vcf.hpp

/*****************************************************************************
Copyright (c) 2019 Reed A. Cartwright, PhD <reed@cartwrig.ht>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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*****************************************************************************/
#ifndef SOFOS_VCF_HPP
#define SOFOS_VCF_HPP

#include <htslib/vcf.h>
#include <htslib/vcfutils.h>

#include <chrono>
#include <memory>
#include <stdexcept>
#include <string>

// The *_free_t classes are used enable RAII on pointers created by htslib.
namespace detail {
struct buffer_free_t {
    void operator()(void *ptr) const {
        free(ptr);  // NOLINT
    }
};
struct file_free_t {
    void operator()(void *ptr) const { hts_close(static_cast<htsFile *>(ptr)); }
};
struct header_free_t {
    void operator()(void *ptr) const { bcf_hdr_destroy(static_cast<bcf_hdr_t *>(ptr)); }
};
struct bcf_free_t {
    void operator()(void *ptr) const { bcf_destroy(static_cast<bcf1_t *>(ptr)); }
};
}  // namespace detail

class BcfReader {
   public:
    explicit BcfReader(const char *path) {
        input_.reset(hts_open(path, "r"));
        if(!input_) {
            throw std::runtime_error(std::string{"unable to open input file: '"} + path + "'.");
        }
        header_.reset(bcf_hdr_read(input_.get()));
        if(!header_) {
            throw std::invalid_argument("unable to read header from input.");
        }
    }

    const bcf_hdr_t *header() const { return header_.get(); }

    template <typename callback_t>
    void operator()(callback_t callback);

   protected:
    std::unique_ptr<htsFile, detail::file_free_t> input_;
    std::unique_ptr<bcf_hdr_t, detail::header_free_t> header_;
};

template <typename callback_t>
void BcfReader::operator()(callback_t callback) {
    std::unique_ptr<bcf1_t, detail::bcf_free_t> record{bcf_init()};
    if(!record) {
        throw std::invalid_argument("unable to allocate vcf record.");
    }
    // process all sites
    while(bcf_read(input_.get(), header_.get(), record.get()) == 0) {
        callback(record.get(), header());
    }
}

// Templates and functions for handling buffers used by htslib
template <typename T>
struct buffer_t {  // NOLINT(cppcoreguidelines-pro-type-member-init)
    std::unique_ptr<T[], detail::buffer_free_t> data;
    int capacity;
};

template <typename T>
inline buffer_t<T> make_buffer(int sz) {
    void *p = std::malloc(sizeof(T) * sz);  // NOLINT(cppcoreguidelines-owning-memory, cppcoreguidelines-no-malloc)
    if(p == nullptr) {
        throw std::bad_alloc{};
    }
    return {std::unique_ptr<T[], detail::buffer_free_t>{static_cast<T *>(p)}, sz};
}

// htslib may call realloc on our pointer. When using a managed buffer,
// we need to check to see if it needs to be updated.
inline int get_info_string(const bcf_hdr_t *header, bcf1_t *record, const char *tag, buffer_t<char> *buffer) {
    char *p = buffer->data.get();
    int n = bcf_get_info_string(header, record, tag, &p, &buffer->capacity);  // NOLINT
    if(n == -4) {
        throw std::bad_alloc{};
    } else if(p != buffer->data.get()) {
        // update pointer
        buffer->data.release();
        buffer->data.reset(p);
    }
    return n;
}

inline int get_info_int32(const bcf_hdr_t *header, bcf1_t *record, const char *tag, buffer_t<int32_t> *buffer) {
    int32_t *p = buffer->data.get();
    int n = bcf_get_info_int32(header, record, tag, &p, &buffer->capacity);  // NOLINT
    if(n == -4) {
        throw std::bad_alloc{};
    } else if(p != buffer->data.get()) {
        // update pointer
        buffer->data.release();
        buffer->data.reset(p);
    }
    return n;
}

inline int get_format_float(const bcf_hdr_t *header, bcf1_t *record, const char *tag, buffer_t<float> *buffer) {
    float *p = buffer->data.get();
    int n = bcf_get_format_float(header, record, tag, &p, &buffer->capacity);  // NOLINT
    if(n == -4) {
        throw std::bad_alloc{};
    } else if(p != buffer->data.get()) {
        // update pointer
        buffer->data.release();
        buffer->data.reset(p);
    }
    return n;
}

inline int get_genotypes(const bcf_hdr_t *header, bcf1_t *record, buffer_t<int32_t> *buffer) {
    int32_t *p = buffer->data.get();
    int n = bcf_get_genotypes(header, record, &p, &buffer->capacity);  // NOLINT
    if(n == -4) {
        throw std::bad_alloc{};
    } else if(p != buffer->data.get()) {
        // update pointer
        buffer->data.release();
        buffer->data.reset(p);
    }
    return n;
}

// an allele is missing if its value is '.', 'N', or 'n'.
inline bool is_allele_missing(const char *a) {
    if(a == nullptr) {
        return true;
    }
    if(a[0] == '\0') {
        return true;
    }
    if((a[0] == '.' || a[0] == 'N' || a[0] == 'n') && a[1] == '\0') {
        return true;
    }
    return false;
}

// determine if the reference allele is missing
inline bool is_ref_missing(bcf1_t *record) {
    if(record->n_allele == 0) {
        return true;
    }
    bcf_unpack(record, BCF_UN_STR);
    return is_allele_missing(record->d.allele[0]);
}

#endif  // SOFOS_VCF_HPP