swh:1:snp:76adc8cf123d92909f09e46db9ddfcbecf4cd1aa
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Tip revision: 0135d929301d24c464d843573e4ea56cd0f3e139 authored by Johnathan Wong on 22 April 2021, 00:47:28 UTC
ntcard.cpp: update low kmer sample check to evaluate entire expression
Tip revision: 0135d92
StringUtil.h
#ifndef STRINGUTIL_H
#define STRINGUTIL_H 1

#include <cassert>
#include <iomanip>
#include <sstream>
#include <string>
#include <cmath>

/** Return the last character of s and remove it. */
static inline char chop(std::string& s)
{
    assert(s.length() > 1);
    unsigned back = s.length() - 1;
    char c = s[back];
    s.erase(back);
    return c;
}

/** If the last character of s is c, remove it and return true. */
static inline bool chomp(std::string& s, char c = '\n')
{
    unsigned back = s.length() - 1;
    if (!s.empty() && s[back] == c) {
        s.erase(back);
        return true;
    } else
        return false;
}

/** Return the SI representation of n. */
static inline std::string toSI(double n)
{
    std::ostringstream s;
    s << std::setprecision(3);
    if (n < 1e3)
        s << n << ' ';
    else if (n < 1e6)
        s << n/1e3 << " k";
    else if (n < 1e9)
        s << n/1e6 << " M";
    else if (n < 1e12)
        s << n/1e9 << " G";
    else
        s << n/1e12 << " T";
    return s.str();
}

/** Return the SI representation of a number in bytes. */
static inline std::string bytesToSI(size_t n)
{
    std::ostringstream s;
    s << std::setprecision(3);
    if (n < 1024)
        s << n;
    else if (n < (1ULL<<20))
        s << (double)n/(1ULL<<10) << "k";
    else if (n < (1ULL<<30))
        s << (double)n/(1ULL<<20) << "M";
    else
        s << (double)n/(1ULL<<30) << "G";
    return s.str();
}

/**
 * Convert a quantity with SI units to the equivalent floating
 * point number.
 */
static inline double fromSI(std::istringstream& iss)
{
    double size;
    std::string units;

    iss >> size;
    if (iss.fail()) {
        // not prefixed by a number
        return 0;
    }

    iss >> units;
    if (iss.fail() && iss.eof()) {
        // no units given; clear fail flag
        // and just return the number
        iss.clear(std::ios::eofbit);
        return size;
    }

    if (units.size() > 1) {
        // unrecognized multichar suffix
        iss.setstate(std::ios::failbit);
        return 0;
    }

    switch(tolower(units[0])) {
    case 'k':
        size *= 1000ULL;
        break;
    case 'm':
        size *= 1000ULL*1000;
        break;
    case 'g':
        size *= 1000ULL*1000*1000;
        break;
    case 't':
        size *= 1000ULL*1000*1000*1000;
        break;
    default:
        iss.setstate(std::ios::failbit);
        return 0;
    }

    return size;
}

/**
 * Convert a quantity with SI units to the equivalent floating
 * point number.
 */
static inline double fromSI(const std::string& str)
{
    std::istringstream iss(str);
    return fromSI(iss);
}

/** Return the engineering string representation of n. */
template <typename T>
static inline std::string toEng(T n)
{
    std::ostringstream s;
    s << std::setprecision(4);
    if (n < 10000000)
        s << n;
    else if (n < 1e9)
        s << n/1e6 << "e6";
    else if (n < 1e12)
        s << n/1e9 << "e9";
    else
        s << n/1e12 << "e12";
    return s.str();
}

/** Return true if the second string is a prefix of the string s. */
template <size_t N>
bool startsWith(const std::string& s, const char (&prefix)[N])
{
    size_t n = N - 1;
    return s.size() > n && equal(s.begin(), s.begin() + n, prefix);
}

/** Return true if the second string is a suffix of the string s. */
template <size_t N>
bool endsWith(const std::string& s, const char (&suffix)[N])
{
    size_t n = N - 1;
    return s.size() > n && equal(s.end() - n, s.end(), suffix);
}

/** Return true if the second string is a suffix of the string s. */
static inline
bool endsWith(const std::string& s, const std::string& suffix)
{
    size_t n = suffix.size();
    return s.size() > n && equal(s.end() - n, s.end(),
                                 suffix.begin());
}

static inline
bool isReadNamePair(const std::string& name1, const std::string& name2)
{
    assert(!name1.empty() && !name2.empty());

    if (name1 == name2)
        return true;

    if (endsWith(name1,"/1") && endsWith(name2,"/2")) {
        int len1 = name1.length();
        int len2 = name2.length();
        assert(len1 > 2 && len2 > 2);
        return name1.compare(0, len1-2, name2, 0, len2-2) == 0;
    }

    return false;
}

static inline size_t SIToBytes(std::istringstream& iss)
{
    double size;
    std::string units;

    iss >> size;
    if (iss.fail()) {
        // not prefixed by a number
        return 0;
    }

    iss >> units;
    if (iss.fail() && iss.eof()) {
        // no units given; clear fail flag
        // and assume bytes
        iss.clear(std::ios::eofbit);
        return (size_t)ceil(size);
    }

    if (units.size() > 1) {
        // unrecognized multichar suffix
        iss.setstate(std::ios::failbit);
        return 0;
    }

    switch(tolower(units[0])) {
    case 'k':
        size *= (size_t)1<<10;
        break;
    case 'm':
        size *= (size_t)1<<20;
        break;
    case 'g':
        size *= (size_t)1<<30;
        break;
    default:
        iss.setstate(std::ios::failbit);
        return 0;
    }

    return (size_t)ceil(size);
}

static inline size_t SIToBytes(const std::string& str)
{
    std::istringstream iss(str);
    return SIToBytes(iss);
}

#endif
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