394 lines
8.1 KiB
C
394 lines
8.1 KiB
C
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/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef WORD_IO_H_
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#define WORD_IO_H_
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#include <stdint.h>
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#include <unistd.h>
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#include <iostream>
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#include <fstream>
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#include "assert_helpers.h"
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#include "endian_swap.h"
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/**
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* Write a 32-bit unsigned to an output stream being careful to
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* re-endianize if caller-requested endianness differs from current
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* host.
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*/
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static inline void writeU32(std::ostream& out, uint32_t x, bool toBigEndian) {
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uint32_t y = endianizeU32(x, toBigEndian);
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out.write((const char*)&y, 4);
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}
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/**
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* Write a 32-bit unsigned to an output stream using the native
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* endianness.
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*/
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static inline void writeU32(std::ostream& out, uint32_t x) {
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out.write((const char*)&x, 4);
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}
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/**
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* Write a 32-bit signed int to an output stream being careful to
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* re-endianize if caller-requested endianness differs from current
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* host.
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*/
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static inline void writeI32(std::ostream& out, int32_t x, bool toBigEndian) {
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int32_t y = endianizeI32(x, toBigEndian);
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out.write((const char*)&y, 4);
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}
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/**
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* Write a 32-bit unsigned to an output stream using the native
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* endianness.
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*/
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static inline void writeI32(std::ostream& out, int32_t x) {
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out.write((const char*)&x, 4);
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}
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/**
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* Write a 16-bit unsigned to an output stream being careful to
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* re-endianize if caller-requested endianness differs from current
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* host.
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*/
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static inline void writeU16(std::ostream& out, uint16_t x, bool toBigEndian) {
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uint16_t y = endianizeU16(x, toBigEndian);
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out.write((const char*)&y, 2);
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}
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/**
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* Write a 16-bit unsigned to an output stream using the native
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* endianness.
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*/
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static inline void writeU16(std::ostream& out, uint16_t x) {
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out.write((const char*)&x, 2);
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}
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/**
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* Write a 16-bit signed int to an output stream being careful to
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* re-endianize if caller-requested endianness differs from current
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* host.
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*/
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static inline void writeI16(std::ostream& out, int16_t x, bool toBigEndian) {
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int16_t y = endianizeI16(x, toBigEndian);
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out.write((const char*)&y, 2);
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}
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/**
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* Write a 16-bit unsigned to an output stream using the native
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* endianness.
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*/
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static inline void writeI16(std::ostream& out, int16_t x) {
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out.write((const char*)&x, 2);
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}
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/**
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* Write a 8-bit unsigned to an output stream.
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*/
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static inline void writeU8(std::ostream& out, uint8_t x) {
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out.write((const char*)&x, 1);
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}
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/**
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* Read a 32-bit unsigned from an input stream, inverting endianness
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* if necessary.
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*/
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static inline uint32_t readU32(std::istream& in, bool swap) {
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uint32_t x;
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in.read((char *)&x, 4);
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assert_eq(4, in.gcount());
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if(swap) {
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return endianSwapU32(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 32-bit unsigned from a file descriptor, optionally inverting
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* endianness.
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*/
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#ifdef BOWTIE_MM
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static inline uint32_t readU32(int in, bool swap) {
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uint32_t x;
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if(read(in, (void *)&x, 4) != 4) {
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assert(false);
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}
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if(swap) {
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return endianSwapU32(x);
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} else {
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return x;
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}
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}
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#endif
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/**
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* Read a 32-bit unsigned from a FILE*, optionally inverting
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* endianness.
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*/
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static inline uint32_t readU32(FILE* in, bool swap) {
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uint32_t x;
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if(fread((void *)&x, 1, 4, in) != 4) {
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assert(false);
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}
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if(swap) {
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return endianSwapU32(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 32-bit signed from an input stream, inverting endianness
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* if necessary.
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*/
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static inline int32_t readI32(std::istream& in, bool swap) {
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int32_t x;
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in.read((char *)&x, 4);
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assert_eq(4, in.gcount());
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if(swap) {
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return endianSwapI32(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 32-bit unsigned from a file descriptor, optionally inverting
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* endianness.
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*/
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#ifdef BOWTIE_MM
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static inline uint32_t readI32(int in, bool swap) {
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int32_t x;
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if(read(in, (void *)&x, 4) != 4) {
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assert(false);
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}
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if(swap) {
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return endianSwapI32(x);
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} else {
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return x;
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}
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}
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#endif
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/**
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* Read a 32-bit unsigned from a FILE*, optionally inverting
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* endianness.
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*/
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static inline uint32_t readI32(FILE* in, bool swap) {
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int32_t x;
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if(fread((void *)&x, 1, 4, in) != 4) {
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assert(false);
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}
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if(swap) {
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return endianSwapI32(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 16-bit unsigned from an input stream, inverting endianness
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* if necessary.
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*/
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static inline uint16_t readU16(std::istream& in, bool swap) {
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uint16_t x;
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in.read((char *)&x, 2);
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assert_eq(2, in.gcount());
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if(swap) {
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return endianSwapU16(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 16-bit unsigned from a file descriptor, optionally inverting
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* endianness.
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*/
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#ifdef BOWTIE_MM
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static inline uint16_t readU16(int in, bool swap) {
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uint16_t x;
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if(read(in, (void *)&x, 2) != 2) {
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assert(false);
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}
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if(swap) {
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return endianSwapU16(x);
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} else {
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return x;
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}
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}
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#endif
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/**
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* Read a 16-bit unsigned from a FILE*, optionally inverting
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* endianness.
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*/
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static inline uint16_t readU16(FILE* in, bool swap) {
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uint16_t x;
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if(fread((void *)&x, 1, 2, in) != 2) {
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assert(false);
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}
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if(swap) {
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return endianSwapU32(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 16-bit signed from an input stream, inverting endianness
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* if necessary.
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*/
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static inline int32_t readI16(std::istream& in, bool swap) {
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int16_t x;
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in.read((char *)&x, 2);
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assert_eq(2, in.gcount());
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if(swap) {
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return endianSwapI16(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 16-bit unsigned from a file descriptor, optionally inverting
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* endianness.
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*/
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#ifdef BOWTIE_MM
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static inline uint16_t readI16(int in, bool swap) {
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int16_t x;
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if(read(in, (void *)&x, 2) != 2) {
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assert(false);
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}
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if(swap) {
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return endianSwapI16(x);
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} else {
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return x;
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}
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}
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#endif
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/**
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* Read a 16-bit unsigned from a FILE*, optionally inverting
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* endianness.
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*/
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static inline uint16_t readI16(FILE* in, bool swap) {
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int16_t x;
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if(fread((void *)&x, 1, 2, in) != 2) {
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assert(false);
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}
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if(swap) {
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return endianSwapI16(x);
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} else {
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return x;
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}
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}
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/**
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* Read a 8-bit unsigned from an input stream
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*/
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static inline uint8_t readU8(std::istream& in) {
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uint8_t x;
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in.read((char *)&x, 1);
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assert_eq(1, in.gcount());
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return x;
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}
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template <typename index_t>
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void writeIndex(std::ostream& out, index_t x, bool toBigEndian) {
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index_t y = endianizeIndex(x, toBigEndian);
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out.write((const char*)&y, sizeof(index_t));
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}
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/**
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* Read a unsigned from an input stream, inverting endianness
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* if necessary.
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*/
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template <typename index_t>
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static inline index_t readIndex(std::istream& in, bool swap) {
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index_t x;
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in.read((char *)&x, sizeof(index_t));
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assert_eq(sizeof(index_t), in.gcount());
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if(swap) {
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return endianSwapIndex(x);
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} else {
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return x;
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}
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}
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/**
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* Read a unsigned from a file descriptor, optionally inverting
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* endianness.
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*/
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#ifdef BOWTIE_MM
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template <typename index_t>
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static inline index_t readIndex(int in, bool swap) {
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index_t x;
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if(read(in, (void *)&x, sizeof(index_t)) != sizeof(index_t)) {
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assert(false);
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}
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if(swap) {
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if(sizeof(index_t) == 8) {
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assert(false);
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return 0;
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} else if(sizeof(index_t) == 4) {
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return endianSwapU32(x);
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} else {
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assert_eq(sizeof(index_t), 2);
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return endianSwapU16(x);
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}
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} else {
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return x;
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}
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}
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#endif
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/**
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* Read a unsigned from a FILE*, optionally inverting
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* endianness.
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*/
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template <typename index_t>
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static inline index_t readIndex(FILE* in, bool swap) {
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index_t x;
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if(fread((void *)&x, 1, sizeof(index_t), in) != sizeof(index_t)) {
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assert(false);
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}
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if(swap) {
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if(sizeof(index_t) == 8) {
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assert(false);
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return 0;
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} else if(sizeof(index_t) == 4) {
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return endianSwapU32(x);
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} else {
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assert_eq(sizeof(index_t), 2);
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return endianSwapU16(x);
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}
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} else {
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return x;
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}
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}
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#endif /*WORD_IO_H_*/
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