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Merge pull request #234 from smithlabcode/xcounts-utils
Adding xcounts_utils.cpp source file
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,130 @@ | ||
| /* xcounts_utils: code for doing things with xcounts format and some | ||
| * for counts format that is common to several tools. | ||
| * | ||
| * Copyright (C) 2023-2024 Andrew D. Smith | ||
| * | ||
| * Authors: Andrew D. Smith | ||
| * | ||
| * This program is free software: you can redistribute it and/or | ||
| * modify it under the terms of the GNU General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but | ||
| * WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| * General Public License for more details. | ||
| */ | ||
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| #include "xcounts_utils.hpp" | ||
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| #include <iostream> | ||
| #include <fstream> | ||
| #include <string> | ||
| #include <vector> | ||
| #include <cassert> | ||
| #include <cstdint> | ||
| #include <sstream> | ||
| #include <charconv> | ||
| #include <unordered_map> | ||
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| #include "counts_header.hpp" | ||
| #include "bam_record_utils.hpp" | ||
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| #include "bamxx.hpp" | ||
| #include "dnmt_error.hpp" | ||
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| using std::vector; | ||
| using std::string; | ||
| using std::to_string; | ||
| using std::unordered_map; | ||
| using std::runtime_error; | ||
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| using bamxx::bgzf_file; | ||
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| // careful: this could get big | ||
| unordered_map<string, vector<xcounts_entry>> | ||
| read_xcounts_by_chrom(const uint32_t n_threads, const string &xcounts_file) { | ||
| bamxx::bam_tpool tp(n_threads); | ||
| bamxx::bgzf_file in(xcounts_file, "r"); | ||
| if (!in) throw runtime_error("failed to open input file"); | ||
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| // set the threads for the input file decompression | ||
| if (n_threads > 1 && in.is_bgzf()) tp.set_io(in); | ||
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| kstring_t line{0, 0, nullptr}; | ||
| string chrom_name; | ||
| uint64_t pos = 0; | ||
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| unordered_map<string, vector<xcounts_entry>> sites_by_chrom; | ||
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| vector<xcounts_entry> curr_chrom; | ||
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| while (bamxx::getline(in, line)) { | ||
| if (is_counts_header_line(line.s)) continue; // ADS: early loop exit | ||
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| if (!std::isdigit(line.s[0])) { // check if we have a chrom line | ||
| if (!chrom_name.empty()) { | ||
| sites_by_chrom.insert({chrom_name, curr_chrom}); | ||
| curr_chrom.clear(); | ||
| } | ||
| chrom_name = string{line.s}; | ||
| pos = 0; | ||
| continue; | ||
| } | ||
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| uint32_t pos_step = 0, n_meth = 0, n_unmeth = 0; | ||
| const auto end_line = line.s + line.l; | ||
| auto res = std::from_chars(line.s, end_line, pos_step); | ||
| res = std::from_chars(res.ptr + 1, end_line, n_meth); | ||
| res = std::from_chars(res.ptr + 1, end_line, n_unmeth); | ||
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| const auto curr_pos = pos + pos_step; | ||
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| curr_chrom.push_back({curr_pos, n_meth, n_unmeth}); | ||
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| pos = curr_pos; | ||
| } | ||
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| if (!chrom_name.empty()) sites_by_chrom.insert({chrom_name, curr_chrom}); | ||
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| return sites_by_chrom; | ||
| } | ||
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| bool | ||
| get_is_xcounts_file(const std::string &filename) { | ||
| static constexpr auto max_lines_to_check = 1000ul; | ||
| bamxx::bgzf_file in(filename, "r"); | ||
| if (!in) throw dnmt_error{"failed to open input file: " + filename}; | ||
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| kstring_t line{0, 0, nullptr}; | ||
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| bool found_header = false; | ||
| bool found_chrom = false; | ||
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| auto line_count = 0ul; | ||
| while (line_count++ < max_lines_to_check && bamxx::getline(in, line)) { | ||
| if (is_counts_header_line(line.s)) { | ||
| found_header = true; | ||
| } | ||
| else if (!std::isdigit(line.s[0])) { // check if we have a chrom line | ||
| if (!found_header) | ||
| return false; | ||
| found_chrom = true; | ||
| } | ||
| else { | ||
| if (!found_chrom) return false; | ||
| int64_t pos_step = 0, n_meth = 0, n_unmeth = 0; | ||
| const auto end_line = line.s + line.l; | ||
| auto res = std::from_chars(line.s, end_line, pos_step); | ||
| if (res.ec != std::errc()) return false; | ||
| res = std::from_chars(res.ptr + 1, end_line, n_meth); | ||
| if (res.ec != std::errc()) return false; | ||
| res = std::from_chars(res.ptr + 1, end_line, n_unmeth); | ||
| if (res.ec != std::errc()) return false; | ||
| } | ||
| } | ||
| return true; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| /* xcounts_utils: code for doing things with xcounts format and some | ||
| * for counts format that is common to several tools. | ||
| * | ||
| * Copyright (C) 2023-2024 Andrew D. Smith | ||
| * | ||
| * Authors: Andrew D. Smith | ||
| * | ||
| * This program is free software: you can redistribute it and/or | ||
| * modify it under the terms of the GNU General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but | ||
| * WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| * General Public License for more details. | ||
| */ | ||
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| #ifndef XCOUNTS_UTILS_HPP | ||
| #define XCOUNTS_UTILS_HPP | ||
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| #include <string> | ||
| #include <vector> | ||
| #include <cstdint> | ||
| #include <unordered_map> | ||
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| struct xcounts_entry { | ||
| uint64_t pos{}; // absolute position | ||
| uint32_t n_meth{}; | ||
| uint32_t n_unmeth{}; | ||
| }; | ||
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| std::unordered_map<std::string, std::vector<xcounts_entry>> | ||
| read_xcounts_by_chrom(const uint32_t n_threads, const std::string &xcounts_file); | ||
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| bool | ||
| get_is_xcounts_file(const std::string &filename); | ||
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| #endif |