--- a/mrfast-2.1.0.4/CommandLineParser.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,388 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, 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 names of the University of Washington, Simon Fraser University, 
- *   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
-	Can Alkan
-  Emails: 
-        farhadh AT uw DOT edu
-        fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu
-*/
-
-
-#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						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;
-int 					nosamMode;
-char					*seqFile1;
-char					*seqFile2;
-char					*mappingOutput = "output";
-char					*mappingOutputPath = "";
-char					*unmappedOutput = "unmapped";
-char					fileName[1000][2][FILE_NAME_LENGTH];
-int						fileCnt;
-int 					maxOEAOutput=1000;
-int 					maxDiscordantOutput=10000;
-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 *batchFile = NULL ;
-	int  batchMode = 0;
-		
-	static struct option longOptions[] = 
-	{
-		{"pe",				no_argument,		&pairedEndMode,		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'},
-		{"maxoea",            required_argument,  0,                  'a'},
-		{"maxdis",            required_argument,  0,                  'd'},
-		{"nosam",        no_argument,        &nosamMode,      1},
-		{0,  0,  0, 0},
-	};
-
-	while ( (o = getopt_long ( argc, argv, "bhvn:e:o:u:i:s:x:y:w:l:m:c:a:d:", longOptions, &index)) != -1 )
-	{
-		switch (o)
-		{
-			case 'a':
-				maxOEAOutput = atoi(optarg);
-				break;
-			case 'd':
-				maxDiscordantOutput = atoi(optarg);
-				break;
-			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;
-				/*		        case '?':
- 			        fprintf(stderr, "Unknown parameter: %s\n", longOptions[index].name);
-			        abort();
-				break;*/
-		}
-
-	}
-	if (indexingMode + searchingMode != 1)
-	{
-		fprintf(stdout, "ERROR: Indexing / Searching mode should be selected\n");
-		return 0;
-	}
-
-	if (WINDOW_SIZE > 15 || WINDOW_SIZE < 11)
-	{
-		fprintf(stdout, "ERROR: Window size should be in [12..15]\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;
-
-
-		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,"mrFAST : Micro-Read Fast Alignment Search Tool.\n\n");
-		fprintf(stdout,"Usage: mrfast [options]\n\n");
-		errorType="edit distance";
-	}
-	else
-	{
-		fprintf(stdout,"mrsFAST : Micro-Read Substitutions (only) Fast Alignment Search Tool.\n\n");
-		fprintf(stdout,"mrsFAST is a cache oblivious read mapping tool. mrsFAST capable of mapping\n");
-		fprintf(stdout,"single and paired end reads to the reference genome. Bisulfite treated \n");
-		fprintf(stdout,"sequences are not supported in this version. By default mrsFAST reports  \n");
-		fprintf(stdout,"the output in SAM format.\n\n");
-		fprintf(stdout,"Usage: mrsFAST [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 in the specified genome. Provide the path to the fasta file. \n\t\t\tIndex file should be in the same directory.\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," --pe \t\t\tSearch will be done in Paired-End mode.\n");
-	fprintf(stdout," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpaired end 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\tpaired 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\tpaired end reads.  \n");
-	fprintf(stdout," -o [file]\t\tOutput of the mapped sequences. The default is \"output\".\n");
-	fprintf(stdout," -u [file]\t\tSave unmapped sequences in fasta/fastq format.\n");
-        fprintf(stdout," --best   \t\tOnly the best mapping from all the possible mapping is returned.\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," -e [int]\t\tMaximum allowed %s (default 2).\n", errorType);
-	fprintf(stdout," --min [int]\t\tMin distance allowed between a pair of end sequences.\n");
-	fprintf(stdout," --max [int]\t\tMax distance allowed between a pair of end sequences.\n");
-
-	fprintf(stdout," --maxoea [int]\t\tMax number of One End Anchored (OEA) returned for each read pair. We recommend 100 or above for NovelSeq use.\n");
-	fprintf(stdout," --maxdis [int]\t\tMax number of discordant map locations returned for each read pair. We recommend 300 or above for VariationHunter use.\n");
-}