Mercurial > repos > calkan > mrsfast
view mrsfast-2.3.0.2/Common.c @ 0:ec628ba33878 default tip
Uploaded source code for mrsFAST
author | calkan |
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date | Tue, 21 Feb 2012 10:39:28 -0500 |
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/* * Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University * All rights reserved. * * Redistribution and use in source and binary forms, with or without modification, * are permitted provided that the following conditions are met: * * Redistributions of source code must retain the above copyright notice, this list * of conditions and the following disclaimer. * - Redistributions in binary form must reproduce the above copyright notice, this * list of conditions and the following disclaimer in the documentation and/or other * materials provided with the distribution. * - Neither the name of the <ORGANIZATION> nor the names of its contributors may be * used to endorse or promote products derived from this software without specific * prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * Author : Faraz Hach * Email : fhach AT cs DOT sfu * Last Update : 2009-02-01 */ #include <stdio.h> #include <stdlib.h> #include <sys/time.h> #include <zlib.h> #include <string.h> #include "Common.h" unsigned short SEQ_LENGTH = 0; unsigned short QUAL_LENGTH = 0; long long memUsage = 0; /**********************************************/ FILE *fileOpen(char *fileName, char *mode) { FILE *fp; fp = fopen (fileName, mode); if (fp == NULL) { fprintf(stdout, "Error: Cannot Open the file %s\n", fileName); fflush(stdout); exit(0); } return fp; } /**********************************************/ gzFile fileOpenGZ(char *fileName, char *mode) { gzFile gzfp; gzfp = gzopen (fileName, mode); if (gzfp == Z_NULL) { fprintf(stdout, "Error: Cannot Open the file %s\n", fileName); fflush(stdout); exit(0); } return gzfp; } /**********************************************/ double getTime(void) { struct timeval t; gettimeofday(&t, NULL); return t.tv_sec+t.tv_usec/1000000.0; } /**********************************************/ char reverseCompleteChar(char c) { char ret; switch (c) { case 'A': ret = 'T'; break; case 'T': ret = 'A'; break; case 'C': ret = 'G'; break; case 'G': ret = 'C'; break; default: ret = 'N'; break; } return ret; } /**********************************************/ void reverseComplete (char *seq, char *rcSeq , int length) { int i; for (i=0; i<length; i++) { rcSeq[i]=reverseCompleteChar (seq[length-1-i]) ; } } /**********************************************/ void * getMem(size_t size) { memUsage+=size; return malloc(size); } /**********************************************/ void freeMem(void *ptr, size_t size) { memUsage-=size; free(ptr); } /**********************************************/ double getMemUsage() { return memUsage/1048576.0; } /**********************************************/ void reverse (char *seq, char *rcSeq , int length) { int i; for (i=0; i<length; i++) { rcSeq[i]=seq[length-1-i]; } } /**********************************************/ void stripPath(char *full, char **path, char **fileName) { int i; int pos = -1; for (i=strlen(full)-1; i>=0; i--) { if (full[i]=='/') { pos = i; break; } } if (pos != -1) { sprintf(*fileName, "%s%c", (full+pos+1), '\0'); full[pos+1]='\0'; sprintf(*path,"%s%c", full, '\0'); } else { sprintf(*fileName, "%s%c", full, '\0'); sprintf(*path,"%c", '\0'); } }