CommandLineParser.c

/*
 * Copyright (c) <2008 - 2020>, 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 (fhach AT cs DOT sfu DOT ca)
 *        Iman Sarrafi (isarrafi AT cs DOT sfu DOT ca)
 */

#include <stdio.h>
#include <stdlib.h>
#include <getopt.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include "Common.h"
#include "CommandLineParser.h"

int						uniqueMode=1;
int						indexingMode;
int						searchingMode;
int						pairedEndMode;
int						pairedEndDiscordantMode;
int						pairedEndProfilingMode = 0;
int						bestMappingMode = 0;
int						SNPMode = 0;
int						seqCompressed;
int						outCompressed;
int						cropSize = 0;
int						tailCropSize = 0;
int						progressRep = 0;
int						nohitDisabled = 0;
int						noSamHeader = 0;
int						minPairEndedDistance=-1;
int						maxPairEndedDistance=-1;
int						minPairEndedDiscordantDistance=-1;
int						maxPairEndedDiscordantDistance=-1;
int						errThreshold = -1;
char					*seqFile1;
char					*seqFile2;
char					fileName[3][FILE_NAME_LENGTH];
char					*unmappedOutput;
char					*mappingOutputPath;
char					*concordantStatOutput;
short					maxHits = 0;
unsigned char			WINDOW_SIZE = 12;
unsigned int			CONTIG_SIZE;
unsigned int			CONTIG_MAX_SIZE;
unsigned int			THREAD_COUNT = 1;
unsigned short			DISCORDANT_CUT_OFF = 300;
double					MAX_MEMORY = 4;// GB
int						THREAD_ID[255];
int						SNP_QUAL_THRESHOLD = 53;



#if (defined(__MACH__) && defined(__APPLE__))
#include <mach-o/getsect.h>
#else
extern char _binary_HELP_start;
extern char _binary_HELP_end;
#endif


void printHelp()
{
#if (defined(__MACH__) && defined(__APPLE__))
	size_t i, sz = getsectbyname("binary", "HELP")->size;
	const uint8_t *c =  (const uint8_t*) getsectbyname("binary", "HELP")->addr;
	for (i = 0; i < sz; i++) 
		putchar(c[i]); 
#else
	char *c;
	for (c = &_binary_HELP_start; c != &_binary_HELP_end; c++)
		putchar(*c);
#endif
	exit(EXIT_SUCCESS);
}

int parseCommandLine (int argc, char *argv[])
{
	int index, len, o;
	char *fastaFile = NULL;
	char *fastaOutputFile = NULL;
	char *indexFile = NULL;
	char *SNPFile = NULL;

	mappingOutput = getMem(FILE_NAME_LENGTH);
	mappingOutputPath = getMem(FILE_NAME_LENGTH);
	unmappedOutput = getMem(FILE_NAME_LENGTH);
	concordantStatOutput = getMem(FILE_NAME_LENGTH);
	strcpy(mappingOutput, "output");
	strcpy(unmappedOutput, "output.nohit");
	strcpy(concordantStatOutput, "concordant.statistic");
	mappingOutputPath[0] = '\0';

	static struct option longOptions[] = 
	{
		{"pe",						no_argument,		&pairedEndMode,		1},
		{"discordant-vh",			no_argument,		&pairedEndDiscordantMode,	1},
		{"seqcomp",					no_argument,		&seqCompressed,		1},
		{"outcomp",					no_argument,		&outCompressed,		1},
		{"progress",				no_argument,		&progressRep,		1},
		{"best",					no_argument,		&bestMappingMode,	1},
		{"disable-nohits",			no_argument,		&nohitDisabled,		1},
		{"disable-sam-header",		no_argument,		&noSamHeader,		1},
		{"index",					required_argument,	0, 					'i'},
		{"search",					required_argument,	0,					's'},
		{"help",					no_argument,		0,					'h'},
		{"version",					no_argument,		0,					'v'},
		{"seq",						required_argument,	0,					'x'},
		{"seq1",					required_argument,	0,					'x'},
		{"seq2",					required_argument,	0,					'y'},
		{"ws",						required_argument,  0,					'w'},
		{"min",						required_argument,  0,					'l'},
		{"max",						required_argument,  0,					'm'},
		{"crop",					required_argument,  0,					'c'},
		{"tail-crop",				required_argument,  0,					'f'},
		{"threads",					required_argument,  0,					't'},
		{"mem",						required_argument,  0,					'z'},
		{"snp",						required_argument,  0,					'p'},
		{"max-discordant-cutoff",	required_argument,  0,                  'd'},
		{"snp-qual",				required_argument,  0,                  'q'},
		{0,0,0,0}
	};



	while ( (o = getopt_long ( argc, argv, "f:i:u:o:s:e:n:bhv", longOptions, &index))!= -1 )
	{
		switch (o)
		{
			case 'i':
				indexingMode = 1;
				fastaFile = optarg;
				break;
			case 's':
				searchingMode = 1;
				fastaFile = optarg;
				break;
			case 'c': 
				cropSize = atoi(optarg);
				break;
			case 'f': 
				tailCropSize = atoi(optarg);
				break;
			case 'w':
				if (searchingMode == 1)
				{
					fprintf(stderr, "Error: Window size can only be set in indexing mode.\n");
					return 0;
				}
				WINDOW_SIZE = atoi(optarg);
				break;
			case 'x':
				seqFile1 = optarg;
				break;
			case 'y':
				seqFile2 = optarg;
				break;
			case 'u':
				strcpy(unmappedOutput, optarg);
				break;
			case 'o':
				stripPath (optarg, &mappingOutputPath, &mappingOutput);
				sprintf(unmappedOutput, "%s%s.nohit", mappingOutputPath, mappingOutput );
				break;
			case 'n':
				maxHits = atoi(optarg);
				break;
			case 'e':
				errThreshold = atoi(optarg);
				break;
			case 'q':
				SNP_QUAL_THRESHOLD = atoi(optarg);
				break;
			case 'l':
				minPairEndedDistance = atoi(optarg);
				break;
			case 'm':
				maxPairEndedDistance = atoi(optarg);
				break;					
			case 'h':
				printHelp();
				return 0;
				break;
			case 'v':
				fprintf(stdout, "Version: %s\nBuild Date: %s\n", MRSFAST_VERSION, BUILD_DATE);
				return 0;
				break;
			case 't':
				THREAD_COUNT = atoi(optarg);
				if (THREAD_COUNT == 0 || THREAD_COUNT > sysconf( _SC_NPROCESSORS_ONLN ))
					THREAD_COUNT = sysconf( _SC_NPROCESSORS_ONLN );
				break;
			case 'z':
				MAX_MEMORY = atoi(optarg);
				break;
			case 'd':
				DISCORDANT_CUT_OFF = atoi(optarg);
				break;
			case 'p':
				SNPMode = 1;
				SNPFile = optarg;
				break;
		}

	}

#ifndef MRSFAST_SSE4
	if (searchingMode)
		fprintf(stdout, "==> This version is compiled without any SSE4 optimization <==\n");
#endif
	if (bestMappingMode)
	{
		nohitDisabled = 1;
	}

	if (indexingMode + searchingMode != 1)
	{
		fprintf(stdout, "ERROR: Indexing / Searching mode should be selected\n");
		return 0;
	}

	if (WINDOW_SIZE > 14 || WINDOW_SIZE < 8)
	{
		fprintf(stdout, "ERROR: Window size should be in [8..14]\n");
		return 0;
	}

	if (MAX_MEMORY < 2)
		fprintf(stdout, "ERROR: At least 2 GB of memory is required for running mrsFAST\n");


	if ( indexingMode )
	{
		CONTIG_SIZE		= 80000000;
		CONTIG_MAX_SIZE	= 120000000;

		if (fastaFile == NULL)
		{
			fprintf(stdout, "ERROR: Reference(s) should be indicated for indexing\n");
			return 0;
		}
	}

	if (maxHits)
	{
		if (maxHits < 0)
		{
			fprintf(stdout, "ERROR: Number of maximum hits must be greater than 0\n");
			return 0;
		}

		if (bestMappingMode)
		{
			fprintf(stdout, "ERROR: Maximum number of mappings could not be set in best mapping mode. Maximum mappings input ignored\n");
			maxHits = 0;
		}
	}

	if ( searchingMode )
	{
		CONTIG_SIZE		= 300000000;
		CONTIG_MAX_SIZE	= 300000000;

		if ( cropSize && tailCropSize)
		{
			fprintf(stdout, "ERROR: Sequences can be cropped from only one side\n");
			return 0;
		}

		if (pairedEndDiscordantMode)
		{
			pairedEndDiscordantMode = pairedEndMode = 1;
		}
		
		if (fastaFile == NULL)
		{
			fprintf(stdout, "ERROR: Index File(s) should be indiciated for searching\n");
			return 0;
		}

		if (seqFile1 == NULL && seqFile2 == NULL)
		{
			fprintf(stdout, "ERROR: Please indicate a sequence file for searching.\n");
			return 0;
		}
		
		if (!pairedEndMode && seqFile2 != NULL)
		{
			fprintf(stdout, "ERROR: Second File can be indicated in pairedend mode\n");
			return 0;
		}

		if (pairedEndMode)
		{
			if (minPairEndedDistance < 0 && maxPairEndedDistance < 0)
			{
				pairedEndProfilingMode = 1;
			}
			else if ( minPairEndedDistance <0 || maxPairEndedDistance < 0 || minPairEndedDistance > maxPairEndedDistance )
			{
				fprintf(stdout, "ERROR: Please enter a valid range for pairedend sequences.\n");
				return 0;
			}

			if (seqFile1 == NULL)
			{
				fprintf(stdout, "ERROR: Please indicate the first file for pairedend search.\n");
				return 0;
			}
		}
	}

	int i = 0;

	sprintf(fileName[0], "%s", fastaFile);
	sprintf(fileName[1], "%s.index", fileName[0]);
	if (SNPMode)
		sprintf(fileName[2], "%s", SNPFile);

	if (!indexingMode)
	{
		fprintf(stdout, "# Threads: %d\n", THREAD_COUNT);
		for (i = 0; i < 255; i++)
			THREAD_ID[i] = i;
	}

	char fname1[FILE_NAME_LENGTH];
	char fname2[FILE_NAME_LENGTH];
	char fname3[FILE_NAME_LENGTH];
	char fname4[FILE_NAME_LENGTH];
	char fname5[FILE_NAME_LENGTH];

	// Why is this one here?
	if (pairedEndMode)
	{
		sprintf(fname1, "%s__%s__1", mappingOutputPath, mappingOutput);
		sprintf(fname2, "%s__%s__2", mappingOutputPath, mappingOutput);
		sprintf(fname3, "%s__%s__disc", mappingOutputPath, mappingOutput);
		sprintf(fname4, "%s__%s__oea1", mappingOutputPath, mappingOutput);
		sprintf(fname5, "%s__%s__oea2", mappingOutputPath, mappingOutput);
		unlink(fname1);
		unlink(fname2);
		unlink(fname3);
		unlink(fname4);
		unlink(fname5);
	}
	initCommon();
	return 1;
}
/**********************************************/
void finalizeCommandParser()
{
	freeMem(mappingOutput, FILE_NAME_LENGTH);
	freeMem(unmappedOutput, FILE_NAME_LENGTH);
	freeMem(mappingOutputPath, FILE_NAME_LENGTH);
	freeMem(concordantStatOutput, FILE_NAME_LENGTH);
}