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/* -*- Mode: C ; indent-tabs-mode: nil ; c-file-style: "stroustrup" ; column-number-mode: t -*-
Project: YAHA, DNA alignment tool designed to find optimal split-read mappings on single-end queries.
Author: Greg Faust (gf4ea@virginia.edu)
File: FileHelpers.c Helper routines for both mempory mapped and stream file IO, and outputting time.
Key elements of the file processing use GNU extensions, and not portable.
License Information:
Copyright 2009-2015 Gregory G. Faust
Licensed under the MIT license (the "License");
You may not use this file except in compliance with the License.
You may obtain a copy of the License at http://opensource.org/licenses/MIT
*/
#include <time.h>
#include <stdlib.h>
#include <stdio_ext.h>
#include <errno.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/stat.h>
#include <sys/mman.h>
#include "Math.h"
// This is the function used in ASSERT.
#ifdef DEBUG
void outputDebugString (char * str)
{
fprintf(stderr, str);
}
#endif
// Call this for fatal run time errors.
void fatalError(const char * errorStr)
{
fprintf(stderr, "%s\n", errorStr);
exit(1);
}
// Find the next occurrence of the char in the str.
// Assumes the char will exist, since it doesn't know when end of string will be reached.
// The contract is that offset + retval will point to the search char.
int findChar(char * str, FSIZE offset, char search)
{
// Make sure we move at least one char ahead.
int count = 1;
while (TRUE)
{
if (str[offset+count] == search) return count;
count += 1;
}
}
static inline int fputchar(FILE * out, char outchar)
{
return putc_unlocked(outchar, out);
}
void printChars(FILE * out, char * str, int start, int len)
{
int i;
for (i=start; i<(start+len); i++) fputchar(out, str[i]);
}
// A convenience function for outputing time is seconds in a more useful metric.
void fprintTimeSeconds (FILE * out, double seconds, int precision)
{
double totalseconds = seconds;
int hours = seconds/3600.;
if (hours > 0)
{
seconds -= hours * 3600;
fprintf(out, "%dH", hours);
}
int minutes = seconds/60.;
if (minutes > 0)
{
seconds -= minutes * 60;
fprintf(out, "%dM", minutes);
}
if (hours + minutes > 0)
{
fprintf(out, "%.0fS", seconds);
fprintf(out, "(%.*fS)", precision, totalseconds);
}
else fprintf(out, "%.*fS", precision, totalseconds);
}
void fprintTimeMicroSeconds (FILE * out, UINT64 microSeconds, int precision)
{
fprintTimeSeconds(out, ((double)microSeconds/1000000.0), precision);
}
// Check for a file system error. If present, output message on stderr.
void checkFSerr (SFSIZE returnCode)
{
if (returnCode == -1)
{
fprintf(stderr, "File system error: %d.\n", errno);
exit(1);
}
}
// Check for a file system error. If present, output better message on stderr.
void checkFSerrWithFilename (SFSIZE returnCode, char * filename)
{
if (returnCode == -1)
{
if (errno == ENOENT)
fprintf(stderr, "File '%s' does not exist.\n", filename);
else if (errno == ENOMEM)
if (filename != NULL)
fprintf(stderr, "Insufficient memory available to open '%s'.\n", filename);
else
fprintf(stderr, "Insufficient memory available to satisfy allocation request.\n");
else
fprintf(stderr, "File system error %d on file '%s'.\n", errno, filename);
exit(1);
}
}
// Check if one file is newer than another.
BOOL fileNewerThan (char * file1Name, char * file2Name)
{
struct stat file1stat;
struct stat file2stat;
int retcode;
retcode = stat(file2Name, &file2stat);
// If file2 does not exist, then we will say file1 is newer.
if (retcode == -1 && errno == ENOENT) return TRUE;
checkFSerrWithFilename(retcode, file2Name);
retcode = stat(file1Name, &file1stat);
checkFSerrWithFilename(retcode, file1Name);
// Both files exist, and we have the stats.
// Now compare the modification times.
struct timespec file1ts = file1stat.st_mtim;
struct timespec file2ts = file2stat.st_mtim;
if (file1ts.tv_sec < file2ts.tv_sec) return FALSE;
if (file1ts.tv_sec > file2ts.tv_sec) return TRUE;
if (file1ts.tv_nsec > file2ts.tv_nsec) return TRUE;
return FALSE;
}
/////
// INPUT FILES
/////
// Open the file for read.
// We will use memory mapped IO.
// And also check file stats to get the file size.
FDES openForRead(char * filename, FSIZE *fileSize, char **contentPtr, BOOL preload)
{
// First open the file.
FDES file;
file = open(filename, O_RDONLY);
checkFSerrWithFilename(file, filename);
// Now get its size.
struct stat * sbuf = (struct stat *)malloc(sizeof(struct stat));
int err;
err = fstat(file, sbuf);
checkFSerrWithFilename(err, filename);
FSIZE size = sbuf->st_size;
#ifdef DEBUG
fprintf(stderr, "File %s is %d bytes long.\n", filename, size);
#endif
// Now memory map the IO.
char * filePtr = (char *)mmap(NULL, sbuf->st_size, PROT_READ, MAP_SHARED, file, 0);
checkFSerrWithFilename((SFSIZE)filePtr, filename);
if (preload)
{
// Try reading in each page to pre-load the page tables in sequential order.
// This seems to vastly speed virtual page table creation or something
// relative to paging in things as they are used.
int count = 0;
for (char * ptr=filePtr; ptr<filePtr+size; ptr+=sbuf->st_blksize) count += ptr[0];
// We call a silly function here to avoid the loop being optimized out for having no effect.
emptyFunction(count);
}
// If we are here, we have successfully opened and mapped the file.
// Fill in OUT parameters, and return.
free(sbuf);
*fileSize = size;
*contentPtr = filePtr;
return file;
}
// We will close the file, and unmap the memory mapped IO.
void closeForRead(FDES ifp, FSIZE fileSize, char *contentPtr)
{
// First unmap the IO.
int err = munmap(contentPtr, fileSize);
checkFSerr(err);
err = close(ifp);
checkFSerr(err);
}
// Open the file for seq read, such as query files.
// We will not use memory mapped IO.
// We will use char IO.
FILE * openForSeqRead(char * filename)
{
FILE * inFile;
if (strcmp(filename, "stdin") == 0 || strcmp(filename, "-") == 0)
{
fprintf(stderr, "Reading queries from stdin.\n");
inFile = stdin;
}
else
inFile = fopen(filename, "r");
if (inFile == NULL)
{
fprintf(stderr, "Failure to open input file: %s. Error number:%d\n", filename, errno);
exit(1);
}
// We will tell the OS that we will do our own locking and unlocking to improve input speed.
__fsetlocking (inFile, FSETLOCKING_BYCALLER);
return inFile;
}
void closeForSeqRead(FILE * inFile)
{
fclose(inFile);
}
/////
// OUTPUT FILES
/////
// Output files are much more complicated in the flag settings and in the closing operation.
// All of our output files are now either stream (for alignment output) or require a preamble.
// Therefore, we will no longer mmap as part of opening the file, nor unmap or write as part of closing.
// Instead we will provide some helper functions for mmapping and writing.
/////
// Allocate a big block of memory as anonymous memory mapped "file".
char * blockMalloc(FSIZE size, char * string)
{
char * retval = (char *)mmap(NULL, size, PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_ANON, 0, 0);
checkFSerrWithFilename((SFSIZE)retval, string);
return retval;
}
// Free big blocks of memory. Note the size is needed.
void blockFree(char * ptr, FSIZE size)
{
int err = munmap(ptr, size);
checkFSerrWithFilename(err, NULL);
}
// Write blocks of memory.
// As write may not always write out all the buffer in one call, repeat until success.
void blockWrite(FDES ofp, char * ptr, FSIZE size)
{
FSIZE done = 0;
while (done < size)
{
SFSIZE curr = write(ofp, ptr+done, size-done);
checkFSerr(curr);
done += curr;
}
}
// Open for write will now only open the file and return the file descriptor.
FDES openForWrite(char * filename)
{
// First we will open the file
// Create it if it doesn't already exist.
// Truncate it to zero length.
// If it is created, set the permission bits.
// User can RWX. Everyone can read.
FDES file;
file = open(filename, O_RDWR | O_CREAT | O_TRUNC, S_IRWXU | S_IRGRP | S_IROTH);
checkFSerrWithFilename(file, filename);
return file;
}
// Just close the file and check for errors.
void closeForWrite(FDES ofp)
{
// Now we can close the file.
int err = close(ofp);
checkFSerr(err);
}
// Open for stream IO.
FILE * openForPrint(char * filename)
{
FILE * outFile;
if (strcmp(filename, "stdout") == 0)
outFile = stdout;
else
outFile = fopen(filename, "w");
if (outFile == NULL)
{
fprintf(stderr, "Failure to open output file: %s. Error number:%d\n", filename, errno);
exit(1);
}
// We will tell the OS that we will do our own locking and unlocking to improve output speed.
// By doing it here we presumably also speed up calls to functions such as fprintf and fputs,
// not just the calls to putc_unlocked.
__fsetlocking (outFile, FSETLOCKING_BYCALLER);
return outFile;
}
void closeForPrint(FILE * outFile)
{
fclose(outFile);
}
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