int32_t> & pos_map, int32_t rpos) {
auto it = pos_map.find(rpos);
if (it != pos_map.end()) {
++(it->second);
}
else {
pos_map.insert({rpos, 1});
}
}
void help() {
fprintf(stderr, "Usage: bamsifter [-c max_coverage] [-i max_identical_cigar_pos] [-o out.bam] [--FLAGS] <in.bam>\n");
fprintf(stderr, "\n");
fprintf(stderr, "-c: Max coverage value.\n");
fprintf(stderr, "-o: Output file name. Default is to stdout.\n");
fprintf(stderr, "-i: Max number of reads with an identical cigar starting at the some position to keep.\n");
fprintf(stderr, "--keep_unmapped: keep unmapped reads (0x4 flag). \n");
fprintf(stderr, "--keep_secondary: keep alignments flagged as secondary (0x100 flag).\n");
fprintf(stderr, "--keep_supplementary: keep alignments flagged as supplementary (0x800 flag).\n");
fprintf(stderr, "--keep_chimeric: keep chimeric alignments (SA: tag).\n");
fprintf(stderr, "File to process.\n");
fprintf(stderr, "\n");
}
int main(int argc, char *argv[])
{
samFile *in; // open input alignment file
int flag = 0;
int clevel = -1; // compression level
bam_hdr_t *input_header; // alignment header
htsFile *out;
char modew[800];
int exit_code = 0;
int coverage_limit = 100;
int similar_cigar_limit = INT_MAX;
int keep_unmapped = 0;
int keep_supplementary = 0;
int keep_secondary = 0;
int keep_chimeric = 0;
const char *out_name = "-";
int c; // for parsing input arguments
// add option to keep only "proper pairs" (both reads mapped)
// add option to run strand specificlly
// add option for BAM index loading (+ generation if needed) to be able to run each chromosome on a seperate thread
// while ((c = getopt(argc, argv, "DSIt:i:bCul:o:N:BZ:@:M")) >= 0) {
while (1) {
static struct option long_options[] = {
/* These options set a flag. */
{"keep_unmapped", no_argument, &keep_unmapped, 1},
{"keep_supplementary", no_argument, &keep_supplementary, 1},
{"keep_secondary", no_argument, &keep_secondary, 1},
{"keep_chimeric", no_argument, &keep_chimeric, 1},
/* No flags set. */
{"coverage_limit", required_argument, 0, 'c'},
{"out_name", required_argument, 0, 'o'},
{"similar_cigar_limit", required_argument, 0, 'i'},
{NULL, 0, NULL, 0}
};
int option_index = 0;
c = getopt_long(argc, argv, "c:o:i:", long_options, &option_index);
if (c == -1) {
break;
}
switch (c)
{
case 0:
if (long_options[option_index].flag != 0)
break;
printf("option %s", long_options[option_index].name);
if (optarg)
printf (" with arg %s", optarg);
printf ("\n");
break;
case 'c': coverage_limit = atoi(optarg); break;
case 'o': out_name = optarg; break;
case 'i': similar_cigar_limit = atoi(optarg); break;
default:
help();
exit(2);
}
}
if (argc == optind) { // missing input file, print help
help();
return (1);
}
in = sam_open(argv[optind], "r");
const htsFormat *in_format = hts_get_format(in);
// Enable multi-threading (only effective when the library was compiled with -DBGZF_MT)
// bgzf_mt(in, n_threads, 0);
if (in == NULL) {
fprintf(stderr, "Error opening \"%s\"\n", argv[optind]);
return EXIT_FAILURE;
}
input_header = sam_hdr_read(in);
if (input_header == NULL) {
fprintf(stderr, "Couldn't read header for \"%s\"\n", argv[optind]);
return EXIT_FAILURE;
}
// check that sort order (SO) flag is set
std::string tmp_text(input_header->text, input_header->l_text);
size_t start_pos = tmp_text.find("@HD");
if (start_pos == std::string::npos) {
fprintf(stderr, "Error, missing @HD field in header.\n");
return EXIT_FAILURE;
}
size_t end_pos = tmp_text.find("\n", start_pos);
if (end_pos == std::string::npos) {
end_pos = tmp_text.length();
}
tmp_text = tmp_text.substr(start_pos, end_pos - start_pos);
start_pos = tmp_text.find("SO:");
if (start_pos == std::string::npos) {
fprintf(stderr, "Error, missing SO field in @HD header line.\n");
return EXIT_FAILURE;
}
tmp_text.find("coordinate", start_pos);
if (start_pos == std::string::npos) {
fprintf(stderr, "Error, file is not coordinate sorted.\n");
return EXIT_FAILURE;
}
strcpy(modew, "w");
if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
if (flag & WRITE_CRAM) strcat(modew, "c");
else if (flag & WRITE_COMPRESSED) strcat(modew, "b");
else if (flag & WRITE_UNCOMPRESSED) strcat(modew, "bu");
// out = hts_open(out_name, modew);
out = hts_open_format(out_name, modew, in_format);
if (out == NULL) {
fprintf(stderr, "Error opening standard output\n");
return EXIT_FAILURE;
}
if (sam_hdr_write(out, input_header) < 0) { // write header from input to output
fprintf(stderr, "Error writing output header.\n");
exit_code = 1;
}
// map for start/end positions of alignments that are already selected
std::map<int32_t, int32_t> starts;
std::map<int32_t, int32_t> ends;
// keep a set of mate reads we decided to keep when encountering the first read
std::set<std::string> mates_to_keep;
std::map<std::vector<uint32_t>, int> current_cigar_counts;
bam1_t *aln = bam_init1(); //initialize an alignment
int32_t current_rname_index = 0; // index compared to header: input_header->target_name[current_rname_index]
int32_t current_coverage = 0;
bool chimeric_to_keep;
int32_t current_pos = 0;
while(sam_read1(in, input_header, aln) > 0) {
if (current_rname_index != aln->core.tid) {
// should have finished writing reads from current_rname_index contig, so can just reset vars
current_coverage = 0;
starts.clear();
ends.clear();
fprintf(stdout, "Done with chr %s.\n", input_header->target_name[current_rname_index]);
current_rname_index = aln->core.tid;
}
// make sure the read is mapped
if (!keep_unmapped && ((aln->core.flag & BAM_FUNMAP) != 0))
continue;
// check if the read has a chimeric alignement and only keep if asked to
// then check if the alignment is a secondary alignment or a supplementary alignment, and keep only if asked to
chimeric_to_keep = false;
if (keep_chimeric && (bam_aux_get(aln, "SA") != NULL)) {
chimeric_to_keep = true;
}
else if ((!keep_secondary && (aln->core.flag & BAM_FSECONDARY) != 0) || (!keep_supplementary && (aln->core.flag & BAM_FSUPPLEMENTARY) != 0)) // suppl: and not chimeric tag
continue;
if (current_pos != aln->core.pos) { // left most position, does NOT need adjustment for reverse strand if summing their coverage
// add the range we want and then erase all the matching entries at once rather than 1 by 1
auto it = starts.begin();
if (it->first <= aln->core.pos) {
for (; it != starts.end(); ++it) {
if (it->first <= aln->core.pos) { // or equal because already selected reads take priority in coverage
current_coverage += it->second;
}
else break;
}
starts.erase(starts.begin(), it);
}
it = ends.begin();
if (it->first <= aln->core.pos) {
for (; it != ends.end(); ++it) {
if (it->first <= aln->core.pos) { // or equal because already selected reads take priority in coverage
current_coverage -= it->second;
}
else break;
}
ends.erase(ends.begin(), it);
}
current_cigar_counts.clear();
current_pos = aln->core.pos;
}
// if we are below the max coverage or the read has already been selected to keep through its pair or because it is chimeric
if ((current_coverage < coverage_limit) ||
(mates_to_keep.find(bam_get_qname(aln)) != mates_to_keep.end()) ||
chimeric_to_keep) {
// get cigar
uint32_t *cigar = bam_get_cigar(aln);
// check that the cigar
if ((similar_cigar_limit < coverage_limit) && !chimeric_to_keep) {
std::vector<uint32_t> tmp_cigar(aln->core.n_cigar);
std::copy(cigar, cigar + aln->core.n_cigar, tmp_cigar.begin());
auto it = current_cigar_counts.find(tmp_cigar);
if (it != current_cigar_counts.end()) { // found
if (it->second < similar_cigar_limit) {
it->second++;
}
else {
continue;
}
}
else {
current_cigar_counts.emplace(std::move(tmp_cigar), 1);
}
}
int32_t rpos = aln->core.pos; // update position on the ref with cigar
for (uint32_t k = 0; k < aln->core.n_cigar; ++k) {
if ((bam_cigar_type(bam_cigar_op(cigar[k]))&2)) { // consumes reference
if (bam_cigar_op(cigar[k]) == BAM_CREF_SKIP) {
insert_or_increment(ends, rpos);
rpos += bam_cigar_oplen(cigar[k]);
insert_or_increment(starts, rpos);
}
else {
rpos += bam_cigar_oplen(cigar[k]);
}
}
}
insert_or_increment(ends, rpos);
++current_coverage;
// save pair mate
mates_to_keep.insert(bam_get_qname(aln));
}
}
int ret;
// close and reopen input file to seek to start regardless of compression
ret = hts_close(in);
if (ret < 0) {
fprintf(stderr, "Error closing input.\n");
exit_code = EXIT_FAILURE;
}
in = sam_open(argv[optind], "r");
input_header = sam_hdr_read(in);
if (input_header == NULL) {
fprintf(stderr, "Couldn't read header for \"%s\"\n", argv[optind]);
return EXIT_FAILURE;
}
while (sam_read1(in, input_header, aln) > 0) {
// output the alignment
if (mates_to_keep.find(bam_get_qname(aln)) != mates_to_keep.end()) {
if (sam_write1(out, input_header, aln) == -1) {
fprintf(stderr, "Could not write selected record \"%s\"\n", bam_get_qname(aln));
return EXIT_FAILURE;
}
}
}
ret = hts_close(in);
if (ret < 0) {
fprintf(stderr, "Error closing input.\n");
exit_code = EXIT_FAILURE;
}
ret = hts_close(out);
if (ret < 0) {
fprintf(stderr, "Error closing output.\n");
exit_code = EXIT_FAILURE;
}
return exit_code;
}