CommandLineParser.c

/*
 * 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.
 */

/*
  Authors: 
	Farhad Hormozdiari
        Faraz Hach
  Emails: 
	farhadh AT uw DOT edu
	fhach AT cs DOT sfu
 */


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

int						uniqueMode=1;
int						indexingMode;
int						searchingMode;
int						pairedEndMode;
int						pairedEndModeMP;
int						pairedEndModePE;
int						pairedEndDiscordantMode;
int						transChromosal=0;
int						pairedEndProfilingMode;
int						seqCompressed;
int						outCompressed;
int						cropSize = 0;
int						progressRep = 0;
int						minPairEndedDistance=-1;
int						maxPairEndedDistance=-1;
int						minPairEndedDiscordantDistance=-1;
int						maxPairEndedDiscordantDistance=-1;
int 					bestMode;
char					*seqFile1;
char					*seqFile2;
char					*mappingOutput = "output";
char					*mappingOutputPath = "";
char					*unmappedOutput = "unmapped";
char					fileName[1000][2][FILE_NAME_LENGTH];
int						fileCnt;
unsigned char			errThreshold=2;
unsigned char			maxHits=0;
unsigned char			WINDOW_SIZE = 12;
unsigned int			CONTIG_SIZE;
unsigned int			CONTIG_MAX_SIZE;

void printHelp();

int parseCommandLine (int argc, char *argv[])
{

	int o;
	int index;
	char *fastaFile = NULL;
	char *fastaOutputFile = NULL;
	char *indexFile = NULL;
	char *batchFile = NULL ;
	int  batchMode = 0;
		
	static struct option longOptions[] = 
	{

		{"mp",				no_argument,		&pairedEndModeMP,		1},
		{"pe",				no_argument,		&pairedEndModePE,		1},
		{"discordant-vh",	no_argument,		&pairedEndDiscordantMode,	1},
		{"trans",           no_argument,            &transChromosal        ,       1},
		{"profile",			no_argument, 		&pairedEndProfilingMode,	1},
		{"seqcomp",			no_argument,		&seqCompressed,		1},
		{"outcomp",			no_argument,		&outCompressed,		1},
		{"progress",		no_argument,		&progressRep,		1},
		{"best",			no_argument,		&bestMode,		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'}

	};

	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 'b':
				batchMode = 1;
				break;
			case 'c': 
				cropSize = atoi(optarg);
				break;
			case 'w':
				WINDOW_SIZE = atoi(optarg);
				break;
			case 'x':
				seqFile1 = optarg;
				break;
			case 'y':
				seqFile2 = optarg;
				break;
			case 'u':
				unmappedOutput = optarg;
				break;
			case 'o':
				mappingOutput = getMem(FILE_NAME_LENGTH);
				mappingOutputPath = getMem(FILE_NAME_LENGTH);
				stripPath (optarg, &mappingOutputPath, &mappingOutput);
				break;
			case 'n':
				maxHits = atoi(optarg);
				break;
			case 'e':
				errThreshold = 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, "%s.%s\n", versionNumber, versionNumberF);
				return 0;
				break;
		}

	}

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

	if (WINDOW_SIZE > 14 || WINDOW_SIZE < 5)
	{
		fprintf(stdout, "ERROR: Window size should be in [12..14]\n");
		return 0;
	}


	if ( indexingMode )
	{
		CONTIG_SIZE		= 15000000;
		CONTIG_MAX_SIZE	= 40000000;

		if (batchMode)
		{
			batchFile = fastaFile;
			fastaFile = NULL;
		}

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

		if (pairedEndDiscordantMode)
		{
			fprintf(stdout, "ERROR: --discordant cannot be used in indexing mode. \n");
			return 0;
		}

	}


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

		pairedEndMode = (pairedEndModeMP || pairedEndModePE);

		if (batchMode)
		{
			batchFile = fastaFile;
			fastaFile = NULL;
		}

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

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

		if (!pairedEndMode && pairedEndDiscordantMode)
		{
			fprintf(stdout, "ERROR: --discordant should be used with --pe");
			return 0;
		}

		if (!pairedEndMode && pairedEndProfilingMode)
		{
			fprintf(stdout, "ERROR: --profile should be used with --pe");
			return 0;
		}
	}

	int i = 0;


	if (batchMode)
	{
		FILE *fp = fileOpen(batchFile, "r");

		if (fp == NULL)
			return 0;

		fileCnt  = 0;

		while ( fgets(fileName[fileCnt][0], FILE_NAME_LENGTH, fp))
		{
			for (i = strlen(fileName[fileCnt][0])-1; i>=0; i--)
				if ( !isspace(fileName[fileCnt][0][i]))
					break;
			fileName[fileCnt][0][i+1] = '\0';

			if (strcmp(fileName[fileCnt][0], "") != 0)
			{
				sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]); 
				fileCnt++;
			}
		}
	}
	else
	{
		sprintf(fileName[fileCnt][0], "%s", fastaFile);
		sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]); 
		fileCnt++;
	}


	if (pairedEndProfilingMode)
	{

		minPairEndedDistance = 0;
		maxPairEndedDistance = 300000000;

	}

	if (pairedEndDiscordantMode)
	{
		minPairEndedDiscordantDistance = minPairEndedDistance;
		maxPairEndedDiscordantDistance = maxPairEndedDistance;

		minPairEndedDistance = 0;
		maxPairEndedDistance = 300000000;
	}

	return 1;
}


void printHelp()
{
	char *errorType;
	if (mrFAST)
	{
		fprintf(stdout,"drFAST : Di-base Read Fast Alignment Search Tool\n\n");
		fprintf(stdout,"Usage: drFAST [options]\n\n");
		errorType="Hamming distance";
	}
	else
	{
		fprintf(stdout,"drFAST : Di-base Read Fast Alignment Search Tool.\n\n");
		fprintf(stdout,"drFAST is a read mapping tool for AB Solid short reads. drFAST is capable of mapping\n");
		fprintf(stdout,"single and paired end reads to the reference genome. It will return all possible\n");
		fprintf(stdout,"mappings. By default drFAST reports the output in SAM format.\n\n");
		fprintf(stdout,"Usage: drFAST [options]\n\n");
		errorType="hamming distance";
	}

	fprintf(stdout,"General Options:\n");
	fprintf(stdout," -v|--version\t\tCurrent Version.\n");
	fprintf(stdout," -h\t\t\tShows the help file.\n");
	fprintf(stdout,"\n\n");

	fprintf(stdout,"Indexing Options:\n");
	fprintf(stdout," --index [file]\t\tGenerate an index from the specified fasta file. \n");
	fprintf(stdout," -b\t\t\tIndicates the indexing will be done in batch mode.\n\t\t\tThe file specified in --index should contain the \n\t\t\tlist of fasta files.\n");
	fprintf(stdout," -ws [int]\t\tSet window size for indexing (default:12-max:14).\n");
	fprintf(stdout,"\n\n");

	fprintf(stdout,"Searching Options:\n");
	fprintf(stdout," --search [file]\tSearch the specified genome. Index file should be \n\t\t\tin same directory as the fasta file.\n");
	fprintf(stdout," -b\t\t\tIndicates the mapping will be done in batch mode. \n\t\t\tThe file specified in --search should contain the \n\t\t\tlist of fasta files.\n");
	fprintf(stdout," --mp \t\t\tSearch will be done in MatePaired mode.\n");
	fprintf(stdout," --pe \t\t\tSearch will be done in Pairedend mode.\n");
	fprintf(stdout," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpairend reads are interleaved, use this option.\n");
	fprintf(stdout," --seq1 [file]\t\tInput sequences in fasta/fastq format [file] (First \n\t\t\tfile). Use this option to indicate the first file of \n\t\t\tpair-end reads. \n");
	fprintf(stdout," --seq2 [file]\t\tInput sequences in fasta/fastq format [file] (Second \n\t\t\tfile). Use this option to indicate the second file of \n\t\t\tpair-end reads.  \n");
	fprintf(stdout," -o [file]\t\tOutput of the mapped sequences. The default is output.\n");
	fprintf(stdout," --seqcomp \t\tIndicates that the input sequences are compressed(gz).\n");
	fprintf(stdout," --outcomp \t\tIndicates that output file should be compressed(gz).\n");
	//	fprintf(stdout," -u [file]\t\tSave unmapped sequences to the [file] in fasta format.\n");
	fprintf(stdout," -n [int]\t\tMaximum number of locations reported for a sequence \n\t\t\t(default 0, all mappings). \n");
	fprintf(stdout," -e [int]\t\t%s (default 2).\n", errorType);
	fprintf(stdout," --min [int]\t\tMin inferred distance allowed between two pairend sequences.\n");
	fprintf(stdout," --max [int]\t\tMax inferred distance allowed between two pairend sequences.\n");
}