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#include <queue>
#include <vector>
#include <iostream>
#include <map>
#include <cstdlib>
#include <cassert>
#include <api/BamMultiReader.h>
#include <api/BamAlignment.h>
#include "OptionParser.h"
#include "interval.h"
using namespace BamTools;
using namespace std;
typedef uint32_t DepthType; // type for depth of coverage, kept it small
const char ref_char = '>'; // reference prefix for "counts" output
const string VERSION = "%prog 1.2.0"
"\nCopyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin\n"
"https://github.com/telatin/covtobed - License MIT"
".\n"
"This is free software: you are free to change and redistribute it.\n"
"There is NO WARRANTY, to the extent permitted by law.";
#define debug if(false)
// Class that stores info about the end position of alignments, used in the alignment queue
struct CovEnd {
PositionType end;
bool rev;
// order for queuing
bool operator<(const CovEnd &o) const {
return end > o.end;
}
};
// Class for input handling: reads and filters alignments from bams
class Input {
public:
BamMultiReader input_bams;
const int min_mapq;
const int discard_invalid_alignments;
// open all files
Input(const vector<string> &paths, const int q, const int v) : min_mapq(q), discard_invalid_alignments(v) {
if (paths.empty()) {
// no input files, use standard input
cerr << "Reading from STDIN... [try 'covtobed -h' for options]" << endl;
if (!input_bams.OpenFile("-"))
throw string("cannot read BAM from standard input, are you piping a BAM file?");
//throw input_bams.GetErrorString();
} else {
for (const auto &path : paths)
if (!input_bams.OpenFile(path))
throw "cannot open '" + path + "'. File not found, or not a BAM file.";
//throw input_bams.GetErrorString();
}
}
// get next good alignment (if any)
bool get_next_alignment(BamAlignment & alignment) {
bool more_alignments, good_alignment;
do {
debug cerr << "[M] Read on ref#" << alignment.RefID << " pos:" << alignment.Position <<
"\n\t| Is mapped? " << alignment.IsMapped() << " | AlignmentFlag:" << alignment.AlignmentFlag << endl;
more_alignments = input_bams.GetNextAlignmentCore(alignment);
if (discard_invalid_alignments) {
good_alignment = alignment.IsMapped() && alignment.MapQuality >= min_mapq
&& !alignment.IsDuplicate() && !alignment.IsFailedQC() && alignment.IsPrimaryAlignment();
// 1.2.0 ProperPair
if (alignment.IsPaired() && ! alignment.IsProperPair() ) {
good_alignment = false;
}
} else {
good_alignment = alignment.IsMapped() && alignment.MapQuality >= min_mapq;
}
} while (more_alignments && !good_alignment);
return more_alignments;
}
vector<RefData> get_ref_data() { return input_bams.GetReferenceData(); }
int get_ref_id(const string &ref) { return input_bams.GetReferenceID(ref); }
};
// Class that stores info about the current coverage
struct Coverage {
DepthType f = 0, r = 0;
operator DepthType() const { return f + r; }
void inc(bool rev=false) {
if (rev)
++r;
else
++f;
}
void dec(bool rev=false) {
if (rev)
--r;
else
--f;
}
};
// Class for output handling: writes coverage in the specified format
class Output {
public:
enum Format {BED, COUNTS};
// class constructor
Output(ostream *o, const char *f, bool s=false, int m=0, int x=100000, int l=1) : out(o), format(parse_format(f)), strands(s), mincov(m), maxcov(x), minlen(l) {
}
// write interval to bed
void operator() (const Interval &i, const Coverage &c) {
// can the last interval be extended with the same coverage?
if (i.ref == last_interval.ref && i.start == last_interval.end && last_coverage == c)
// extend previous interval
last_interval.end = i.end;
else {
// output previous interval
write(last_interval, last_coverage);
if (i.ref != last_interval.ref)
// new reference
switch(format) {
case BED:
break;
case COUNTS:
*out << ref_char << i.ref << endl;
break;
}
last_interval = i;
last_coverage = c;
}
}
~Output() {
write(last_interval, last_coverage);
}
private:
void write(const Interval &i, const Coverage &c) {
if (i and c >= mincov and c < maxcov and (i.end - i.start >= minlen) ) { // interval not empty plus user constraints
switch(format) {
case Format::BED:
*out << i.ref << '\t' << i.start << '\t' << i.end << '\t';
if (c >= 0) {
write_coverage(c);
}
break;
case Format::COUNTS:
write_coverage(c);
*out << '\t' << i.length();
break;
}
*out << endl;
}
}
void write_coverage(const Coverage &c) {
if (strands)
*out << c.f << '\t' << c.r;
else
*out << static_cast<DepthType>(c);
}
static Format parse_format(const char *format_str) {
const string s = format_str;
if (s == "bed")
return Output::BED;
if (s == "counts")
return Output::COUNTS;
throw string("unkown format specification: \"") + format_str + "\"";
}
ostream *out;
const Format format;
const bool strands;
const int mincov;
const int maxcov;
const int minlen;
Interval last_interval;
Coverage last_coverage;
};
int main(int argc, char *argv[]) {
// general options
optparse::OptionParser parser = optparse::OptionParser().description("Computes coverage from alignments").usage("%prog [options] [BAM]...").version(VERSION);
//parser.add_option("-v") .action("version") .help("prints program version");
// input options
parser.add_option("--physical-coverage").action("store_true").set_default("0").help("compute physical coverage (needs paired alignments in input)");
parser.add_option("-q", "--min-mapq").metavar("MINQ").type("int").set_default("0").help("skip alignments whose mapping quality is less than MINQ (default: %default)");
parser.add_option("-m", "--min-cov").metavar("MINCOV").type("int").set_default("0").help("print BED feature only if the coverage is bigger than (or equal to) MINCOV (default: %default)");
parser.add_option("-x", "--max-cov").metavar("MAXCOV").type("int").set_default("100000").help("print BED feature only if the coverage is lower than MAXCOV (default: %default)");
parser.add_option("-l", "--min-len").metavar("MINLEN").type("int").set_default("1").help("print BED feature only if its length is bigger (or equal to) than MINLELN (default: %default)");
parser.add_option("-z", "--min-ctg-len").metavar("MINCTGLEN").type("int").help("Skip reference sequences (contigs) shorter than this value");
parser.add_option("-d", "--discard-invalid-alignments").action("store_true").set_default("0").help("skip duplicates, failed QC, and non primary alignment, minq>0 (or user-defined if higher) (default: %default)");
// output options
parser.add_option("--output-strands").action("store_true").set_default("0").help("output coverage and stats separately for each strand");
vector<string> choices = {"bed", "counts"};
parser.add_option("--format").choices(choices.begin(), choices.end()).set_default("bed").help("output format");
// parse arguments
optparse::Values options = parser.parse_args(argc, argv);
const bool physical_coverage = options.get("physical_coverage");
const bool only_valid = options.get("discard_invalid_alignments");
const int minimum_coverage = options.get("min_cov");
const int maximum_coverage = options.get("max_cov");
const int minimum_length = options.get("min_len");
const int minimum_contig_len= options.get("min_ctg_len");
int min_mapq = options.get("min_mapq");
if (only_valid and !min_mapq) {
min_mapq = 1;
} else {
min_mapq = options.get("min_mapq");
}
try {
// open input and output
Input input(parser.args(), min_mapq, only_valid);
Output output(&cout,
static_cast<const char *>(options.get("format")),
static_cast<bool>(options.get("output_strands")),
minimum_coverage, maximum_coverage, minimum_length);
// main alignment parsing loop
BamAlignment alignment;
bool more_alignments = input.get_next_alignment(alignment);
for (const auto &ref : input.get_ref_data()) { // loop on reference
// init new reference data
const int ref_id = input.get_ref_id(ref.RefName);
if (ref.RefLength <= minimum_contig_len) {
continue;
}
debug cerr << "[R] Reference: " << ref_id << endl;
PositionType last_pos = 0;
priority_queue<CovEnd> coverage_ends;
Coverage coverage;
bool more_alignments_for_ref = more_alignments && alignment.RefID == ref_id;
// loop current reference
do {
// find next possible coverage change
const PositionType next_change = more_alignments_for_ref ?
(coverage_ends.empty() ? alignment.Position : min(alignment.Position, coverage_ends.top().end)) :
(coverage_ends.empty() ? ref.RefLength : coverage_ends.top().end);
debug cerr << "[-] Coverage is " << coverage << " up to " << next_change << endl;
// output coverage
assert(coverage_ends.size() == coverage);
output({ref.RefName, last_pos, next_change}, coverage);
// increment coverage with alignments that start here
while (more_alignments_for_ref && next_change == alignment.Position) {
if (physical_coverage) {
if (alignment.InsertSize > 0) {
debug cerr << " [phy] pos:" << alignment.Position << " size:" << alignment.InsertSize << endl;
coverage_ends.push({alignment.Position + alignment.InsertSize, alignment.IsReverseStrand()});
coverage.inc(alignment.IsReverseStrand());
}
} else {
coverage_ends.push({alignment.GetEndPosition(), alignment.IsReverseStrand()});
coverage.inc(alignment.IsReverseStrand());
}
more_alignments = input.get_next_alignment(alignment);
more_alignments_for_ref = more_alignments && alignment.RefID == ref_id;
}
// decrement coverage with alignments that end here
while (!coverage_ends.empty() && next_change == coverage_ends.top().end) {
coverage.dec(coverage_ends.top().rev);
coverage_ends.pop();
}
debug cerr << "[<] Coverage is " << coverage << " from " << next_change << endl;
last_pos = next_change;
} while (last_pos != ref.RefLength);
debug cerr << "[_] Completed at " << ref.RefName << ":" << last_pos << " [coverage:" << coverage_ends.size() << "]" << endl;
// reference ended
if (!coverage_ends.empty()) {
cerr << "Coverage is not zero at the end of " << ref.RefName << endl;
cerr << "Try samtools fixmate on the input file" << endl;
}
// 1.2.0 -- removed: assert(coverage_ends.empty());
}
//assert(!more_alignments);
if (more_alignments) {
throw string("Unexpected alignment found, is the BAM sorted?");
}
} catch (const string &msg) {
parser.error(msg);
}
return 0;
}
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